[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-oTACC-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/ACC-TP/10005775/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/10686043/transformed.cor.cli.txt"

nPatients in clinical file=82, in cluster file=64, common to both=56
[1] "Reduce the number of clustering variables from 151 to 125."
[1] 125  56
[1] "ZFPM1 MUTATION ANALYSIS"
[1] 3
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             23              33 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             23              33 
[1] "LACTB MUTATION ANALYSIS"
[1] 3
  LACTB MUTATED LACTB WILD-TYPE 
             17              39 
  LACTB MUTATED LACTB WILD-TYPE 
             17              39 
[1] "CCDC102A MUTATION ANALYSIS"
[1] 3
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                16                 40 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                16                 40 
[1] "ZNF517 MUTATION ANALYSIS"
[1] 3
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              11               45 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              11               45 
[1] "TOR3A MUTATION ANALYSIS"
[1] 3
  TOR3A MUTATED TOR3A WILD-TYPE 
             11              45 
  TOR3A MUTATED TOR3A WILD-TYPE 
             11              45 
[1] "USP42 MUTATION ANALYSIS"
[1] 3
  USP42 MUTATED USP42 WILD-TYPE 
             13              43 
  USP42 MUTATED USP42 WILD-TYPE 
             13              43 
[1] "CLDN23 MUTATION ANALYSIS"
[1] 3
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               46 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               46 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            11             45 
  TP53 MUTATED TP53 WILD-TYPE 
            11             45 
[1] "KCNK17 MUTATION ANALYSIS"
[1] 3
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               8               48 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               8               48 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              4              52 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              4              52 
[1] "APOE MUTATION ANALYSIS"
[1] 3
  APOE MUTATED APOE WILD-TYPE 
             5             51 
  APOE MUTATED APOE WILD-TYPE 
             5             51 
[1] "CCDC105 MUTATION ANALYSIS"
[1] 3
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                50 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                50 
[1] "RINL MUTATION ANALYSIS"
[1] 3
  RINL MUTATED RINL WILD-TYPE 
             7             49 
  RINL MUTATED RINL WILD-TYPE 
             7             49 
[1] "MAL2 MUTATION ANALYSIS"
[1] 3
  MAL2 MUTATED MAL2 WILD-TYPE 
             9             47 
  MAL2 MUTATED MAL2 WILD-TYPE 
             9             47 
[1] "LRIG1 MUTATION ANALYSIS"
[1] 3
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             14              42 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             14              42 
[1] "C19ORF10 MUTATION ANALYSIS"
[1] 3
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 6                 50 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 6                 50 
[1] "C10ORF95 MUTATION ANALYSIS"
[1] 3
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 50 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 50 
[1] "SYT8 MUTATION ANALYSIS"
[1] 3
  SYT8 MUTATED SYT8 WILD-TYPE 
             5             51 
  SYT8 MUTATED SYT8 WILD-TYPE 
             5             51 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             8             48 
  IDUA MUTATED IDUA WILD-TYPE 
             8             48 
[1] "HHIPL1 MUTATION ANALYSIS"
[1] 3
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               50 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               50 
[1] "ASPDH MUTATION ANALYSIS"
[1] 3
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              48 
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              48 
[1] "C1ORF106 MUTATION ANALYSIS"
[1] 3
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 8                 48 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 8                 48 
[1] "THEM4 MUTATION ANALYSIS"
[1] 3
  THEM4 MUTATED THEM4 WILD-TYPE 
              4              52 
  THEM4 MUTATED THEM4 WILD-TYPE 
              4              52 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               6               50 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               6               50 
[1] "GDF1 MUTATION ANALYSIS"
[1] 3
  GDF1 MUTATED GDF1 WILD-TYPE 
             4             52 
  GDF1 MUTATED GDF1 WILD-TYPE 
             4             52 
[1] "TSC22D2 MUTATION ANALYSIS"
[1] 3
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                48 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                48 
[1] "ZAR1 MUTATION ANALYSIS"
[1] 3
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             45 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             45 
[1] "RGS9BP MUTATION ANALYSIS"
[1] 3
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               7               49 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               7               49 
[1] "OPRD1 MUTATION ANALYSIS"
[1] 3
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             11              45 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             11              45 
[1] "C16ORF3 MUTATION ANALYSIS"
[1] 3
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                51 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                51 
[1] "FPGS MUTATION ANALYSIS"
[1] 3
  FPGS MUTATED FPGS WILD-TYPE 
             5             51 
  FPGS MUTATED FPGS WILD-TYPE 
             5             51 
[1] "PLIN5 MUTATION ANALYSIS"
[1] 3
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              51 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              51 
[1] "IRX3 MUTATION ANALYSIS"
[1] 3
  IRX3 MUTATED IRX3 WILD-TYPE 
             4             52 
  IRX3 MUTATED IRX3 WILD-TYPE 
             4             52 
[1] "TRIOBP MUTATION ANALYSIS"
[1] 3
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               46 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               46 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 52 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 52 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              9              47 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              9              47 
[1] "ZNF628 MUTATION ANALYSIS"
[1] 3
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               6               50 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               6               50 
[1] "WDR34 MUTATION ANALYSIS"
[1] 3
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              51 
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              51 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               5               51 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               5               51 
[1] "GARS MUTATION ANALYSIS"
[1] 3
  GARS MUTATED GARS WILD-TYPE 
            17             39 
  GARS MUTATED GARS WILD-TYPE 
            17             39 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10               46 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10               46 
[1] "BHLHE22 MUTATION ANALYSIS"
[1] 3
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                51 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                51 
[1] "PTPLA MUTATION ANALYSIS"
[1] 3
  PTPLA MUTATED PTPLA WILD-TYPE 
              3              53 
  PTPLA MUTATED PTPLA WILD-TYPE 
              3              53 
[1] "CD320 MUTATION ANALYSIS"
[1] 3
  CD320 MUTATED CD320 WILD-TYPE 
              4              52 
  CD320 MUTATED CD320 WILD-TYPE 
              4              52 
[1] "KIAA1984 MUTATION ANALYSIS"
[1] 3
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 3                 53 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 3                 53 
[1] "TPO MUTATION ANALYSIS"
[1] 3
  TPO MUTATED TPO WILD-TYPE 
           10            46 
  TPO MUTATED TPO WILD-TYPE 
           10            46 
[1] "AATK MUTATION ANALYSIS"
[1] 3
  AATK MUTATED AATK WILD-TYPE 
             5             51 
  AATK MUTATED AATK WILD-TYPE 
             5             51 
[1] "PANK2 MUTATION ANALYSIS"
[1] 3
  PANK2 MUTATED PANK2 WILD-TYPE 
              4              52 
  PANK2 MUTATED PANK2 WILD-TYPE 
              4              52 
[1] "SNED1 MUTATION ANALYSIS"
[1] 3
  SNED1 MUTATED SNED1 WILD-TYPE 
              6              50 
  SNED1 MUTATED SNED1 WILD-TYPE 
              6              50 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                52 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                52 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              46 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              46 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
              4              52 
  RREB1 MUTATED RREB1 WILD-TYPE 
              4              52 
[1] "RNF39 MUTATION ANALYSIS"
[1] 3
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              51 
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              51 
[1] "SEMA5B MUTATION ANALYSIS"
[1] 3
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               6               50 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               6               50 
[1] "TAF5 MUTATION ANALYSIS"
[1] 3
  TAF5 MUTATED TAF5 WILD-TYPE 
             3             53 
  TAF5 MUTATED TAF5 WILD-TYPE 
             3             53 
[1] "SARM1 MUTATION ANALYSIS"
[1] 3
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              50 
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              50 
[1] "PRSS27 MUTATION ANALYSIS"
[1] 3
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               53 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               53 
[1] "TMEM189 MUTATION ANALYSIS"
[1] 3
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                53 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                53 
[1] "NOXA1 MUTATION ANALYSIS"
[1] 3
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              4              52 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              4              52 
[1] "LRP11 MUTATION ANALYSIS"
[1] 3
  LRP11 MUTATED LRP11 WILD-TYPE 
              4              52 
  LRP11 MUTATED LRP11 WILD-TYPE 
              4              52 
[1] "RNF149 MUTATION ANALYSIS"
[1] 3
  RNF149 MUTATED RNF149 WILD-TYPE 
               3               53 
  RNF149 MUTATED RNF149 WILD-TYPE 
               3               53 
[1] "DMKN MUTATION ANALYSIS"
[1] 3
  DMKN MUTATED DMKN WILD-TYPE 
             3             53 
  DMKN MUTATED DMKN WILD-TYPE 
             3             53 
[1] "FANK1 MUTATION ANALYSIS"
[1] 3
  FANK1 MUTATED FANK1 WILD-TYPE 
              3              53 
  FANK1 MUTATED FANK1 WILD-TYPE 
              3              53 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             19              37 
  MUC5B MUTATED MUC5B WILD-TYPE 
             19              37 
[1] "GLTPD2 MUTATION ANALYSIS"
[1] 3
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               50 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               50 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             51 
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             51 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             3             53 
  SRPX MUTATED SRPX WILD-TYPE 
             3             53 
[1] "MAP1S MUTATION ANALYSIS"
[1] 3
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              51 
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              51 
[1] "SCRT1 MUTATION ANALYSIS"
[1] 3
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              53 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              53 
[1] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              38 
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              38 
[1] "IER5 MUTATION ANALYSIS"
[1] 3
  IER5 MUTATED IER5 WILD-TYPE 
             3             53 
  IER5 MUTATED IER5 WILD-TYPE 
             3             53 
[1] "TNIP2 MUTATION ANALYSIS"
[1] 3
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              51 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              51 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               51 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               51 
[1] "RASIP1 MUTATION ANALYSIS"
[1] 3
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               7               49 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               7               49 
[1] "NMU MUTATION ANALYSIS"
[1] 3
  NMU MUTATED NMU WILD-TYPE 
            4            52 
  NMU MUTATED NMU WILD-TYPE 
            4            52 
[1] "VARS MUTATION ANALYSIS"
[1] 3
  VARS MUTATED VARS WILD-TYPE 
             6             50 
  VARS MUTATED VARS WILD-TYPE 
             6             50 
[1] "HSD17B1 MUTATION ANALYSIS"
[1] 3
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                52 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                52 
[1] "COQ2 MUTATION ANALYSIS"
[1] 3
  COQ2 MUTATED COQ2 WILD-TYPE 
             4             52 
  COQ2 MUTATED COQ2 WILD-TYPE 
             4             52 
[1] "KNDC1 MUTATION ANALYSIS"
[1] 3
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              47 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              47 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
           4           52 
  AR MUTATED AR WILD-TYPE 
           4           52 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              3              53 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              3              53 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 53 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 53 
[1] "AKAP2 MUTATION ANALYSIS"
[1] 3
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              52 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              52 
[1] "KBTBD13 MUTATION ANALYSIS"
[1] 3
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                47 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                47 
[1] "SPIRE2 MUTATION ANALYSIS"
[1] 3
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               53 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               53 
[1] "NPTX1 MUTATION ANALYSIS"
[1] 3
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              53 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              53 
[1] "ADAD2 MUTATION ANALYSIS"
[1] 3
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              3              53 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              3              53 
[1] "SEZ6L2 MUTATION ANALYSIS"
[1] 3
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               5               51 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               5               51 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             5             51 
  NEFH MUTATED NEFH WILD-TYPE 
             5             51 
[1] "AMDHD1 MUTATION ANALYSIS"
[1] 3
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               46 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               46 
[1] "GLTSCR2 MUTATION ANALYSIS"
[1] 3
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
                4                52 
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
                4                52 
[1] "PLEC MUTATION ANALYSIS"
[1] 3
  PLEC MUTATED PLEC WILD-TYPE 
            10             46 
  PLEC MUTATED PLEC WILD-TYPE 
            10             46 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             53 
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             53 
[1] "DSPP MUTATION ANALYSIS"
[1] 3
  DSPP MUTATED DSPP WILD-TYPE 
             9             47 
  DSPP MUTATED DSPP WILD-TYPE 
             9             47 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               8               48 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               8               48 
[1] "PRKAR1A MUTATION ANALYSIS"
[1] 3
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                50 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                50 
[1] "CYP4A22 MUTATION ANALYSIS"
[1] 3
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                3                53 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                3                53 
[1] "NOM1 MUTATION ANALYSIS"
[1] 3
  NOM1 MUTATED NOM1 WILD-TYPE 
             5             51 
  NOM1 MUTATED NOM1 WILD-TYPE 
             5             51 
[1] "C12ORF65 MUTATION ANALYSIS"
[1] 3
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
                 3                 53 
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
                 3                 53 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              50 
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              50 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   53 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   53 
[1] "UQCRFS1 MUTATION ANALYSIS"
[1] 3
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                51 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                51 
[1] "PDCD6 MUTATION ANALYSIS"
[1] 3
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              53 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              53 
[1] "PTX4 MUTATION ANALYSIS"
[1] 3
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             53 
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             53 
[1] "POLRMT MUTATION ANALYSIS"
[1] 3
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               52 
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               52 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            7            49 
  NF1 MUTATED NF1 WILD-TYPE 
            7            49 
[1] "ADAMTS7 MUTATION ANALYSIS"
[1] 3
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                52 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                52 
[1] "CLIC6 MUTATION ANALYSIS"
[1] 3
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              4              52 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              4              52 
[1] "EMR2 MUTATION ANALYSIS"
[1] 3
  EMR2 MUTATED EMR2 WILD-TYPE 
             4             52 
  EMR2 MUTATED EMR2 WILD-TYPE 
             4             52 
[1] "PCDHB13 MUTATION ANALYSIS"
[1] 3
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                4                52 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                4                52 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              53 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              53 
[1] "ASB16 MUTATION ANALYSIS"
[1] 3
  ASB16 MUTATED ASB16 WILD-TYPE 
              4              52 
  ASB16 MUTATED ASB16 WILD-TYPE 
              4              52 
[1] "GPRIN2 MUTATION ANALYSIS"
[1] 3
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               7               49 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               7               49 
[1] "HNRNPCL1 MUTATION ANALYSIS"
[1] 3
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 3                 53 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 3                 53 
[1] "BTNL9 MUTATION ANALYSIS"
[1] 3
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              3              53 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              3              53 
[1] "KCNJ11 MUTATION ANALYSIS"
[1] 3
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               52 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               52 
[1] "LRRC4B MUTATION ANALYSIS"
[1] 3
  LRRC4B MUTATED LRRC4B WILD-TYPE 
               6               50 
  LRRC4B MUTATED LRRC4B WILD-TYPE 
               6               50 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
              3              53 
  OPLAH MUTATED OPLAH WILD-TYPE 
              3              53 
[1] "MADCAM1 MUTATION ANALYSIS"
[1] 3
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
                3                53 
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
                3                53 
[1] "MSH3 MUTATION ANALYSIS"
[1] 3
  MSH3 MUTATED MSH3 WILD-TYPE 
             3             53 
  MSH3 MUTATED MSH3 WILD-TYPE 
             3             53 
[1] "UTS2R MUTATION ANALYSIS"
[1] 3
  UTS2R MUTATED UTS2R WILD-TYPE 
              3              53 
  UTS2R MUTATED UTS2R WILD-TYPE 
              3              53 
[1] "SMG1 MUTATION ANALYSIS"
[1] 3
  SMG1 MUTATED SMG1 WILD-TYPE 
             3             53 
  SMG1 MUTATED SMG1 WILD-TYPE 
             3             53 
[1] "FEZ2 MUTATION ANALYSIS"
[1] 3
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             53 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             53 
[1] "GLI3 MUTATION ANALYSIS"
[1] 3
  GLI3 MUTATED GLI3 WILD-TYPE 
             5             51 
  GLI3 MUTATED GLI3 WILD-TYPE 
             5             51 
[1] "NOL9 MUTATION ANALYSIS"
[1] 3
  NOL9 MUTATED NOL9 WILD-TYPE 
             3             53 
  NOL9 MUTATED NOL9 WILD-TYPE 
             3             53 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 56 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
          NA           NA         1942           NA           NA         2428 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
          NA           NA           NA           NA           NA         2782 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
        1259         1227         1424         1255          670          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
         674         3688          488         1541         1924          950 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
          NA           NA          528          253           NA         1414 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
        2673         4673         3659         1525         1091           NA 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
        3897          724          840          628          645          487 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
          NA           NA           NA           NA         2222           NA 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-P6-A5OH 
        1949         1583          639           NA           NA           NA 
TCGA-PK-A5H8 TCGA-PK-A5HB 
        3240         1293 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 56 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 25  7 15 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 25  7 15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 6 25  7 15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 25  7 15 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = ZFPM1 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  ZFPM1 MUTATED   12 10
  ZFPM1 WILD-TYPE 23 10
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             22              33 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             10              10 
$`ZFPM1 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JH 
       55.13        63.85        16.11        30.31        18.12        40.34 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY 
       41.26        22.03       121.25        16.04        50.66        18.15 
TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LA 
       11.31       120.30        50.14         4.11        20.65        16.01 
TCGA-OR-A5LC TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5HB 
        5.23        53.03        12.59        42.51 

$`ZFPM1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JC 
       44.55        15.45        12.00        79.82        19.04        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JW 
       91.46        41.39        46.82         4.90        22.16        63.25 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       31.23        32.68        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 
      153.63        35.87       128.12        23.80        27.62        21.21 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
       39.58        39.35        36.33        73.05        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       21.01         6.81       106.52 

  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
           4.11            4.90 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
         121.25          153.63 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
          26.17           39.35 
[1] "4.1 - 121.2 (26.2)" "4.9 - 153.6 (39.4)"
[1] "hr=" "1.8"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ZFPM1 MUTATED         2        8         4        8
  ZFPM1 WILD-TYPE       4       13        10        4
D1V3, multiclass
           clus
vv          ZFPM1 MUTATED ZFPM1 WILD-TYPE
  STAGE I               2               4
  STAGE II              8              13
  STAGE III             4              10
  STAGE IV              8               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  ZFPM1 MUTATED    2 10  3  7
  ZFPM1 WILD-TYPE  4 15  4  8
D1V4, multiclass
    clus
vv   ZFPM1 MUTATED ZFPM1 WILD-TYPE
  T1             2               4
  T2            10              15
  T3             3               4
  T4             7               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                 cls
clus               0  1
  ZFPM1 MUTATED   19  3
  ZFPM1 WILD-TYPE 28  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     19    3
  ZFPM1 WILD-TYPE   28    3
   clus
vv  ZFPM1 MUTATED ZFPM1 WILD-TYPE
  0            19              28
  1             3               3
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus               0  1
  ZFPM1 MUTATED   16  7
  ZFPM1 WILD-TYPE 21 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     16    7
  ZFPM1 WILD-TYPE   21   12
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  FEMALE            16              21
  MALE               7              12
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus               0  1
  ZFPM1 MUTATED    3  8
  ZFPM1 WILD-TYPE  4 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED      3    8
  ZFPM1 WILD-TYPE    4   13
                        clus
vv                       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO             8              13
[1] 2 2
[1] FALSE

Clustering(2) Variable = LACTB MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  LACTB MUTATED   10  7
  LACTB WILD-TYPE 25 13
  LACTB MUTATED LACTB WILD-TYPE 
             17              38 
  LACTB MUTATED LACTB WILD-TYPE 
              7              13 
$`LACTB MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI 
       12.00        79.82        19.04        18.12        57.53        46.82 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K9 TCGA-OR-A5KU 
       22.03        22.16        16.04        63.25        11.31       153.63 
TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5LJ 
       50.14         4.11       128.12        27.62        36.33 

$`LACTB WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA 
       44.55        55.13        63.85        15.45        16.11        30.31 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JR 
       91.46        41.39        40.34        41.26         4.90       121.25 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L4 TCGA-OR-A5L6 
       46.49        87.88       120.30        35.87        23.80        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       21.21        16.01        39.58         5.23        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  LACTB MUTATED LACTB WILD-TYPE 
           4.11            4.90 
  LACTB MUTATED LACTB WILD-TYPE 
         153.63          121.25 
  LACTB MUTATED LACTB WILD-TYPE 
         27.620          39.465 
[1] "4.1 - 153.6 (27.6)" "4.9 - 121.2 (39.5)"
[1] "hr=" "1.2"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LACTB MUTATED         4        7         3        2
  LACTB WILD-TYPE       2       14        11       10
D2V3, multiclass
           clus
vv          LACTB MUTATED LACTB WILD-TYPE
  STAGE I               4               2
  STAGE II              7              14
  STAGE III             3              11
  STAGE IV              2              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              T1 T2 T3 T4
  LACTB MUTATED    4  9  1  2
  LACTB WILD-TYPE  2 16  6 13
D2V4, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  T1             4               2
  T2             9              16
  T3             1               6
  T4             2              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"
D2V5, binary
                 cls
clus               0  1
  LACTB MUTATED   14  2
  LACTB WILD-TYPE 33  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     14    2
  LACTB WILD-TYPE   33    4
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0            14              33
  1             2               4
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus               0  1
  LACTB MUTATED   10  7
  LACTB WILD-TYPE 27 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     10    7
  LACTB WILD-TYPE   27   12
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  FEMALE            10              27
  MALE               7              12
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus               0  1
  LACTB MUTATED    3  6
  LACTB WILD-TYPE  4 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    6
  LACTB WILD-TYPE    4   15
                        clus
vv                       LACTB MUTATED LACTB WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO             6              15
[1] 2 2
[1] FALSE

Clustering(3) Variable = CCDC102A MUTATION ANALYSIS
D3V1, survival
                    sevent
clus2                 0  1
  CCDC102A MUTATED   13  3
  CCDC102A WILD-TYPE 22 17
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                16                 39 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                 3                 17 
$`CCDC102A MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       55.13        46.82        22.03         4.90        22.16       121.25 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       63.25        31.23        17.36        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      153.63        21.21        16.01         5.23 

$`CCDC102A WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 
       40.34        41.26        16.04        50.66        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
        8.32       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ 
       23.80        27.62        20.65        39.58        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  CCDC102A MUTATED CCDC102A WILD-TYPE 
              4.90               4.11 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
            153.63             128.12 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
            26.695             39.350 
[1] "4.9 - 153.6 (26.7)" "4.1 - 128.1 (39.4)"
[1] "hr=" "2.2"
D3V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  CCDC102A MUTATED         4        7         2        3
  CCDC102A WILD-TYPE       2       14        12        9
D3V3, multiclass
           clus
vv          CCDC102A MUTATED CCDC102A WILD-TYPE
  STAGE I                  4                  2
  STAGE II                 7                 14
  STAGE III                2                 12
  STAGE IV                 3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  CCDC102A MUTATED    4  7  2  3
  CCDC102A WILD-TYPE  2 18  5 12
D3V4, multiclass
    clus
vv   CCDC102A MUTATED CCDC102A WILD-TYPE
  T1                4                  2
  T2                7                 18
  T3                2                  5
  T4                3                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                    cls
clus                  0  1
  CCDC102A MUTATED   16  0
  CCDC102A WILD-TYPE 31  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     16    0
  CCDC102A WILD-TYPE   31    6
   clus
vv  CCDC102A MUTATED CCDC102A WILD-TYPE
  0               16                 31
  1                0                  6
[1] 2 2
[1] FALSE
D3V6, binary
                    cls
clus                  0  1
  CCDC102A MUTATED   11  5
  CCDC102A WILD-TYPE 26 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     11    5
  CCDC102A WILD-TYPE   26   14
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  FEMALE               11                 26
  MALE                  5                 14
[1] 2 2
[1] FALSE
D3V7, binary
                    cls
clus                  0  1
  CCDC102A MUTATED    1  6
  CCDC102A WILD-TYPE  6 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED      1    6
  CCDC102A WILD-TYPE    6   15
                        clus
vv                       CCDC102A MUTATED CCDC102A WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                6                 15
[1] 2 2
[1] FALSE

Clustering(4) Variable = ZNF517 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  ZNF517 MUTATED    8  2
  ZNF517 WILD-TYPE 27 18
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              10               45 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
               2               18 
$`ZNF517 MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       18.12        41.39        40.34        17.36         8.32        11.31 
TCGA-OR-A5KV TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-PK-A5HB 
      120.30        20.65        16.01        42.51 

$`ZNF517 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI 
       16.11        19.04        30.31        57.53        91.46        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        22.03         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5KO 
       50.66        63.25        31.23        18.15        32.68        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
       87.88       153.63        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       23.80        27.62        21.21        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
        6.81        12.59       106.52 

  ZNF517 MUTATED ZNF517 WILD-TYPE 
            8.32             4.11 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
          120.30           153.63 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
          19.385           39.350 
[1] "8.3 - 120.3 (19.4)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.4"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF517 MUTATED         0        5         3        2
  ZNF517 WILD-TYPE       6       16        11       10
D4V3, multiclass
           clus
vv          ZNF517 MUTATED ZNF517 WILD-TYPE
  STAGE I                0                6
  STAGE II               5               16
  STAGE III              3               11
  STAGE IV               2               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               T1 T2 T3 T4
  ZNF517 MUTATED    0  6  1  3
  ZNF517 WILD-TYPE  6 19  6 12
D4V4, multiclass
    clus
vv   ZNF517 MUTATED ZNF517 WILD-TYPE
  T1              0                6
  T2              6               19
  T3              1                6
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                  cls
clus                0  1
  ZNF517 MUTATED    9  1
  ZNF517 WILD-TYPE 38  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      9    1
  ZNF517 WILD-TYPE   38    5
   clus
vv  ZNF517 MUTATED ZNF517 WILD-TYPE
  0              9               38
  1              1                5
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                0  1
  ZNF517 MUTATED    8  3
  ZNF517 WILD-TYPE 29 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      8    3
  ZNF517 WILD-TYPE   29   16
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  FEMALE              8               29
  MALE                3               16
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                0  1
  ZNF517 MUTATED    0  4
  ZNF517 WILD-TYPE  7 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      0    4
  ZNF517 WILD-TYPE    7   17
                        clus
vv                       ZNF517 MUTATED ZNF517 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               17
[1] 2 2
[1] FALSE

Clustering(5) Variable = TOR3A MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  TOR3A MUTATED    8  3
  TOR3A WILD-TYPE 27 17
  TOR3A MUTATED TOR3A WILD-TYPE 
             11              44 
  TOR3A MUTATED TOR3A WILD-TYPE 
              3              17 
$`TOR3A MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT 
       79.82        30.31        18.12        22.03       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5KT TCGA-OR-A5L6 TCGA-P6-A5OF TCGA-PK-A5HB 
       50.66        87.88        20.65         6.81        42.51 

$`TOR3A WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       19.04        57.53        91.46        41.39        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       41.26         4.90        22.16        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU 
       32.68        17.36         8.32        11.31        46.49       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  TOR3A MUTATED TOR3A WILD-TYPE 
           6.81            4.11 
  TOR3A MUTATED TOR3A WILD-TYPE 
         121.25          153.63 
  TOR3A MUTATED TOR3A WILD-TYPE 
          30.31           37.84 
[1] "6.8 - 121.2 (30.3)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.4"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TOR3A MUTATED         3        4         1        2
  TOR3A WILD-TYPE       3       17        13       10
D5V3, multiclass
           clus
vv          TOR3A MUTATED TOR3A WILD-TYPE
  STAGE I               3               3
  STAGE II              4              17
  STAGE III             1              13
  STAGE IV              2              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              T1 T2 T3 T4
  TOR3A MUTATED    3  4  0  3
  TOR3A WILD-TYPE  3 21  7 12
D5V4, multiclass
    clus
vv   TOR3A MUTATED TOR3A WILD-TYPE
  T1             3               3
  T2             4              21
  T3             0               7
  T4             3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                 cls
clus               0  1
  TOR3A MUTATED   10  0
  TOR3A WILD-TYPE 37  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED     10    0
  TOR3A WILD-TYPE   37    6
   clus
vv  TOR3A MUTATED TOR3A WILD-TYPE
  0            10              37
  1             0               6
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus               0  1
  TOR3A MUTATED    6  5
  TOR3A WILD-TYPE 31 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      6    5
  TOR3A WILD-TYPE   31   14
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  FEMALE             6              31
  MALE               5              14
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus               0  1
  TOR3A MUTATED    1  3
  TOR3A WILD-TYPE  6 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      1    3
  TOR3A WILD-TYPE    6   18
                        clus
vv                       TOR3A MUTATED TOR3A WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(6) Variable = USP42 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  USP42 MUTATED    9  3
  USP42 WILD-TYPE 26 17
  USP42 MUTATED USP42 WILD-TYPE 
             12              43 
  USP42 MUTATED USP42 WILD-TYPE 
              3              17 
$`USP42 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       63.85        19.04        41.39        40.34        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5KO TCGA-OR-A5KX TCGA-OR-A5LD TCGA-OR-A5LJ 
       22.16       121.25        46.49        35.87        39.35        36.33 

$`USP42 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JP 
       30.31        18.12        57.53        91.46        46.82         4.90 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LK TCGA-OR-A5LL 
       21.21        16.01        39.58         5.23        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  USP42 MUTATED USP42 WILD-TYPE 
          19.04            4.11 
  USP42 MUTATED USP42 WILD-TYPE 
         121.25          153.63 
  USP42 MUTATED USP42 WILD-TYPE 
         39.845          31.230 
[1] "19.0 - 121.2 (39.8)" "4.1 - 153.6 (31.2)" 
[1] "hr=" "1.8"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  USP42 MUTATED         2        3         4        4
  USP42 WILD-TYPE       4       18        10        8
D6V3, multiclass
           clus
vv          USP42 MUTATED USP42 WILD-TYPE
  STAGE I               2               4
  STAGE II              3              18
  STAGE III             4              10
  STAGE IV              4               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  USP42 MUTATED    2  5  2  4
  USP42 WILD-TYPE  4 20  5 11
D6V4, multiclass
    clus
vv   USP42 MUTATED USP42 WILD-TYPE
  T1             2               4
  T2             5              20
  T3             2               5
  T4             4              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"
D6V5, binary
                 cls
clus               0  1
  USP42 MUTATED   11  2
  USP42 WILD-TYPE 36  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED     11    2
  USP42 WILD-TYPE   36    4
   clus
vv  USP42 MUTATED USP42 WILD-TYPE
  0            11              36
  1             2               4
[1] 2 2
[1] FALSE
D6V6, binary
                 cls
clus               0  1
  USP42 MUTATED    9  4
  USP42 WILD-TYPE 28 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED      9    4
  USP42 WILD-TYPE   28   15
        clus
vv       USP42 MUTATED USP42 WILD-TYPE
  FEMALE             9              28
  MALE               4              15
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus               0  1
  USP42 MUTATED    2  5
  USP42 WILD-TYPE  5 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED      2    5
  USP42 WILD-TYPE    5   16
                        clus
vv                       USP42 MUTATED USP42 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             5              16
[1] 2 2
[1] FALSE

Clustering(7) Variable = CLDN23 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  CLDN23 MUTATED    7  3
  CLDN23 WILD-TYPE 28 17
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               45 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
               3               17 
$`CLDN23 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JY TCGA-OR-A5L4 TCGA-OR-A5L9 
       46.82        41.26        22.16        18.15        23.80        21.21 
TCGA-OR-A5LA TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LR 
       16.01        36.33        53.03        21.01 

$`CLDN23 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       41.39        40.34        22.03         4.90       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        63.25        31.23        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB 
       35.87         4.11       128.12        27.62        20.65        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF 
        5.23        39.35        73.05        64.08        52.04         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  CLDN23 MUTATED CLDN23 WILD-TYPE 
           16.01             4.11 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
           53.03           153.63 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
           22.98            39.58 
[1] "16.0 - 53.0 (23.0)" "4.1 - 153.6 (39.6)"
[1] "hr=" "1"  
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CLDN23 MUTATED         1        5         1        3
  CLDN23 WILD-TYPE       5       16        13        9
D7V3, multiclass
           clus
vv          CLDN23 MUTATED CLDN23 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               16
  STAGE III              1               13
  STAGE IV               3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CLDN23 MUTATED    1  6  0  3
  CLDN23 WILD-TYPE  5 19  7 12
D7V4, multiclass
    clus
vv   CLDN23 MUTATED CLDN23 WILD-TYPE
  T1              1                5
  T2              6               19
  T3              0                7
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                  cls
clus                0  1
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 39  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   39    4
   clus
vv  CLDN23 MUTATED CLDN23 WILD-TYPE
  0              8               39
  1              2                4
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                0  1
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 29 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   29   17
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  FEMALE              8               29
  MALE                2               17
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                0  1
  CLDN23 MUTATED    0  4
  CLDN23 WILD-TYPE  7 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      0    4
  CLDN23 WILD-TYPE    7   17
                        clus
vv                       CLDN23 MUTATED CLDN23 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               17
[1] 2 2
[1] FALSE

Clustering(8) Variable = TP53 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    5  6
  TP53 WILD-TYPE 30 14
  TP53 MUTATED TP53 WILD-TYPE 
            11             44 
  TP53 MUTATED TP53 WILD-TYPE 
             6             14 
$`TP53 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JL TCGA-OR-A5JP 
       55.13        12.00        30.31        18.12        22.03         4.90 
TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5LJ TCGA-PK-A5HB 
       17.36        46.49         4.11        36.33        42.51 

$`TP53 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        63.85        15.45        79.82        16.11        19.04 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        91.46        41.39        40.34        46.82        41.26 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       18.15        32.68         8.32        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  TP53 MUTATED TP53 WILD-TYPE 
          4.11           5.23 
  TP53 MUTATED TP53 WILD-TYPE 
         55.13         153.63 
  TP53 MUTATED TP53 WILD-TYPE 
         22.03          39.96 
[1] "4.1 - 55.1 (22.0)"  "5.2 - 153.6 (40.0)"
[1] "hr=" "2.7"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         1        2         2        5
  TP53 WILD-TYPE       5       19        12        7
D8V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              1              5
  STAGE II             2             19
  STAGE III            2             12
  STAGE IV             5              7
[1] 4 2
[1] TRUE
[1] "dimension of 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    1  3  1  5
  TP53 WILD-TYPE  5 22  6 10
D8V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            1              5
  T2            3             22
  T3            1              6
  T4            5             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"
D8V5, binary
                cls
clus              0  1
  TP53 MUTATED    9  1
  TP53 WILD-TYPE 38  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9    1
  TP53 WILD-TYPE   38    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            9             38
  1            1              5
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus              0  1
  TP53 MUTATED    6  5
  TP53 WILD-TYPE 31 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6    5
  TP53 WILD-TYPE   31   14
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            6             31
  MALE              5             14
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE  5 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE    5   18
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(9) Variable = KCNK17 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  KCNK17 MUTATED    6  2
  KCNK17 WILD-TYPE 29 18
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               8               47 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               2               18 
$`KCNK17 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JI TCGA-OR-A5JW TCGA-OR-A5KO 
       63.85        19.04        30.31        46.82        63.25        46.49 
TCGA-OR-A5LO TCGA-PK-A5HB 
       64.08        42.51 

$`KCNK17 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        91.46        41.39        40.34        41.26 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       31.23        18.15        32.68        17.36         8.32        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.58         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       52.04        21.01         6.81        12.59       106.52 

  KCNK17 MUTATED KCNK17 WILD-TYPE 
           19.04             4.11 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
           64.08           153.63 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
          46.655           32.680 
[1] "19.0 - 64.1 (46.7)" "4.1 - 153.6 (32.7)"
[1] "hr=" "2.2"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KCNK17 MUTATED         1        2         2        2
  KCNK17 WILD-TYPE       5       19        12       10
D9V3, multiclass
           clus
vv          KCNK17 MUTATED KCNK17 WILD-TYPE
  STAGE I                1                5
  STAGE II               2               19
  STAGE III              2               12
  STAGE IV               2               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               T1 T2 T3 T4
  KCNK17 MUTATED    1  2  2  2
  KCNK17 WILD-TYPE  5 23  5 13
D9V4, multiclass
    clus
vv   KCNK17 MUTATED KCNK17 WILD-TYPE
  T1              1                5
  T2              2               23
  T3              2                5
  T4              2               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"
D9V5, binary
                  cls
clus                0  1
  KCNK17 MUTATED    7  0
  KCNK17 WILD-TYPE 40  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      7    0
  KCNK17 WILD-TYPE   40    6
   clus
vv  KCNK17 MUTATED KCNK17 WILD-TYPE
  0              7               40
  1              0                6
[1] 2 2
[1] FALSE
D9V6, binary
                  cls
clus                0  1
  KCNK17 MUTATED    4  4
  KCNK17 WILD-TYPE 33 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      4    4
  KCNK17 WILD-TYPE   33   15
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  FEMALE              4               33
  MALE                4               15
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                0  1
  KCNK17 MUTATED    2  1
  KCNK17 WILD-TYPE  5 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      2    1
  KCNK17 WILD-TYPE    5   20
                        clus
vv                       KCNK17 MUTATED KCNK17 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              1               20
[1] 2 2
[1] FALSE

Clustering(10) Variable = LZTR1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  LZTR1 MUTATED    1  3
  LZTR1 WILD-TYPE 34 17
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              4              51 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              3              17 
$`LZTR1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5LB 
       19.04        11.31       120.30        39.58 

$`LZTR1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       20.65        21.21        16.01         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  LZTR1 MUTATED LZTR1 WILD-TYPE 
          11.31            4.11 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
         120.30          153.63 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
          29.31           36.33 
[1] "11.3 - 120.3 (29.3)" "4.1 - 153.6 (36.3)" 
[1] "hr=" "2.4"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LZTR1 MUTATED         0        1         2        1
  LZTR1 WILD-TYPE       6       20        12       11
D10V3, multiclass
           clus
vv          LZTR1 MUTATED LZTR1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             2              12
  STAGE IV              1              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              T1 T2 T3 T4
  LZTR1 MUTATED    0  2  1  1
  LZTR1 WILD-TYPE  6 23  6 14
D10V4, multiclass
    clus
vv   LZTR1 MUTATED LZTR1 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             1               6
  T4             1              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"
D10V5, binary
                 cls
clus               0  1
  LZTR1 MUTATED    3  1
  LZTR1 WILD-TYPE 44  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      3    1
  LZTR1 WILD-TYPE   44    5
   clus
vv  LZTR1 MUTATED LZTR1 WILD-TYPE
  0             3              44
  1             1               5
[1] 2 2
[1] FALSE
D10V6, binary
                 cls
clus               0  1
  LZTR1 MUTATED    2  2
  LZTR1 WILD-TYPE 35 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      2    2
  LZTR1 WILD-TYPE   35   17
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  FEMALE             2              35
  MALE               2              17
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus               0  1
  LZTR1 MUTATED    1  2
  LZTR1 WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      1    2
  LZTR1 WILD-TYPE    6   19
                        clus
vv                       LZTR1 MUTATED LZTR1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(11) Variable = APOE MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  APOE MUTATED    3  2
  APOE WILD-TYPE 32 18
  APOE MUTATED APOE WILD-TYPE 
             5             50 
  APOE MUTATED APOE WILD-TYPE 
             2             18 
$`APOE MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-PK-A5HB 
       18.12        63.25        17.36        11.31        42.51 

$`APOE WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        30.31        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        16.04        50.66        31.23        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
        8.32        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  APOE MUTATED APOE WILD-TYPE 
         11.31           4.11 
  APOE MUTATED APOE WILD-TYPE 
         63.25         153.63 
  APOE MUTATED APOE WILD-TYPE 
         18.12          37.84 
[1] "11.3 - 63.2 (18.1)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.4"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  APOE MUTATED         0        2         1        1
  APOE WILD-TYPE       6       19        13       11
D11V3, multiclass
           clus
vv          APOE MUTATED APOE WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            1             13
  STAGE IV             1             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             T1 T2 T3 T4
  APOE MUTATED    0  2  0  2
  APOE WILD-TYPE  6 23  7 13
D11V4, multiclass
    clus
vv   APOE MUTATED APOE WILD-TYPE
  T1            0              6
  T2            2             23
  T3            0              7
  T4            2             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"
D11V5, binary
                cls
clus              0  1
  APOE MUTATED    4  0
  APOE WILD-TYPE 43  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      4    0
  APOE WILD-TYPE   43    6
   clus
vv  APOE MUTATED APOE WILD-TYPE
  0            4             43
  1            0              6
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus              0  1
  APOE MUTATED    2  3
  APOE WILD-TYPE 35 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      2    3
  APOE WILD-TYPE   35   16
        clus
vv       APOE MUTATED APOE WILD-TYPE
  FEMALE            2             35
  MALE              3             16
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus              0  1
  APOE MUTATED    0  0
  APOE WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      0    0
  APOE WILD-TYPE    7   21

Clustering(12) Variable = CCDC105 MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  CCDC105 MUTATED    3  3
  CCDC105 WILD-TYPE 32 17
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                49 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                3                17 
$`CCDC105 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5L5 TCGA-OR-A5LJ TCGA-OR-A5LL 
       63.85        22.03        11.31        27.62        36.33        53.03 

$`CCDC105 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       50.14        35.87         4.11       128.12        23.80        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       21.21        16.01        39.58         5.23        39.35        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  CCDC105 MUTATED CCDC105 WILD-TYPE 
            11.31              4.11 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
            63.85            153.63 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
           31.975            39.350 
[1] "11.3 - 63.9 (32.0)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC105 MUTATED         2        2         1        1
  CCDC105 WILD-TYPE       4       19        13       11
D12V3, multiclass
           clus
vv          CCDC105 MUTATED CCDC105 WILD-TYPE
  STAGE I                 2                 4
  STAGE II                2                19
  STAGE III               1                13
  STAGE IV                1                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                T1 T2 T3 T4
  CCDC105 MUTATED    2  3  1  0
  CCDC105 WILD-TYPE  4 22  6 15
D12V4, multiclass
    clus
vv   CCDC105 MUTATED CCDC105 WILD-TYPE
  T1               2                 4
  T2               3                22
  T3               1                 6
  T4               0                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"
D12V5, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    5  1
  CCDC105 WILD-TYPE 42  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      5    1
  CCDC105 WILD-TYPE   42    5
   clus
vv  CCDC105 MUTATED CCDC105 WILD-TYPE
  0               5                42
  1               1                 5
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    6  0
  CCDC105 WILD-TYPE 31 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      6    0
  CCDC105 WILD-TYPE   31   19
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  FEMALE               6                31
  MALE                 0                19
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    1  2
  CCDC105 WILD-TYPE  6 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      1    2
  CCDC105 WILD-TYPE    6   19
                        clus
vv                       CCDC105 MUTATED CCDC105 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               2                19
[1] 2 2
[1] FALSE

Clustering(13) Variable = RINL MUTATION ANALYSIS
D13V1, survival
                sevent
clus2             0  1
  RINL MUTATED    3  4
  RINL WILD-TYPE 32 16
  RINL MUTATED RINL WILD-TYPE 
             7             48 
  RINL MUTATED RINL WILD-TYPE 
             4             16 
$`RINL MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5KV 
       55.13        19.04        16.04        63.25        32.68       120.30 
TCGA-OR-A5LC 
        5.23 

$`RINL WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       50.66        31.23        18.15        17.36         8.32        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       46.49        87.88       153.63        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       39.58        39.35        36.33        73.05        53.03        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       52.04        21.01         6.81        12.59       106.52        42.51 

  RINL MUTATED RINL WILD-TYPE 
          5.23           4.11 
  RINL MUTATED RINL WILD-TYPE 
        120.30         153.63 
  RINL MUTATED RINL WILD-TYPE 
         32.68          37.84 
[1] "5.2 - 120.3 (32.7)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.6"
D13V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RINL MUTATED         0        2         3        2
  RINL WILD-TYPE       6       19        11       10
D13V3, multiclass
           clus
vv          RINL MUTATED RINL WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            3             11
  STAGE IV             2             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             T1 T2 T3 T4
  RINL MUTATED    0  3  2  2
  RINL WILD-TYPE  6 22  5 13
D13V4, multiclass
    clus
vv   RINL MUTATED RINL WILD-TYPE
  T1            0              6
  T2            3             22
  T3            2              5
  T4            2             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"
D13V5, binary
                cls
clus              0  1
  RINL MUTATED    6  1
  RINL WILD-TYPE 41  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      6    1
  RINL WILD-TYPE   41    5
   clus
vv  RINL MUTATED RINL WILD-TYPE
  0            6             41
  1            1              5
[1] 2 2
[1] FALSE
D13V6, binary
                cls
clus              0  1
  RINL MUTATED    5  2
  RINL WILD-TYPE 32 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      5    2
  RINL WILD-TYPE   32   17
        clus
vv       RINL MUTATED RINL WILD-TYPE
  FEMALE            5             32
  MALE              2             17
[1] 2 2
[1] FALSE
D13V7, binary
                cls
clus              0  1
  RINL MUTATED    2  2
  RINL WILD-TYPE  5 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      2    2
  RINL WILD-TYPE    5   19
                        clus
vv                       RINL MUTATED RINL WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(14) Variable = MAL2 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  MAL2 MUTATED    6  3
  MAL2 WILD-TYPE 29 17
  MAL2 MUTATED MAL2 WILD-TYPE 
             9             46 
  MAL2 MUTATED MAL2 WILD-TYPE 
             3             17 
$`MAL2 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JT TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KX TCGA-OR-A5L9 
       41.39        16.04         8.32        11.31        35.87        21.21 
TCGA-OR-A5LA TCGA-OR-A5LJ TCGA-P6-A5OG 
       16.01        36.33        12.59 

$`MAL2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       17.36        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB 
        4.11       128.12        23.80        27.62        20.65        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       21.01         6.81       106.52        42.51 

  MAL2 MUTATED MAL2 WILD-TYPE 
          8.32           4.11 
  MAL2 MUTATED MAL2 WILD-TYPE 
         41.39         153.63 
  MAL2 MUTATED MAL2 WILD-TYPE 
         16.04          40.80 
[1] "8.3 - 41.4 (16.0)"  "4.1 - 153.6 (40.8)"
[1] "hr=" "1.8"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAL2 MUTATED         0        5         2        2
  MAL2 WILD-TYPE       6       16        12       10
D14V3, multiclass
           clus
vv          MAL2 MUTATED MAL2 WILD-TYPE
  STAGE I              0              6
  STAGE II             5             16
  STAGE III            2             12
  STAGE IV             2             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             T1 T2 T3 T4
  MAL2 MUTATED    0  7  1  1
  MAL2 WILD-TYPE  6 18  6 14
D14V4, multiclass
    clus
vv   MAL2 MUTATED MAL2 WILD-TYPE
  T1            0              6
  T2            7             18
  T3            1              6
  T4            1             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"
D14V5, binary
                cls
clus              0  1
  MAL2 MUTATED    7  2
  MAL2 WILD-TYPE 40  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      7    2
  MAL2 WILD-TYPE   40    4
   clus
vv  MAL2 MUTATED MAL2 WILD-TYPE
  0            7             40
  1            2              4
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus              0  1
  MAL2 MUTATED    9  0
  MAL2 WILD-TYPE 28 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      9    0
  MAL2 WILD-TYPE   28   19
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  FEMALE            9             28
  MALE              0             19
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus              0  1
  MAL2 MUTATED    0  5
  MAL2 WILD-TYPE  7 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      0    5
  MAL2 WILD-TYPE    7   16
                        clus
vv                       MAL2 MUTATED MAL2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            5             16
[1] 2 2
[1] FALSE

Clustering(15) Variable = LRIG1 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  LRIG1 MUTATED   10  3
  LRIG1 WILD-TYPE 25 17
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             13              42 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
              3              17 
$`LRIG1 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5K5 
       15.45        41.39        40.34        46.82        22.03         8.32 
TCGA-OR-A5KX TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-P6-A5OG 
       35.87        23.80        21.21        36.33        73.05        12.59 
TCGA-PK-A5HB 
       42.51 

$`LRIG1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JK 
       19.04        30.31        18.12        57.53        91.46        41.26 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
        4.90        22.16       121.25        16.04        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO 
       31.23        18.15        32.68        17.36        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 
       87.88       153.63       120.30        50.14         4.11       128.12 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        16.01        39.58         5.23        39.35 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01         6.81       106.52 

  LRIG1 MUTATED LRIG1 WILD-TYPE 
           8.32            4.11 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          73.05          153.63 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
         35.870          39.465 
[1] "8.3 - 73.0 (35.9)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.4"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRIG1 MUTATED         2        4         3        4
  LRIG1 WILD-TYPE       4       17        11        8
D15V3, multiclass
           clus
vv          LRIG1 MUTATED LRIG1 WILD-TYPE
  STAGE I               2               4
  STAGE II              4              17
  STAGE III             3              11
  STAGE IV              4               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  LRIG1 MUTATED    2  6  2  3
  LRIG1 WILD-TYPE  4 19  5 12
D15V4, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  T1             2               4
  T2             6              19
  T3             2               5
  T4             3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                 cls
clus               0  1
  LRIG1 MUTATED   10  3
  LRIG1 WILD-TYPE 37  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     10    3
  LRIG1 WILD-TYPE   37    3
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0            10              37
  1             3               3
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus               0  1
  LRIG1 MUTATED   11  3
  LRIG1 WILD-TYPE 26 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     11    3
  LRIG1 WILD-TYPE   26   16
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  FEMALE            11              26
  MALE               3              16
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  LRIG1 MUTATED    1  6
  LRIG1 WILD-TYPE  6 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      1    6
  LRIG1 WILD-TYPE    6   15
                        clus
vv                       LRIG1 MUTATED LRIG1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             6              15
[1] 2 2
[1] FALSE

Clustering(16) Variable = C19ORF10 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  C19ORF10 MUTATED    5  1
  C19ORF10 WILD-TYPE 30 19
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 6                 49 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 1                 19 
$`C19ORF10 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JW TCGA-OR-A5K5 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-P6-A5OF 
       63.85        63.25         8.32       153.63       120.30         6.81 

$`C19ORF10 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        16.04        50.66        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX 
       17.36        11.31        46.49        87.88        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
              6.81               4.11 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
            153.63             128.12 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
             63.55              35.87 
[1] "6.8 - 153.6 (63.5)" "4.1 - 128.1 (35.9)"
[1] "hr=" "3.2"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C19ORF10 MUTATED         0        2         4        0
  C19ORF10 WILD-TYPE       6       19        10       12
D16V3, multiclass
           clus
vv          C19ORF10 MUTATED C19ORF10 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 2                 19
  STAGE III                4                 10
  STAGE IV                 0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  C19ORF10 MUTATED    0  3  2  1
  C19ORF10 WILD-TYPE  6 22  5 14
D16V4, multiclass
    clus
vv   C19ORF10 MUTATED C19ORF10 WILD-TYPE
  T1                0                  6
  T2                3                 22
  T3                2                  5
  T4                1                 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"
D16V5, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    5  1
  C19ORF10 WILD-TYPE 42  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      5    1
  C19ORF10 WILD-TYPE   42    5
   clus
vv  C19ORF10 MUTATED C19ORF10 WILD-TYPE
  0                5                 42
  1                1                  5
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    5  1
  C19ORF10 WILD-TYPE 32 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      5    1
  C19ORF10 WILD-TYPE   32   18
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  FEMALE                5                 32
  MALE                  1                 18
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    1  3
  C19ORF10 WILD-TYPE  6 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      1    3
  C19ORF10 WILD-TYPE    6   18
                        clus
vv                       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                3                 18
[1] 2 2
[1] FALSE

Clustering(17) Variable = C10ORF95 MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  C10ORF95 MUTATED    3  3
  C10ORF95 WILD-TYPE 32 17
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 49 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 3                 17 
$`C10ORF95 MUTATED`
TCGA-OR-A5JQ TCGA-OR-A5K9 TCGA-OR-A5LB TCGA-OR-A5LO TCGA-P6-A5OG TCGA-PK-A5H8 
       22.16        11.31        39.58        64.08        12.59       106.52 

$`C10ORF95 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        73.05        53.03        52.04        21.01         6.81 
TCGA-PK-A5HB 
       42.51 

  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
             11.31               4.11 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
            106.52             153.63 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
             30.87              36.33 
[1] "11.3 - 106.5 (30.9)" "4.1 - 153.6 (36.3)" 
[1] "hr=" "1.4"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C10ORF95 MUTATED         0        3         0        2
  C10ORF95 WILD-TYPE       6       18        14       10
D17V3, multiclass
           clus
vv          C10ORF95 MUTATED C10ORF95 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 3                 18
  STAGE III                0                 14
  STAGE IV                 2                 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                 T1 T2 T3 T4
  C10ORF95 MUTATED    0  3  0  2
  C10ORF95 WILD-TYPE  6 22  7 13
D17V4, multiclass
    clus
vv   C10ORF95 MUTATED C10ORF95 WILD-TYPE
  T1                0                  6
  T2                3                 22
  T3                0                  7
  T4                2                 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"
D17V5, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    5  0
  C10ORF95 WILD-TYPE 42  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      5    0
  C10ORF95 WILD-TYPE   42    6
   clus
vv  C10ORF95 MUTATED C10ORF95 WILD-TYPE
  0                5                 42
  1                0                  6
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    4  2
  C10ORF95 WILD-TYPE 33 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      4    2
  C10ORF95 WILD-TYPE   33   17
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  FEMALE                4                 33
  MALE                  2                 17
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    0  3
  C10ORF95 WILD-TYPE  7 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      0    3
  C10ORF95 WILD-TYPE    7   18
                        clus
vv                       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                 18
[1] 2 2
[1] FALSE

Clustering(18) Variable = SYT8 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  SYT8 MUTATED    4  1
  SYT8 WILD-TYPE 31 19
  SYT8 MUTATED SYT8 WILD-TYPE 
             5             50 
  SYT8 MUTATED SYT8 WILD-TYPE 
             1             19 
$`SYT8 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5KO TCGA-OR-A5LB TCGA-OR-A5LO TCGA-OR-A5LR 
       41.39        46.49        39.58        64.08        21.01 

$`SYT8 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-P6-A5OF TCGA-P6-A5OG 
       36.33        73.05        53.03        52.04         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  SYT8 MUTATED SYT8 WILD-TYPE 
         21.01           4.11 
  SYT8 MUTATED SYT8 WILD-TYPE 
         64.08         153.63 
  SYT8 MUTATED SYT8 WILD-TYPE 
        41.390         34.275 
[1] "21.0 - 64.1 (41.4)" "4.1 - 153.6 (34.3)"
[1] "hr=" "2.3"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SYT8 MUTATED         0        3         0        2
  SYT8 WILD-TYPE       6       18        14       10
D18V3, multiclass
           clus
vv          SYT8 MUTATED SYT8 WILD-TYPE
  STAGE I              0              6
  STAGE II             3             18
  STAGE III            0             14
  STAGE IV             2             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             T1 T2 T3 T4
  SYT8 MUTATED    0  3  0  2
  SYT8 WILD-TYPE  6 22  7 13
D18V4, multiclass
    clus
vv   SYT8 MUTATED SYT8 WILD-TYPE
  T1            0              6
  T2            3             22
  T3            0              7
  T4            2             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"
D18V5, binary
                cls
clus              0  1
  SYT8 MUTATED    5  0
  SYT8 WILD-TYPE 42  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      5    0
  SYT8 WILD-TYPE   42    6
   clus
vv  SYT8 MUTATED SYT8 WILD-TYPE
  0            5             42
  1            0              6
[1] 2 2
[1] FALSE
D18V6, binary
                cls
clus              0  1
  SYT8 MUTATED    4  1
  SYT8 WILD-TYPE 33 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      4    1
  SYT8 WILD-TYPE   33   18
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  FEMALE            4             33
  MALE              1             18
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus              0  1
  SYT8 MUTATED    0  2
  SYT8 WILD-TYPE  7 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      0    2
  SYT8 WILD-TYPE    7   19
                        clus
vv                       SYT8 MUTATED SYT8 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(19) Variable = IDUA MUTATION ANALYSIS
D19V1, survival
                sevent
clus2             0  1
  IDUA MUTATED    6  2
  IDUA WILD-TYPE 29 18
  IDUA MUTATED IDUA WILD-TYPE 
             8             47 
  IDUA MUTATED IDUA WILD-TYPE 
             2             18 
$`IDUA MUTATED`
TCGA-OR-A5JP TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-OR-A5LK TCGA-OR-A5LO 
        4.90        11.31       153.63       128.12        73.05        64.08 
TCGA-P6-A5OG TCGA-PK-A5HB 
       12.59        42.51 

$`IDUA WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ 
       41.39        40.34        46.82        41.26        22.03        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV 
       32.68        17.36         8.32        46.49        87.88       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14        35.87         4.11        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        52.04        21.01         6.81       106.52 

  IDUA MUTATED IDUA WILD-TYPE 
          4.90           4.11 
  IDUA MUTATED IDUA WILD-TYPE 
        153.63         121.25 
  IDUA MUTATED IDUA WILD-TYPE 
        53.295         35.870 
[1] "4.9 - 153.6 (53.3)" "4.1 - 121.2 (35.9)"
[1] "hr=" "1.8"
D19V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         1        5         0        1
  IDUA WILD-TYPE       5       16        14       11
D19V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              1              5
  STAGE II             5             16
  STAGE III            0             14
  STAGE IV             1             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             T1 T2 T3 T4
  IDUA MUTATED    1  5  0  1
  IDUA WILD-TYPE  5 20  7 14
D19V4, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  T1            1              5
  T2            5             20
  T3            0              7
  T4            1             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"
D19V5, binary
                cls
clus              0  1
  IDUA MUTATED    7  0
  IDUA WILD-TYPE 40  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      7    0
  IDUA WILD-TYPE   40    6
   clus
vv  IDUA MUTATED IDUA WILD-TYPE
  0            7             40
  1            0              6
[1] 2 2
[1] FALSE
D19V6, binary
                cls
clus              0  1
  IDUA MUTATED    5  3
  IDUA WILD-TYPE 32 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      5    3
  IDUA WILD-TYPE   32   16
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  FEMALE            5             32
  MALE              3             16
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus              0  1
  IDUA MUTATED    0  3
  IDUA WILD-TYPE  7 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      0    3
  IDUA WILD-TYPE    7   18
                        clus
vv                       IDUA MUTATED IDUA WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(20) Variable = HHIPL1 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2               0  1
  HHIPL1 MUTATED    3  3
  HHIPL1 WILD-TYPE 32 17
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               49 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               3               17 
$`HHIPL1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-P6-A5OG 
       19.04        41.26        22.03       120.30         4.11        12.59 

$`HHIPL1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       40.34        46.82         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       35.87       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01         6.81       106.52 
TCGA-PK-A5HB 
       42.51 

  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
            4.11             4.90 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          120.30           153.63 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          20.535           39.350 
[1] "4.1 - 120.3 (20.5)" "4.9 - 153.6 (39.4)"
[1] "hr=" "1.9"
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HHIPL1 MUTATED         1        1         2        2
  HHIPL1 WILD-TYPE       5       20        12       10
D20V3, multiclass
           clus
vv          HHIPL1 MUTATED HHIPL1 WILD-TYPE
  STAGE I                1                5
  STAGE II               1               20
  STAGE III              2               12
  STAGE IV               2               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               T1 T2 T3 T4
  HHIPL1 MUTATED    1  2  1  2
  HHIPL1 WILD-TYPE  5 23  6 13
D20V4, multiclass
    clus
vv   HHIPL1 MUTATED HHIPL1 WILD-TYPE
  T1              1                5
  T2              2               23
  T3              1                6
  T4              2               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"
D20V5, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    5  1
  HHIPL1 WILD-TYPE 42  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      5    1
  HHIPL1 WILD-TYPE   42    5
   clus
vv  HHIPL1 MUTATED HHIPL1 WILD-TYPE
  0              5               42
  1              1                5
[1] 2 2
[1] FALSE
D20V6, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    3  3
  HHIPL1 WILD-TYPE 34 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      3    3
  HHIPL1 WILD-TYPE   34   16
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  FEMALE              3               34
  MALE                3               16
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    1  3
  HHIPL1 WILD-TYPE  6 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      1    3
  HHIPL1 WILD-TYPE    6   18
                        clus
vv                       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(21) Variable = ASPDH MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2              0  1
  ASPDH MUTATED    5  3
  ASPDH WILD-TYPE 30 17
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              47 
  ASPDH MUTATED ASPDH WILD-TYPE 
              3              17 
$`ASPDH MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KW 
       30.31        57.53        32.68        17.36         8.32        50.14 
TCGA-OR-A5KX TCGA-PK-A5HB 
       35.87        42.51 

$`ASPDH WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        19.04        18.12        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K9 
       16.04        50.66        63.25        31.23        18.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-OR-A5L3 
       46.49        87.88       153.63       120.30         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        20.65        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        73.05        53.03        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       52.04        21.01         6.81        12.59       106.52 

  ASPDH MUTATED ASPDH WILD-TYPE 
           8.32            4.11 
  ASPDH MUTATED ASPDH WILD-TYPE 
          57.53          153.63 
  ASPDH MUTATED ASPDH WILD-TYPE 
         34.275          39.350 
[1] "8.3 - 57.5 (34.3)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1.2"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASPDH MUTATED         0        0         5        1
  ASPDH WILD-TYPE       6       21         9       11
D21V3, multiclass
           clus
vv          ASPDH MUTATED ASPDH WILD-TYPE
  STAGE I               0               6
  STAGE II              0              21
  STAGE III             5               9
  STAGE IV              1              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              T1 T2 T3 T4
  ASPDH MUTATED    0  2  1  3
  ASPDH WILD-TYPE  6 23  6 12
D21V4, multiclass
    clus
vv   ASPDH MUTATED ASPDH WILD-TYPE
  T1             0               6
  T2             2              23
  T3             1               6
  T4             3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                 cls
clus               0  1
  ASPDH MUTATED    4  2
  ASPDH WILD-TYPE 43  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      4    2
  ASPDH WILD-TYPE   43    4
   clus
vv  ASPDH MUTATED ASPDH WILD-TYPE
  0             4              43
  1             2               4
[1] 2 2
[1] FALSE
D21V6, binary
                 cls
clus               0  1
  ASPDH MUTATED    6  2
  ASPDH WILD-TYPE 31 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      6    2
  ASPDH WILD-TYPE   31   17
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  FEMALE             6              31
  MALE               2              17
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus               0  1
  ASPDH MUTATED    0  2
  ASPDH WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      0    2
  ASPDH WILD-TYPE    7   19
                        clus
vv                       ASPDH MUTATED ASPDH WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(22) Variable = C1ORF106 MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  C1ORF106 MUTATED    7  1
  C1ORF106 WILD-TYPE 28 19
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 8                 47 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 1                 19 
$`C1ORF106 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX 
       22.03         4.90        18.15        87.88       153.63        35.87 
TCGA-OR-A5LA TCGA-OR-A5LO 
       16.01        64.08 

$`C1ORF106 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR 
       41.39        40.34        46.82        41.26        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ 
        8.32        11.31        46.49       120.30        50.14         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB 
      128.12        23.80        27.62        20.65        21.21        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
        5.23        39.35        36.33        73.05        53.03        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       21.01         6.81        12.59       106.52        42.51 

  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
              4.90               4.11 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
            153.63             128.12 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
             28.95              39.35 
[1] "4.9 - 153.6 (28.9)" "4.1 - 128.1 (39.4)"
[1] "hr=" "3.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C1ORF106 MUTATED         2        4         1        1
  C1ORF106 WILD-TYPE       4       17        13       11
D22V3, multiclass
           clus
vv          C1ORF106 MUTATED C1ORF106 WILD-TYPE
  STAGE I                  2                  4
  STAGE II                 4                 17
  STAGE III                1                 13
  STAGE IV                 1                 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                 T1 T2 T3 T4
  C1ORF106 MUTATED    2  5  0  1
  C1ORF106 WILD-TYPE  4 20  7 14
D22V4, multiclass
    clus
vv   C1ORF106 MUTATED C1ORF106 WILD-TYPE
  T1                2                  4
  T2                5                 20
  T3                0                  7
  T4                1                 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"
D22V5, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    6  2
  C1ORF106 WILD-TYPE 41  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      6    2
  C1ORF106 WILD-TYPE   41    4
   clus
vv  C1ORF106 MUTATED C1ORF106 WILD-TYPE
  0                6                 41
  1                2                  4
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    7  1
  C1ORF106 WILD-TYPE 30 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      7    1
  C1ORF106 WILD-TYPE   30   18
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  FEMALE                7                 30
  MALE                  1                 18
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    0  4
  C1ORF106 WILD-TYPE  7 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      0    4
  C1ORF106 WILD-TYPE    7   17
                        clus
vv                       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                4                 17
[1] 2 2
[1] FALSE

Clustering(23) Variable = THEM4 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2              0  1
  THEM4 MUTATED    2  2
  THEM4 WILD-TYPE 33 18
  THEM4 MUTATED THEM4 WILD-TYPE 
              4              51 
  THEM4 MUTATED THEM4 WILD-TYPE 
              2              18 
$`THEM4 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5LJ TCGA-PK-A5HB 
       22.03        11.31        36.33        42.51 

$`THEM4 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        46.82        41.26         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
        6.81        12.59       106.52 

  THEM4 MUTATED THEM4 WILD-TYPE 
          11.31            4.11 
  THEM4 MUTATED THEM4 WILD-TYPE 
          42.51          153.63 
  THEM4 MUTATED THEM4 WILD-TYPE 
          29.18           39.35 
[1] "11.3 - 42.5 (29.2)" "4.1 - 153.6 (39.4)"
[1] "hr=" "2"  
D23V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  THEM4 MUTATED         1        1         0        1
  THEM4 WILD-TYPE       5       20        14       11
D23V3, multiclass
           clus
vv          THEM4 MUTATED THEM4 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              20
  STAGE III             0              14
  STAGE IV              1              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              T1 T2 T3 T4
  THEM4 MUTATED    1  2  0  0
  THEM4 WILD-TYPE  5 23  7 15
D23V4, multiclass
    clus
vv   THEM4 MUTATED THEM4 WILD-TYPE
  T1             1               5
  T2             2              23
  T3             0               7
  T4             0              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"
D23V5, binary
                 cls
clus               0  1
  THEM4 MUTATED    2  1
  THEM4 WILD-TYPE 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      2    1
  THEM4 WILD-TYPE   45    5
   clus
vv  THEM4 MUTATED THEM4 WILD-TYPE
  0             2              45
  1             1               5
[1] 2 2
[1] FALSE
D23V6, binary
                 cls
clus               0  1
  THEM4 MUTATED    3  1
  THEM4 WILD-TYPE 34 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      3    1
  THEM4 WILD-TYPE   34   18
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  FEMALE             3              34
  MALE               1              18
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus               0  1
  THEM4 MUTATED    0  1
  THEM4 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      0    1
  THEM4 WILD-TYPE    7   20
                        clus
vv                       THEM4 MUTATED THEM4 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(24) Variable = CTNNB1 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED    3  3
  CTNNB1 WILD-TYPE 32 17
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               6               49 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               17 
$`CTNNB1 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-OR-A5LJ 
       18.15         8.32        11.31       153.63       128.12        36.33 

$`CTNNB1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       32.68        17.36        46.49        87.88       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       35.87         4.11        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       16.01        39.58         5.23        39.35        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            8.32             4.11 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          153.63           121.25 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           27.24            39.35 
[1] "8.3 - 153.6 (27.2)" "4.1 - 121.2 (39.4)"
[1] "hr=" "1.6"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CTNNB1 MUTATED         1        2         1        2
  CTNNB1 WILD-TYPE       5       19        13       10
D24V3, multiclass
           clus
vv          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                1                5
  STAGE II               2               19
  STAGE III              1               13
  STAGE IV               2               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               T1 T2 T3 T4
  CTNNB1 MUTATED    1  3  1  1
  CTNNB1 WILD-TYPE  5 22  6 14
D24V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              1                5
  T2              3               22
  T3              1                6
  T4              1               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"
D24V5, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    4  2
  CTNNB1 WILD-TYPE 43  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      4    2
  CTNNB1 WILD-TYPE   43    4
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0              4               43
  1              2                4
[1] 2 2
[1] FALSE
D24V6, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    6  0
  CTNNB1 WILD-TYPE 31 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6    0
  CTNNB1 WILD-TYPE   31   19
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              6               31
  MALE                0               19
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    0  3
  CTNNB1 WILD-TYPE  7 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0    3
  CTNNB1 WILD-TYPE    7   18
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(25) Variable = GDF1 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2             0  1
  GDF1 MUTATED    4  0
  GDF1 WILD-TYPE 31 20
  GDF1 MUTATED GDF1 WILD-TYPE 
             4             51 
  GDF1 MUTATED GDF1 WILD-TYPE 
             0             20 
$`GDF1 MUTATED`
TCGA-OR-A5JW TCGA-OR-A5KU TCGA-OR-A5L9 TCGA-PK-A5HB 
       63.25       153.63        21.21        42.51 

$`GDF1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        16.04        50.66        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
        6.81        12.59       106.52 

  GDF1 MUTATED GDF1 WILD-TYPE 
         21.21           4.11 
  GDF1 MUTATED GDF1 WILD-TYPE 
        153.63         128.12 
  GDF1 MUTATED GDF1 WILD-TYPE 
         52.88          35.87 
[1] "21.2 - 153.6 (52.9)" "4.1 - 128.1 (35.9)" 
[1] "hr="     "7.8e+07"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GDF1 MUTATED         0        3         0        0
  GDF1 WILD-TYPE       6       18        14       12
D25V3, multiclass
           clus
vv          GDF1 MUTATED GDF1 WILD-TYPE
  STAGE I              0              6
  STAGE II             3             18
  STAGE III            0             14
  STAGE IV             0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  GDF1 MUTATED    0  3  0  0
  GDF1 WILD-TYPE  6 22  7 15
D25V4, multiclass
    clus
vv   GDF1 MUTATED GDF1 WILD-TYPE
  T1            0              6
  T2            3             22
  T3            0              7
  T4            0             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"
D25V5, binary
                cls
clus              0  1
  GDF1 MUTATED    3  0
  GDF1 WILD-TYPE 44  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      3    0
  GDF1 WILD-TYPE   44    6
   clus
vv  GDF1 MUTATED GDF1 WILD-TYPE
  0            3             44
  1            0              6
[1] 2 2
[1] FALSE
D25V6, binary
                cls
clus              0  1
  GDF1 MUTATED    2  2
  GDF1 WILD-TYPE 35 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      2    2
  GDF1 WILD-TYPE   35   17
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  FEMALE            2             35
  MALE              2             17
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus              0  1
  GDF1 MUTATED    0  2
  GDF1 WILD-TYPE  7 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      0    2
  GDF1 WILD-TYPE    7   19
                        clus
vv                       GDF1 MUTATED GDF1 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(26) Variable = TSC22D2 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  TSC22D2 MUTATED    3  4
  TSC22D2 WILD-TYPE 32 16
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                7                48 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                4                16 
$`TSC22D2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JQ TCGA-OR-A5K2 TCGA-OR-A5LC TCGA-OR-A5LP 
       19.04        30.31        22.16        32.68         5.23        52.04 
TCGA-PK-A5HB 
       42.51 

$`TSC22D2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26        22.03         4.90       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        63.25        31.23        18.15        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.21        16.01        39.58        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       53.03        64.08        21.01         6.81        12.59       106.52 

  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
             5.23              4.11 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
            52.04            153.63 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
           30.310            39.465 
[1] "5.2 - 52.0 (30.3)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2.4"
D26V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TSC22D2 MUTATED         0        2         2        3
  TSC22D2 WILD-TYPE       6       19        12        9
D26V3, multiclass
           clus
vv          TSC22D2 MUTATED TSC22D2 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                19
  STAGE III               2                12
  STAGE IV                3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  TSC22D2 MUTATED    0  2  1  4
  TSC22D2 WILD-TYPE  6 23  6 11
D26V4, multiclass
    clus
vv   TSC22D2 MUTATED TSC22D2 WILD-TYPE
  T1               0                 6
  T2               2                23
  T3               1                 6
  T4               4                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"
D26V5, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    7  0
  TSC22D2 WILD-TYPE 40  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      7    0
  TSC22D2 WILD-TYPE   40    6
   clus
vv  TSC22D2 MUTATED TSC22D2 WILD-TYPE
  0               7                40
  1               0                 6
[1] 2 2
[1] FALSE
D26V6, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    6  2
  TSC22D2 WILD-TYPE 31 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      6    2
  TSC22D2 WILD-TYPE   31   17
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  FEMALE               6                31
  MALE                 2                17
[1] 2 2
[1] FALSE
D26V7, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    1  2
  TSC22D2 WILD-TYPE  6 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      1    2
  TSC22D2 WILD-TYPE    6   19
                        clus
vv                       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               2                19
[1] 2 2
[1] FALSE

Clustering(27) Variable = ZAR1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2             0  1
  ZAR1 MUTATED    6  4
  ZAR1 WILD-TYPE 29 16
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            10             45 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
             4             16 
$`ZAR1 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K9 
       30.31        40.34        22.16        18.15        32.68        11.31 
TCGA-OR-A5KW TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LK 
       50.14        21.21        16.01        73.05 

$`ZAR1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        18.12        57.53        91.46        41.39 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26        22.03         4.90       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
       50.66        63.25        31.23        17.36         8.32        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
       87.88       153.63       120.30        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       23.80        27.62        20.65        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  ZAR1 MUTATED ZAR1 WILD-TYPE 
         11.31           4.11 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
         73.05         153.63 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
        26.235         39.580 
[1] "11.3 - 73.0 (26.2)" "4.1 - 153.6 (39.6)"
[1] "hr=" "1.4"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ZAR1 MUTATED         0        6         2        3
  ZAR1 WILD-TYPE       6       15        12        9
D27V3, multiclass
           clus
vv          ZAR1 MUTATED ZAR1 WILD-TYPE
  STAGE I              0              6
  STAGE II             6             15
  STAGE III            2             12
  STAGE IV             3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  ZAR1 MUTATED    0  7  0  4
  ZAR1 WILD-TYPE  6 18  7 11
D27V4, multiclass
    clus
vv   ZAR1 MUTATED ZAR1 WILD-TYPE
  T1            0              6
  T2            7             18
  T3            0              7
  T4            4             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"
D27V5, binary
                cls
clus              0  1
  ZAR1 MUTATED    9  2
  ZAR1 WILD-TYPE 38  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      9    2
  ZAR1 WILD-TYPE   38    4
   clus
vv  ZAR1 MUTATED ZAR1 WILD-TYPE
  0            9             38
  1            2              4
[1] 2 2
[1] FALSE
D27V6, binary
                cls
clus              0  1
  ZAR1 MUTATED   10  1
  ZAR1 WILD-TYPE 27 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED     10    1
  ZAR1 WILD-TYPE   27   18
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  FEMALE           10             27
  MALE              1             18
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus              0  1
  ZAR1 MUTATED    0  4
  ZAR1 WILD-TYPE  7 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      0    4
  ZAR1 WILD-TYPE    7   17
                        clus
vv                       ZAR1 MUTATED ZAR1 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            4             17
[1] 2 2
[1] FALSE

Clustering(28) Variable = RGS9BP MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2               0  1
  RGS9BP MUTATED    5  2
  RGS9BP WILD-TYPE 30 18
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               7               48 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               2               18 
$`RGS9BP MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JR TCGA-OR-A5JX TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5LA 
       15.45       121.25        31.23         8.32        11.31        16.01 
TCGA-PK-A5HB 
       42.51 

$`RGS9BP WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        18.15        32.68        17.36 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.58         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 

  RGS9BP MUTATED RGS9BP WILD-TYPE 
            8.32             4.11 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
          121.25           153.63 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
          16.010           39.465 
[1] "8.3 - 121.2 (16.0)" "4.1 - 153.6 (39.5)"
[1] "hr=" "1.2"
D28V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RGS9BP MUTATED         1        2         2        1
  RGS9BP WILD-TYPE       5       19        12       11
D28V3, multiclass
           clus
vv          RGS9BP MUTATED RGS9BP WILD-TYPE
  STAGE I                1                5
  STAGE II               2               19
  STAGE III              2               12
  STAGE IV               1               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               T1 T2 T3 T4
  RGS9BP MUTATED    1  2  3  0
  RGS9BP WILD-TYPE  5 23  4 15
D28V4, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  T1              1                5
  T2              2               23
  T3              3                4
  T4              0               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"
D28V5, binary
                  cls
clus                0  1
  RGS9BP MUTATED    5  1
  RGS9BP WILD-TYPE 42  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      5    1
  RGS9BP WILD-TYPE   42    5
   clus
vv  RGS9BP MUTATED RGS9BP WILD-TYPE
  0              5               42
  1              1                5
[1] 2 2
[1] FALSE
D28V6, binary
                  cls
clus                0  1
  RGS9BP MUTATED    4  3
  RGS9BP WILD-TYPE 33 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      4    3
  RGS9BP WILD-TYPE   33   16
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  FEMALE              4               33
  MALE                3               16
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                0  1
  RGS9BP MUTATED    1  1
  RGS9BP WILD-TYPE  6 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      1    1
  RGS9BP WILD-TYPE    6   20
                        clus
vv                       RGS9BP MUTATED RGS9BP WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              1               20
[1] 2 2
[1] FALSE

Clustering(29) Variable = OPRD1 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  OPRD1 MUTATED    7  3
  OPRD1 WILD-TYPE 28 17
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             10              45 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
              3              17 
$`OPRD1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5K2 
       19.04        30.31        41.39        22.03         4.90        32.68 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5LP TCGA-OR-A5LR 
      153.63       120.30        52.04        21.01 

$`OPRD1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       16.11        18.12        57.53        91.46        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       41.26        22.16       121.25        16.04        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       31.23        18.15        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       87.88        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-P6-A5OF 
       39.35        36.33        73.05        53.03        64.08         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  OPRD1 MUTATED OPRD1 WILD-TYPE 
           4.90            4.11 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         153.63          128.12 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         31.495          39.350 
[1] "4.9 - 153.6 (31.5)" "4.1 - 128.1 (39.4)"
[1] "hr=" "1.2"
D29V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OPRD1 MUTATED         1        5         3        2
  OPRD1 WILD-TYPE       5       16        11       10
D29V3, multiclass
           clus
vv          OPRD1 MUTATED OPRD1 WILD-TYPE
  STAGE I               1               5
  STAGE II              5              16
  STAGE III             3              11
  STAGE IV              2              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              T1 T2 T3 T4
  OPRD1 MUTATED    1  6  1  3
  OPRD1 WILD-TYPE  5 19  6 12
D29V4, multiclass
    clus
vv   OPRD1 MUTATED OPRD1 WILD-TYPE
  T1             1               5
  T2             6              19
  T3             1               6
  T4             3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                 cls
clus               0  1
  OPRD1 MUTATED   10  1
  OPRD1 WILD-TYPE 37  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED     10    1
  OPRD1 WILD-TYPE   37    5
   clus
vv  OPRD1 MUTATED OPRD1 WILD-TYPE
  0            10              37
  1             1               5
[1] 2 2
[1] FALSE
D29V6, binary
                 cls
clus               0  1
  OPRD1 MUTATED    9  2
  OPRD1 WILD-TYPE 28 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      9    2
  OPRD1 WILD-TYPE   28   17
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  FEMALE             9              28
  MALE               2              17
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus               0  1
  OPRD1 MUTATED    1  3
  OPRD1 WILD-TYPE  6 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      1    3
  OPRD1 WILD-TYPE    6   18
                        clus
vv                       OPRD1 MUTATED OPRD1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(30) Variable = C16ORF3 MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  C16ORF3 MUTATED    4  1
  C16ORF3 WILD-TYPE 31 19
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                50 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                1                19 
$`C16ORF3 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5LR 
       55.13        46.49        50.14       128.12        21.01 

$`C16ORF3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
      120.30        35.87         4.11        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF TCGA-P6-A5OG 
       73.05        53.03        64.08        52.04         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
            21.01              4.11 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
           128.12            153.63 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
           50.140            34.275 
[1] "21.0 - 128.1 (50.1)" "4.1 - 153.6 (34.3)" 
[1] "hr=" "2.6"
D30V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C16ORF3 MUTATED         1        1         1        2
  C16ORF3 WILD-TYPE       5       20        13       10
D30V3, multiclass
           clus
vv          C16ORF3 MUTATED C16ORF3 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                20
  STAGE III               1                13
  STAGE IV                2                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                T1 T2 T3 T4
  C16ORF3 MUTATED    1  2  1  1
  C16ORF3 WILD-TYPE  5 23  6 14
D30V4, multiclass
    clus
vv   C16ORF3 MUTATED C16ORF3 WILD-TYPE
  T1               1                 5
  T2               2                23
  T3               1                 6
  T4               1                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"
D30V5, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    4  1
  C16ORF3 WILD-TYPE 43  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      4    1
  C16ORF3 WILD-TYPE   43    5
   clus
vv  C16ORF3 MUTATED C16ORF3 WILD-TYPE
  0               4                43
  1               1                 5
[1] 2 2
[1] FALSE
D30V6, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    5  0
  C16ORF3 WILD-TYPE 32 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      5    0
  C16ORF3 WILD-TYPE   32   19
        clus
vv       C16ORF3 MUTATED C16ORF3 WILD-TYPE
  FEMALE               5                32
  MALE                 0                19
[1] 2 2
[1] FALSE
D30V7, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    1  3
  C16ORF3 WILD-TYPE  6 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      1    3
  C16ORF3 WILD-TYPE    6   18
                        clus
vv                       C16ORF3 MUTATED C16ORF3 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               3                18
[1] 2 2
[1] FALSE

Clustering(31) Variable = FPGS MUTATION ANALYSIS
D31V1, survival
                sevent
clus2             0  1
  FPGS MUTATED    3  1
  FPGS WILD-TYPE 32 19
  FPGS MUTATED FPGS WILD-TYPE 
             4             51 
  FPGS MUTATED FPGS WILD-TYPE 
             1             19 
$`FPGS MUTATED`
TCGA-OR-A5JR TCGA-OR-A5K5 TCGA-OR-A5L6 TCGA-OR-A5LJ 
      121.25         8.32        20.65        36.33 

$`FPGS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  FPGS MUTATED FPGS WILD-TYPE 
          8.32           4.11 
  FPGS MUTATED FPGS WILD-TYPE 
        121.25         153.63 
  FPGS MUTATED FPGS WILD-TYPE 
         28.49          39.35 
[1] "8.3 - 121.2 (28.5)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.3"
D31V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FPGS MUTATED         1        1         1        2
  FPGS WILD-TYPE       5       20        13       10
D31V3, multiclass
           clus
vv          FPGS MUTATED FPGS WILD-TYPE
  STAGE I              1              5
  STAGE II             1             20
  STAGE III            1             13
  STAGE IV             2             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             T1 T2 T3 T4
  FPGS MUTATED    1  2  1  1
  FPGS WILD-TYPE  5 23  6 14
D31V4, multiclass
    clus
vv   FPGS MUTATED FPGS WILD-TYPE
  T1            1              5
  T2            2             23
  T3            1              6
  T4            1             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"
D31V5, binary
                cls
clus              0  1
  FPGS MUTATED    4  1
  FPGS WILD-TYPE 43  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      4    1
  FPGS WILD-TYPE   43    5
   clus
vv  FPGS MUTATED FPGS WILD-TYPE
  0            4             43
  1            1              5
[1] 2 2
[1] FALSE
D31V6, binary
                cls
clus              0  1
  FPGS MUTATED    3  2
  FPGS WILD-TYPE 34 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      3    2
  FPGS WILD-TYPE   34   17
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  FEMALE            3             34
  MALE              2             17
[1] 2 2
[1] FALSE
D31V7, binary
                cls
clus              0  1
  FPGS MUTATED    0  3
  FPGS WILD-TYPE  7 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      0    3
  FPGS WILD-TYPE    7   18
                        clus
vv                       FPGS MUTATED FPGS WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(32) Variable = PLIN5 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 31 19
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              50 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              1              19 
$`PLIN5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JF TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5L9 
       63.85        41.39        63.25        18.15        21.21 

$`PLIN5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       19.04        30.31        18.12        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       16.04        50.66        31.23        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  PLIN5 MUTATED PLIN5 WILD-TYPE 
          18.15            4.11 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
          63.85          153.63 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
          41.39           36.10 
[1] "18.1 - 63.9 (41.4)" "4.1 - 153.6 (36.1)"
[1] "hr=" "2.4"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PLIN5 MUTATED         0        3         1        1
  PLIN5 WILD-TYPE       6       18        13       11
D32V3, multiclass
           clus
vv          PLIN5 MUTATED PLIN5 WILD-TYPE
  STAGE I               0               6
  STAGE II              3              18
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  PLIN5 MUTATED    0  3  1  1
  PLIN5 WILD-TYPE  6 22  6 14
D32V4, multiclass
    clus
vv   PLIN5 MUTATED PLIN5 WILD-TYPE
  T1             0               6
  T2             3              22
  T3             1               6
  T4             1              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"
D32V5, binary
                 cls
clus               0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 43  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      4    1
  PLIN5 WILD-TYPE   43    5
   clus
vv  PLIN5 MUTATED PLIN5 WILD-TYPE
  0             4              43
  1             1               5
[1] 2 2
[1] FALSE
D32V6, binary
                 cls
clus               0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 33 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      4    1
  PLIN5 WILD-TYPE   33   18
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  FEMALE             4              33
  MALE               1              18
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus               0  1
  PLIN5 MUTATED    1  1
  PLIN5 WILD-TYPE  6 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      1    1
  PLIN5 WILD-TYPE    6   20
                        clus
vv                       PLIN5 MUTATED PLIN5 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(33) Variable = IRX3 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2             0  1
  IRX3 MUTATED    2  2
  IRX3 WILD-TYPE 33 18
  IRX3 MUTATED IRX3 WILD-TYPE 
             4             51 
  IRX3 MUTATED IRX3 WILD-TYPE 
             2             18 
$`IRX3 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5L3 TCGA-OR-A5LO 
       30.31        18.12       128.12        64.08 

$`IRX3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        19.04        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87         4.11        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        73.05        53.03        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  IRX3 MUTATED IRX3 WILD-TYPE 
         18.12           4.11 
  IRX3 MUTATED IRX3 WILD-TYPE 
        128.12         153.63 
  IRX3 MUTATED IRX3 WILD-TYPE 
        47.195         36.330 
[1] "18.1 - 128.1 (47.2)" "4.1 - 153.6 (36.3)" 
[1] "hr=" "1.1"
D33V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IRX3 MUTATED         1        1         0        2
  IRX3 WILD-TYPE       5       20        14       10
D33V3, multiclass
           clus
vv          IRX3 MUTATED IRX3 WILD-TYPE
  STAGE I              1              5
  STAGE II             1             20
  STAGE III            0             14
  STAGE IV             2             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             T1 T2 T3 T4
  IRX3 MUTATED    1  1  0  2
  IRX3 WILD-TYPE  5 24  7 13
D33V4, multiclass
    clus
vv   IRX3 MUTATED IRX3 WILD-TYPE
  T1            1              5
  T2            1             24
  T3            0              7
  T4            2             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"
D33V5, binary
                cls
clus              0  1
  IRX3 MUTATED    4  0
  IRX3 WILD-TYPE 43  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      4    0
  IRX3 WILD-TYPE   43    6
   clus
vv  IRX3 MUTATED IRX3 WILD-TYPE
  0            4             43
  1            0              6
[1] 2 2
[1] FALSE
D33V6, binary
                cls
clus              0  1
  IRX3 MUTATED    3  1
  IRX3 WILD-TYPE 34 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      3    1
  IRX3 WILD-TYPE   34   18
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  FEMALE            3             34
  MALE              1             18
[1] 2 2
[1] FALSE
D33V7, binary
                cls
clus              0  1
  IRX3 MUTATED    0  1
  IRX3 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      0    1
  IRX3 WILD-TYPE    7   20
                        clus
vv                       IRX3 MUTATED IRX3 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(34) Variable = TRIOBP MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2               0  1
  TRIOBP MUTATED    6  4
  TRIOBP WILD-TYPE 29 16
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               45 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               4               16 
$`TRIOBP MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5KV TCGA-OR-A5L5 
       15.45        50.66        32.68        17.36       120.30        27.62 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LJ TCGA-P6-A5OG 
       21.21        16.01        36.33        12.59 

$`TRIOBP WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K5 
      121.25        16.04        63.25        31.23        18.15         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        46.49        87.88       153.63        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC 
        4.11       128.12        23.80        20.65        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81       106.52        42.51 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
           12.59             4.11 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          120.30           153.63 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          24.415           40.340 
[1] "12.6 - 120.3 (24.4)" "4.1 - 153.6 (40.3)" 
[1] "hr=" "1.6"
D34V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TRIOBP MUTATED         1        3         3        3
  TRIOBP WILD-TYPE       5       18        11        9
D34V3, multiclass
           clus
vv          TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                1                5
  STAGE II               3               18
  STAGE III              3               11
  STAGE IV               3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  TRIOBP MUTATED    1  5  1  3
  TRIOBP WILD-TYPE  5 20  6 12
D34V4, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  T1              1                5
  T2              5               20
  T3              1                6
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                  cls
clus                0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 40  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      7    3
  TRIOBP WILD-TYPE   40    3
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0              7               40
  1              3                3
[1] 2 2
[1] FALSE
D34V6, binary
                  cls
clus                0  1
  TRIOBP MUTATED    9  1
  TRIOBP WILD-TYPE 28 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      9    1
  TRIOBP WILD-TYPE   28   18
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  FEMALE              9               28
  MALE                1               18
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                0  1
  TRIOBP MUTATED    1  6
  TRIOBP WILD-TYPE  6 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      1    6
  TRIOBP WILD-TYPE    6   15
                        clus
vv                       TRIOBP MUTATED TRIOBP WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              6               15
[1] 2 2
[1] FALSE

Clustering(35) Variable = KRTAP4-5 MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  KRTAP4-5 MUTATED    4  0
  KRTAP4-5 WILD-TYPE 31 20
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 51 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 0                 20 
$`KRTAP4-5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5L3 TCGA-OR-A5L9 
       63.85         4.90       128.12        21.21 

$`KRTAP4-5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26        22.03        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87         4.11        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       20.65        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
              4.90               4.11 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
            128.12             153.63 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             42.53              36.33 
[1] "4.9 - 128.1 (42.5)" "4.1 - 153.6 (36.3)"
[1] "hr="     "7.6e+07"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP4-5 MUTATED         1        2         1        0
  KRTAP4-5 WILD-TYPE       5       19        13       12
D35V3, multiclass
           clus
vv          KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  STAGE I                  1                  5
  STAGE II                 2                 19
  STAGE III                1                 13
  STAGE IV                 0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  KRTAP4-5 MUTATED    1  2  1  0
  KRTAP4-5 WILD-TYPE  5 23  6 15
D35V4, multiclass
    clus
vv   KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  T1                1                  5
  T2                2                 23
  T3                1                  6
  T4                0                 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"
D35V5, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    4  0
  KRTAP4-5 WILD-TYPE 43  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      4    0
  KRTAP4-5 WILD-TYPE   43    6
   clus
vv  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  0                4                 43
  1                0                  6
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    3  1
  KRTAP4-5 WILD-TYPE 34 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      3    1
  KRTAP4-5 WILD-TYPE   34   18
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  FEMALE                3                 34
  MALE                  1                 18
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    1  2
  KRTAP4-5 WILD-TYPE  6 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      1    2
  KRTAP4-5 WILD-TYPE    6   19
                        clus
vv                       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                2                 19
[1] 2 2
[1] FALSE

Clustering(36) Variable = ATXN1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2              0  1
  ATXN1 MUTATED    6  3
  ATXN1 WILD-TYPE 29 17
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              9              46 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              3              17 
$`ATXN1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5KO TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5LC 
       12.00        41.39        46.49       128.12        23.80         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        64.08        52.04 

$`ATXN1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       19.04        30.31        18.12        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       50.14        35.87         4.11        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LR 
       16.01        39.58        39.35        73.05        53.03        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  ATXN1 MUTATED ATXN1 WILD-TYPE 
           5.23            4.11 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         128.12          153.63 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         41.390          34.275 
[1] "5.2 - 128.1 (41.4)" "4.1 - 153.6 (34.3)"
[1] "hr=" "1.2"
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ATXN1 MUTATED         1        3         2        3
  ATXN1 WILD-TYPE       5       18        12        9
D36V3, multiclass
           clus
vv          ATXN1 MUTATED ATXN1 WILD-TYPE
  STAGE I               1               5
  STAGE II              3              18
  STAGE III             2              12
  STAGE IV              3               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  ATXN1 MUTATED    1  4  0  4
  ATXN1 WILD-TYPE  5 21  7 11
D36V4, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  T1             1               5
  T2             4              21
  T3             0               7
  T4             4              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"
D36V5, binary
                 cls
clus               0  1
  ATXN1 MUTATED    8  1
  ATXN1 WILD-TYPE 39  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      8    1
  ATXN1 WILD-TYPE   39    5
   clus
vv  ATXN1 MUTATED ATXN1 WILD-TYPE
  0             8              39
  1             1               5
[1] 2 2
[1] FALSE
D36V6, binary
                 cls
clus               0  1
  ATXN1 MUTATED    8  1
  ATXN1 WILD-TYPE 29 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      8    1
  ATXN1 WILD-TYPE   29   18
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  FEMALE             8              29
  MALE               1              18
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus               0  1
  ATXN1 MUTATED    1  5
  ATXN1 WILD-TYPE  6 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      1    5
  ATXN1 WILD-TYPE    6   16
                        clus
vv                       ATXN1 MUTATED ATXN1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             5              16
[1] 2 2
[1] FALSE

Clustering(37) Variable = ZNF628 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2               0  1
  ZNF628 MUTATED    2  3
  ZNF628 WILD-TYPE 33 17
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               5               50 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               3               17 
$`ZNF628 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5K5 TCGA-OR-A5K9 
       55.13        18.12        63.25         8.32        11.31 

$`ZNF628 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        30.31        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        31.23        18.15        32.68        17.36 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  ZNF628 MUTATED ZNF628 WILD-TYPE 
            8.32             4.11 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
           63.25           153.63 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
           18.12            37.84 
[1] "8.3 - 63.2 (18.1)"  "4.1 - 153.6 (37.8)"
[1] "hr=" "2.1"
D37V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF628 MUTATED         0        2         1        3
  ZNF628 WILD-TYPE       6       19        13        9
D37V3, multiclass
           clus
vv          ZNF628 MUTATED ZNF628 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               19
  STAGE III              1               13
  STAGE IV               3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ZNF628 MUTATED    0  2  2  2
  ZNF628 WILD-TYPE  6 23  5 13
D37V4, multiclass
    clus
vv   ZNF628 MUTATED ZNF628 WILD-TYPE
  T1              0                6
  T2              2               23
  T3              2                5
  T4              2               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"
D37V5, binary
                  cls
clus                0  1
  ZNF628 MUTATED    6  0
  ZNF628 WILD-TYPE 41  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      6    0
  ZNF628 WILD-TYPE   41    6
   clus
vv  ZNF628 MUTATED ZNF628 WILD-TYPE
  0              6               41
  1              0                6
[1] 2 2
[1] FALSE
D37V6, binary
                  cls
clus                0  1
  ZNF628 MUTATED    4  2
  ZNF628 WILD-TYPE 33 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      4    2
  ZNF628 WILD-TYPE   33   17
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  FEMALE              4               33
  MALE                2               17
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                0  1
  ZNF628 MUTATED    1  1
  ZNF628 WILD-TYPE  6 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      1    1
  ZNF628 WILD-TYPE    6   20
                        clus
vv                       ZNF628 MUTATED ZNF628 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              1               20
[1] 2 2
[1] FALSE

Clustering(38) Variable = WDR34 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2              0  1
  WDR34 MUTATED    4  1
  WDR34 WILD-TYPE 31 19
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              50 
  WDR34 MUTATED WDR34 WILD-TYPE 
              1              19 
$`WDR34 MUTATED`
TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5LD TCGA-PK-A5HB 
       91.46        41.26         4.90        39.35        42.51 

$`WDR34 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JF 
       16.11        19.04        30.31        18.12        57.53        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       40.34        46.82        22.03        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       20.65        21.21        16.01        39.58         5.23        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  WDR34 MUTATED WDR34 WILD-TYPE 
           4.90            4.11 
  WDR34 MUTATED WDR34 WILD-TYPE 
          91.46          153.63 
  WDR34 MUTATED WDR34 WILD-TYPE 
         41.260          34.275 
[1] "4.9 - 91.5 (41.3)"  "4.1 - 153.6 (34.3)"
[1] "hr=" "2"  
D38V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  WDR34 MUTATED         0        2         1        1
  WDR34 WILD-TYPE       6       19        13       11
D38V3, multiclass
           clus
vv          WDR34 MUTATED WDR34 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              19
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  WDR34 MUTATED    0  2  0  2
  WDR34 WILD-TYPE  6 23  7 13
D38V4, multiclass
    clus
vv   WDR34 MUTATED WDR34 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             0               7
  T4             2              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"
D38V5, binary
                 cls
clus               0  1
  WDR34 MUTATED    4  0
  WDR34 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      4    0
  WDR34 WILD-TYPE   43    6
   clus
vv  WDR34 MUTATED WDR34 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D38V6, binary
                 cls
clus               0  1
  WDR34 MUTATED    1  4
  WDR34 WILD-TYPE 36 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      1    4
  WDR34 WILD-TYPE   36   15
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  FEMALE             1              36
  MALE               4              15
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus               0  1
  WDR34 MUTATED    0  1
  WDR34 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      0    1
  WDR34 WILD-TYPE    7   20
                        clus
vv                       WDR34 MUTATED WDR34 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(39) Variable = BTBD11 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2               0  1
  BTBD11 MUTATED    3  2
  BTBD11 WILD-TYPE 32 18
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               5               50 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               2               18 
$`BTBD11 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5KW TCGA-OR-A5L5 
       12.00        22.03        32.68        50.14        27.62 

$`BTBD11 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        18.15        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       35.87         4.11       128.12        23.80        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
           12.00             4.11 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           50.14           153.63 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
          27.620           39.465 
[1] "12.0 - 50.1 (27.6)" "4.1 - 153.6 (39.5)"
[1] "hr=" "1.6"
D39V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BTBD11 MUTATED         2        0         3        0
  BTBD11 WILD-TYPE       4       21        11       12
D39V3, multiclass
           clus
vv          BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                2                4
  STAGE II               0               21
  STAGE III              3               11
  STAGE IV               0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  BTBD11 MUTATED    2  1  0  2
  BTBD11 WILD-TYPE  4 24  7 13
D39V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              2                4
  T2              1               24
  T3              0                7
  T4              2               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"
D39V5, binary
                  cls
clus                0  1
  BTBD11 MUTATED    4  1
  BTBD11 WILD-TYPE 43  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      4    1
  BTBD11 WILD-TYPE   43    5
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0              4               43
  1              1                5
[1] 2 2
[1] FALSE
D39V6, binary
                  cls
clus                0  1
  BTBD11 MUTATED    4  1
  BTBD11 WILD-TYPE 33 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      4    1
  BTBD11 WILD-TYPE   33   18
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE              4               33
  MALE                1               18
[1] 2 2
[1] FALSE
D39V7, binary
                  cls
clus                0  1
  BTBD11 MUTATED    1  2
  BTBD11 WILD-TYPE  6 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      1    2
  BTBD11 WILD-TYPE    6   19
                        clus
vv                       BTBD11 MUTATED BTBD11 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               19
[1] 2 2
[1] FALSE

Clustering(40) Variable = GARS MUTATION ANALYSIS
D40V1, survival
                sevent
clus2             0  1
  GARS MUTATED   13  3
  GARS WILD-TYPE 22 17
  GARS MUTATED GARS WILD-TYPE 
            16             39 
  GARS MUTATED GARS WILD-TYPE 
             3             17 
$`GARS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JC TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ 
       79.82        57.53        40.34        46.82        22.03        22.16 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L5 
       16.04        50.66        87.88        35.87         4.11        27.62 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OG 
       73.05        64.08        52.04        12.59 

$`GARS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JK 
       19.04        30.31        18.12        91.46        41.39        41.26 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
        4.90       121.25        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        11.31        46.49       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
       50.14       128.12        23.80        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LR 
       39.58         5.23        39.35        36.33        53.03        21.01 
TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81       106.52        42.51 

  GARS MUTATED GARS WILD-TYPE 
          4.11           4.90 
  GARS MUTATED GARS WILD-TYPE 
         87.88         153.63 
  GARS MUTATED GARS WILD-TYPE 
         43.58          32.68 
[1] "4.1 - 87.9 (43.6)"  "4.9 - 153.6 (32.7)"
[1] "hr=" "2.7"
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GARS MUTATED         4        9         1        2
  GARS WILD-TYPE       2       12        13       10
D40V3, multiclass
           clus
vv          GARS MUTATED GARS WILD-TYPE
  STAGE I              4              2
  STAGE II             9             12
  STAGE III            1             13
  STAGE IV             2             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             T1 T2 T3 T4
  GARS MUTATED    4 10  0  2
  GARS WILD-TYPE  2 15  7 13
D40V4, multiclass
    clus
vv   GARS MUTATED GARS WILD-TYPE
  T1            4              2
  T2           10             15
  T3            0              7
  T4            2             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"
D40V5, binary
                cls
clus              0  1
  GARS MUTATED   15  1
  GARS WILD-TYPE 32  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     15    1
  GARS WILD-TYPE   32    5
   clus
vv  GARS MUTATED GARS WILD-TYPE
  0           15             32
  1            1              5
[1] 2 2
[1] FALSE
D40V6, binary
                cls
clus              0  1
  GARS MUTATED   12  5
  GARS WILD-TYPE 25 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     12    5
  GARS WILD-TYPE   25   14
        clus
vv       GARS MUTATED GARS WILD-TYPE
  FEMALE           12             25
  MALE              5             14
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus              0  1
  GARS MUTATED    1  6
  GARS WILD-TYPE  6 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED      1    6
  GARS WILD-TYPE    6   15
                        clus
vv                       GARS MUTATED GARS WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            6             15
[1] 2 2
[1] FALSE

Clustering(41) Variable = ZNF598 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2               0  1
  ZNF598 MUTATED    5  4
  ZNF598 WILD-TYPE 30 16
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               9               46 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               4               16 
$`ZNF598 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JP TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K9 
       12.00        19.04         4.90        16.04        50.66        11.31 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-PK-A5HB 
       39.35        73.05        42.51 

$`ZNF598 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JW 
       46.82        41.26        22.03        22.16       121.25        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
       31.23        18.15        32.68        17.36         8.32        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.58         5.23        36.33        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
            4.90             4.11 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           73.05           153.63 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          19.040           37.955 
[1] "4.9 - 73.0 (19.0)"  "4.1 - 153.6 (38.0)"
[1] "hr=" "1.8"
D41V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         0        5         3        1
  ZNF598 WILD-TYPE       6       16        11       11
D41V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                0                6
  STAGE II               5               16
  STAGE III              3               11
  STAGE IV               1               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               T1 T2 T3 T4
  ZNF598 MUTATED    0  5  1  3
  ZNF598 WILD-TYPE  6 20  6 12
D41V4, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  T1              0                6
  T2              5               20
  T3              1                6
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                  cls
clus                0  1
  ZNF598 MUTATED    9  0
  ZNF598 WILD-TYPE 38  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      9    0
  ZNF598 WILD-TYPE   38    6
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0              9               38
  1              0                6
[1] 2 2
[1] FALSE
D41V6, binary
                  cls
clus                0  1
  ZNF598 MUTATED    3  7
  ZNF598 WILD-TYPE 34 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      3    7
  ZNF598 WILD-TYPE   34   12
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              3               34
  MALE                7               12
[1] 2 2
[1] FALSE
D41V7, binary
                  cls
clus                0  1
  ZNF598 MUTATED    2  2
  ZNF598 WILD-TYPE  5 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    2
  ZNF598 WILD-TYPE    5   19
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              2               19
[1] 2 2
[1] FALSE

Clustering(42) Variable = BHLHE22 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  BHLHE22 MUTATED    2  3
  BHLHE22 WILD-TYPE 33 17
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                50 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                3                17 
$`BHLHE22 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5JT TCGA-OR-A5KW TCGA-OR-A5LJ 
       55.13        12.00        16.04        50.14        36.33 

$`BHLHE22 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        63.85        15.45        79.82        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       21.21        16.01        39.58         5.23        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
            12.00              4.11 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
            55.13            153.63 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
            36.33             37.61 
[1] "12.0 - 55.1 (36.3)" "4.1 - 153.6 (37.6)"
[1] "hr=" "2"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  BHLHE22 MUTATED         0        1         2        2
  BHLHE22 WILD-TYPE       6       20        12       10
D42V3, multiclass
           clus
vv          BHLHE22 MUTATED BHLHE22 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                1                20
  STAGE III               2                12
  STAGE IV                2                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                T1 T2 T3 T4
  BHLHE22 MUTATED    0  3  1  1
  BHLHE22 WILD-TYPE  6 22  6 14
D42V4, multiclass
    clus
vv   BHLHE22 MUTATED BHLHE22 WILD-TYPE
  T1               0                 6
  T2               3                22
  T3               1                 6
  T4               1                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"
D42V5, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    3  2
  BHLHE22 WILD-TYPE 44  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      3    2
  BHLHE22 WILD-TYPE   44    4
   clus
vv  BHLHE22 MUTATED BHLHE22 WILD-TYPE
  0               3                44
  1               2                 4
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    4  1
  BHLHE22 WILD-TYPE 33 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      4    1
  BHLHE22 WILD-TYPE   33   18
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  FEMALE               4                33
  MALE                 1                18
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    2  2
  BHLHE22 WILD-TYPE  5 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      2    2
  BHLHE22 WILD-TYPE    5   19
                        clus
vv                       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               2                19
[1] 2 2
[1] FALSE

Clustering(43) Variable = PTPLA MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  PTPLA MUTATED    2  1
  PTPLA WILD-TYPE 33 19
  PTPLA MUTATED PTPLA WILD-TYPE 
              3              52 
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              19 
$`PTPLA MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JW TCGA-OR-A5L3 
       12.00        63.25       128.12 

$`PTPLA WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        16.04        50.66        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87         4.11        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PTPLA MUTATED PTPLA WILD-TYPE 
          12.00            4.11 
  PTPLA MUTATED PTPLA WILD-TYPE 
         128.12          153.63 
  PTPLA MUTATED PTPLA WILD-TYPE 
          63.25           36.10 
[1] "12.0 - 128.1 (63.2)" "4.1 - 153.6 (36.1)" 
[1] "hr=" "1.5"
D43V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTPLA MUTATED         1        1         1        0
  PTPLA WILD-TYPE       5       20        13       12
D43V3, multiclass
           clus
vv          PTPLA MUTATED PTPLA WILD-TYPE
  STAGE I               1               5
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  PTPLA MUTATED    1  1  0  1
  PTPLA WILD-TYPE  5 24  7 14
D43V4, multiclass
    clus
vv   PTPLA MUTATED PTPLA WILD-TYPE
  T1             1               5
  T2             1              24
  T3             0               7
  T4             1              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"
D43V5, binary
                 cls
clus               0  1
  PTPLA MUTATED    3  0
  PTPLA WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      3    0
  PTPLA WILD-TYPE   44    6
   clus
vv  PTPLA MUTATED PTPLA WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D43V6, binary
                 cls
clus               0  1
  PTPLA MUTATED    1  2
  PTPLA WILD-TYPE 36 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      1    2
  PTPLA WILD-TYPE   36   17
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  FEMALE             1              36
  MALE               2              17
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus               0  1
  PTPLA MUTATED    1  1
  PTPLA WILD-TYPE  6 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      1    1
  PTPLA WILD-TYPE    6   20
                        clus
vv                       PTPLA MUTATED PTPLA WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(44) Variable = CD320 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  CD320 MUTATED    3  1
  CD320 WILD-TYPE 32 19
  CD320 MUTATED CD320 WILD-TYPE 
              4              51 
  CD320 MUTATED CD320 WILD-TYPE 
              1              19 
$`CD320 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5K5 TCGA-OR-A5L4 
       12.00        79.82         8.32        23.80 

$`CD320 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14        35.87         4.11       128.12        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  CD320 MUTATED CD320 WILD-TYPE 
           8.32            4.11 
  CD320 MUTATED CD320 WILD-TYPE 
          79.82          153.63 
  CD320 MUTATED CD320 WILD-TYPE 
          17.90           39.35 
[1] "8.3 - 79.8 (17.9)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1.1"
D44V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CD320 MUTATED         0        1         3        0
  CD320 WILD-TYPE       6       20        11       12
D44V3, multiclass
           clus
vv          CD320 MUTATED CD320 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             3              11
  STAGE IV              0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  CD320 MUTATED    0  1  1  2
  CD320 WILD-TYPE  6 24  6 13
D44V4, multiclass
    clus
vv   CD320 MUTATED CD320 WILD-TYPE
  T1             0               6
  T2             1              24
  T3             1               6
  T4             2              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"
D44V5, binary
                 cls
clus               0  1
  CD320 MUTATED    4  0
  CD320 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      4    0
  CD320 WILD-TYPE   43    6
   clus
vv  CD320 MUTATED CD320 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D44V6, binary
                 cls
clus               0  1
  CD320 MUTATED    3  1
  CD320 WILD-TYPE 34 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      3    1
  CD320 WILD-TYPE   34   18
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  FEMALE             3              34
  MALE               1              18
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus               0  1
  CD320 MUTATED    2  1
  CD320 WILD-TYPE  5 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      2    1
  CD320 WILD-TYPE    5   20
                        clus
vv                       CD320 MUTATED CD320 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(45) Variable = KIAA1984 MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                 0  1
  KIAA1984 MUTATED    2  1
  KIAA1984 WILD-TYPE 33 19
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 3                 52 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 1                 19 
$`KIAA1984 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KO TCGA-PK-A5HB 
       19.04        46.49        42.51 

$`KIAA1984 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
             19.04               4.11 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
             46.49             153.63 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
             42.51              36.10 
[1] "19.0 - 46.5 (42.5)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.1"
D45V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1984 MUTATED         0        0         1        1
  KIAA1984 WILD-TYPE       6       21        13       11
D45V3, multiclass
[1] "Remove cluster labels:" "KIAA1984 MUTATED"      
clus
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 2                 51 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5JA         TCGA-OR-A5JB 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JD         TCGA-OR-A5JF         TCGA-OR-A5JH 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JI         TCGA-OR-A5JK         TCGA-OR-A5JL 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JP         TCGA-OR-A5JQ         TCGA-OR-A5JR 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JW 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JX         TCGA-OR-A5JY         TCGA-OR-A5K2 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5K4         TCGA-OR-A5K5         TCGA-OR-A5K9 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5KT         TCGA-OR-A5KU         TCGA-OR-A5KV 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5KW         TCGA-OR-A5KX         TCGA-OR-A5KZ 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5L3         TCGA-OR-A5L4         TCGA-OR-A5L5 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5L6         TCGA-OR-A5L9         TCGA-OR-A5LA 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LB         TCGA-OR-A5LC         TCGA-OR-A5LD 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LJ         TCGA-OR-A5LK         TCGA-OR-A5LL 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LR 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-P6-A5OF         TCGA-P6-A5OG         TCGA-P6-A5OH 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
                    vv
clus                 T1 T2 T3 T4
  KIAA1984 MUTATED    0  0  1  1
  KIAA1984 WILD-TYPE  6 25  6 14
D45V4, multiclass
[1] "Remove cluster labels:" "KIAA1984 MUTATED"      
clus
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 2                 51 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5JA         TCGA-OR-A5JB 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JD         TCGA-OR-A5JF         TCGA-OR-A5JH 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JI         TCGA-OR-A5JK         TCGA-OR-A5JL 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JP         TCGA-OR-A5JQ         TCGA-OR-A5JR 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JW 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JX         TCGA-OR-A5JY         TCGA-OR-A5K2 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5K4         TCGA-OR-A5K5         TCGA-OR-A5K9 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5KT         TCGA-OR-A5KU         TCGA-OR-A5KV 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5KW         TCGA-OR-A5KX         TCGA-OR-A5KZ 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5L3         TCGA-OR-A5L4         TCGA-OR-A5L5 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5L6         TCGA-OR-A5L9         TCGA-OR-A5LA 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LB         TCGA-OR-A5LC         TCGA-OR-A5LD 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LJ         TCGA-OR-A5LK         TCGA-OR-A5LL 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LR 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-P6-A5OF         TCGA-P6-A5OG         TCGA-P6-A5OH 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
D45V5, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    2  0
  KIAA1984 WILD-TYPE 45  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      2    0
  KIAA1984 WILD-TYPE   45    6
   clus
vv  KIAA1984 MUTATED KIAA1984 WILD-TYPE
  0                2                 45
  1                0                  6
[1] 2 2
[1] FALSE
D45V6, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    1  2
  KIAA1984 WILD-TYPE 36 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      1    2
  KIAA1984 WILD-TYPE   36   17
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  FEMALE                1                 36
  MALE                  2                 17
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    1  1
  KIAA1984 WILD-TYPE  6 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      1    1
  KIAA1984 WILD-TYPE    6   20
                        clus
vv                       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                1                 20
[1] 2 2
[1] FALSE

Clustering(46) Variable = TPO MUTATION ANALYSIS
D46V1, survival
               sevent
clus2            0  1
  TPO MUTATED    5  5
  TPO WILD-TYPE 30 15
  TPO MUTATED TPO WILD-TYPE 
           10            45 
  TPO MUTATED TPO WILD-TYPE 
            5            15 
$`TPO MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5K9 
       19.04        18.12        41.39        40.34        46.82        11.31 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5LD TCGA-OR-A5LJ 
      120.30        50.14        39.35        36.33 

$`TPO WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JL 
       16.11        30.31        57.53        91.46        41.26        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
        4.90        22.16       121.25        16.04        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
       31.23        18.15        32.68        17.36         8.32        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       87.88       153.63        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  TPO MUTATED TPO WILD-TYPE 
        11.31          4.11 
  TPO MUTATED TPO WILD-TYPE 
       120.30        153.63 
  TPO MUTATED TPO WILD-TYPE 
       39.845        32.680 
[1] "11.3 - 120.3 (39.8)" "4.1 - 153.6 (32.7)" 
[1] "hr=" "1.5"
D46V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TPO MUTATED         1        3         4        2
  TPO WILD-TYPE       5       18        10       10
D46V3, multiclass
           clus
vv          TPO MUTATED TPO WILD-TYPE
  STAGE I             1             5
  STAGE II            3            18
  STAGE III           4            10
  STAGE IV            2            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            T1 T2 T3 T4
  TPO MUTATED    1  6  1  2
  TPO WILD-TYPE  5 19  6 13
D46V4, multiclass
    clus
vv   TPO MUTATED TPO WILD-TYPE
  T1           1             5
  T2           6            19
  T3           1             6
  T4           2            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"
D46V5, binary
               cls
clus             0  1
  TPO MUTATED    7  3
  TPO WILD-TYPE 40  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      7    3
  TPO WILD-TYPE   40    3
   clus
vv  TPO MUTATED TPO WILD-TYPE
  0           7            40
  1           3             3
[1] 2 2
[1] FALSE
D46V6, binary
               cls
clus             0  1
  TPO MUTATED    6  4
  TPO WILD-TYPE 31 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      6    4
  TPO WILD-TYPE   31   15
        clus
vv       TPO MUTATED TPO WILD-TYPE
  FEMALE           6            31
  MALE             4            15
[1] 2 2
[1] FALSE
D46V7, binary
               cls
clus             0  1
  TPO MUTATED    1  4
  TPO WILD-TYPE  6 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      1    4
  TPO WILD-TYPE    6   17
                        clus
vv                       TPO MUTATED TPO WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           4            17
[1] 2 2
[1] FALSE

Clustering(47) Variable = AATK MUTATION ANALYSIS
D47V1, survival
                sevent
clus2             0  1
  AATK MUTATED    4  1
  AATK WILD-TYPE 31 19
  AATK MUTATED AATK WILD-TYPE 
             5             50 
  AATK MUTATED AATK WILD-TYPE 
             1             19 
$`AATK MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JH TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5LR 
       12.00        40.34       153.63        50.14        21.01 

$`AATK WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV 
       17.36         8.32        11.31        46.49        87.88       120.30 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF TCGA-P6-A5OG 
       73.05        53.03        64.08        52.04         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  AATK MUTATED AATK WILD-TYPE 
         12.00           4.11 
  AATK MUTATED AATK WILD-TYPE 
        153.63         128.12 
  AATK MUTATED AATK WILD-TYPE 
         40.34          36.10 
[1] "12.0 - 153.6 (40.3)" "4.1 - 128.1 (36.1)" 
[1] "hr=" "2"  
D47V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  AATK MUTATED         0        3         2        0
  AATK WILD-TYPE       6       18        12       12
D47V3, multiclass
           clus
vv          AATK MUTATED AATK WILD-TYPE
  STAGE I              0              6
  STAGE II             3             18
  STAGE III            2             12
  STAGE IV             0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  AATK MUTATED    0  4  0  1
  AATK WILD-TYPE  6 21  7 14
D47V4, multiclass
    clus
vv   AATK MUTATED AATK WILD-TYPE
  T1            0              6
  T2            4             21
  T3            0              7
  T4            1             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"
D47V5, binary
                cls
clus              0  1
  AATK MUTATED    4  1
  AATK WILD-TYPE 43  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      4    1
  AATK WILD-TYPE   43    5
   clus
vv  AATK MUTATED AATK WILD-TYPE
  0            4             43
  1            1              5
[1] 2 2
[1] FALSE
D47V6, binary
                cls
clus              0  1
  AATK MUTATED    4  1
  AATK WILD-TYPE 33 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      4    1
  AATK WILD-TYPE   33   18
        clus
vv       AATK MUTATED AATK WILD-TYPE
  FEMALE            4             33
  MALE              1             18
[1] 2 2
[1] FALSE
D47V7, binary
                cls
clus              0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE  6 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    2
  AATK WILD-TYPE    6   19
                        clus
vv                       AATK MUTATED AATK WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(48) Variable = PANK2 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2              0  1
  PANK2 MUTATED    0  3
  PANK2 WILD-TYPE 35 17
  PANK2 MUTATED PANK2 WILD-TYPE 
              3              52 
  PANK2 MUTATED PANK2 WILD-TYPE 
              3              17 
$`PANK2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KZ TCGA-OR-A5LD 
       19.04         4.11        39.35 

$`PANK2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        50.14        35.87       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PANK2 MUTATED PANK2 WILD-TYPE 
           4.11            4.90 
  PANK2 MUTATED PANK2 WILD-TYPE 
          39.35          153.63 
  PANK2 MUTATED PANK2 WILD-TYPE 
         19.040          37.955 
[1] "4.1 - 39.4 (19.0)"  "4.9 - 153.6 (38.0)"
[1] "hr=" "5.8"
D48V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PANK2 MUTATED         0        1         2        1
  PANK2 WILD-TYPE       6       20        12       11
D48V3, multiclass
           clus
vv          PANK2 MUTATED PANK2 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             2              12
  STAGE IV              1              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              T1 T2 T3 T4
  PANK2 MUTATED    0  1  1  2
  PANK2 WILD-TYPE  6 24  6 13
D48V4, multiclass
    clus
vv   PANK2 MUTATED PANK2 WILD-TYPE
  T1             0               6
  T2             1              24
  T3             1               6
  T4             2              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"
D48V5, binary
                 cls
clus               0  1
  PANK2 MUTATED    4  0
  PANK2 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      4    0
  PANK2 WILD-TYPE   43    6
   clus
vv  PANK2 MUTATED PANK2 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D48V6, binary
                 cls
clus               0  1
  PANK2 MUTATED    1  3
  PANK2 WILD-TYPE 36 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      1    3
  PANK2 WILD-TYPE   36   16
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  FEMALE             1              36
  MALE               3              16
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus               0  1
  PANK2 MUTATED    1  3
  PANK2 WILD-TYPE  6 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      1    3
  PANK2 WILD-TYPE    6   18
                        clus
vv                       PANK2 MUTATED PANK2 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(49) Variable = SNED1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  SNED1 MUTATED    4  2
  SNED1 WILD-TYPE 31 18
  SNED1 MUTATED SNED1 WILD-TYPE 
              6              49 
  SNED1 MUTATED SNED1 WILD-TYPE 
              2              18 
$`SNED1 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JY TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-P6-A5OG 
       41.39        46.82        18.15       120.30       128.12        12.59 

$`SNED1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       35.87         4.11        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01         6.81       106.52 
TCGA-PK-A5HB 
       42.51 

  SNED1 MUTATED SNED1 WILD-TYPE 
          12.59            4.11 
  SNED1 MUTATED SNED1 WILD-TYPE 
         128.12          153.63 
  SNED1 MUTATED SNED1 WILD-TYPE 
         44.105          35.870 
[1] "12.6 - 128.1 (44.1)" "4.1 - 153.6 (35.9)" 
[1] "hr=" "1.3"
D49V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SNED1 MUTATED         2        1         1        2
  SNED1 WILD-TYPE       4       20        13       10
D49V3, multiclass
           clus
vv          SNED1 MUTATED SNED1 WILD-TYPE
  STAGE I               2               4
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              2              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              T1 T2 T3 T4
  SNED1 MUTATED    2  2  0  2
  SNED1 WILD-TYPE  4 23  7 13
D49V4, multiclass
    clus
vv   SNED1 MUTATED SNED1 WILD-TYPE
  T1             2               4
  T2             2              23
  T3             0               7
  T4             2              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"
D49V5, binary
                 cls
clus               0  1
  SNED1 MUTATED    4  2
  SNED1 WILD-TYPE 43  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      4    2
  SNED1 WILD-TYPE   43    4
   clus
vv  SNED1 MUTATED SNED1 WILD-TYPE
  0             4              43
  1             2               4
[1] 2 2
[1] FALSE
D49V6, binary
                 cls
clus               0  1
  SNED1 MUTATED    5  1
  SNED1 WILD-TYPE 32 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      5    1
  SNED1 WILD-TYPE   32   18
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  FEMALE             5              32
  MALE               1              18
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus               0  1
  SNED1 MUTATED    0  3
  SNED1 WILD-TYPE  7 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      0    3
  SNED1 WILD-TYPE    7   18
                        clus
vv                       SNED1 MUTATED SNED1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(50) Variable = CCDC150 MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  CCDC150 MUTATED    1  3
  CCDC150 WILD-TYPE 34 17
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                51 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                3                17 
$`CCDC150 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5KV 
       16.11        19.04        30.31       120.30 

$`CCDC150 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        91.46        41.39        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        22.03         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
            16.11              4.11 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           120.30            153.63 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           24.675            39.350 
[1] "16.1 - 120.3 (24.7)" "4.1 - 153.6 (39.4)" 
[1] "hr=" "2.5"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC150 MUTATED         0        0         3        1
  CCDC150 WILD-TYPE       6       21        11       11
D50V3, multiclass
           clus
vv          CCDC150 MUTATED CCDC150 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                0                21
  STAGE III               3                11
  STAGE IV                1                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                T1 T2 T3 T4
  CCDC150 MUTATED    0  1  2  1
  CCDC150 WILD-TYPE  6 24  5 14
D50V4, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  T1               0                 6
  T2               1                24
  T3               2                 5
  T4               1                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"
D50V5, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    3  1
  CCDC150 WILD-TYPE 44  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      3    1
  CCDC150 WILD-TYPE   44    5
   clus
vv  CCDC150 MUTATED CCDC150 WILD-TYPE
  0               3                44
  1               1                 5
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    3  1
  CCDC150 WILD-TYPE 34 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      3    1
  CCDC150 WILD-TYPE   34   18
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  FEMALE               3                34
  MALE                 1                18
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    2  1
  CCDC150 WILD-TYPE  5 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      2    1
  CCDC150 WILD-TYPE    5   20
                        clus
vv                       CCDC150 MUTATED CCDC150 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(51) Variable = ERCC2 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2              0  1
  ERCC2 MUTATED    7  3
  ERCC2 WILD-TYPE 28 17
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              45 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
              3              17 
$`ERCC2 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 
       63.85         4.90       121.25        63.25        32.68         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KW TCGA-OR-A5LJ TCGA-OR-A5LO 
       11.31        50.14        36.33        64.08 

$`ERCC2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT 
       40.34        46.82        41.26        22.03        22.16        16.04 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT 
       50.66        31.23        18.15        17.36        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       39.35        73.05        53.03        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  ERCC2 MUTATED ERCC2 WILD-TYPE 
           4.90            4.11 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         121.25          153.63 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         43.235          35.870 
[1] "4.9 - 121.2 (43.2)" "4.1 - 153.6 (35.9)"
[1] "hr=" "1.4"
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         1        4         4        1
  ERCC2 WILD-TYPE       5       17        10       11
D51V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               1               5
  STAGE II              4              17
  STAGE III             4              10
  STAGE IV              1              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              T1 T2 T3 T4
  ERCC2 MUTATED    1  6  2  1
  ERCC2 WILD-TYPE  5 19  5 14
D51V4, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  T1             1               5
  T2             6              19
  T3             2               5
  T4             1              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"
D51V5, binary
                 cls
clus               0  1
  ERCC2 MUTATED    8  2
  ERCC2 WILD-TYPE 39  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      8    2
  ERCC2 WILD-TYPE   39    4
   clus
vv  ERCC2 MUTATED ERCC2 WILD-TYPE
  0             8              39
  1             2               4
[1] 2 2
[1] FALSE
D51V6, binary
                 cls
clus               0  1
  ERCC2 MUTATED    7  3
  ERCC2 WILD-TYPE 30 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      7    3
  ERCC2 WILD-TYPE   30   16
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  FEMALE             7              30
  MALE               3              16
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus               0  1
  ERCC2 MUTATED    1  2
  ERCC2 WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      1    2
  ERCC2 WILD-TYPE    6   19
                        clus
vv                       ERCC2 MUTATED ERCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(52) Variable = RREB1 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    2  2
  RREB1 WILD-TYPE 33 18
  RREB1 MUTATED RREB1 WILD-TYPE 
              4              51 
  RREB1 MUTATED RREB1 WILD-TYPE 
              2              18 
$`RREB1 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       15.45        50.66        31.23        18.15 

$`RREB1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
      121.25        16.04        63.25        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  RREB1 MUTATED RREB1 WILD-TYPE 
          15.45            4.11 
  RREB1 MUTATED RREB1 WILD-TYPE 
          50.66          153.63 
  RREB1 MUTATED RREB1 WILD-TYPE 
          24.69           39.35 
[1] "15.4 - 50.7 (24.7)" "4.1 - 153.6 (39.4)"
[1] "hr=" "2"  
D52V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RREB1 MUTATED         0        1         1        2
  RREB1 WILD-TYPE       6       20        13       10
D52V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              2              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              T1 T2 T3 T4
  RREB1 MUTATED    0  1  2  1
  RREB1 WILD-TYPE  6 24  5 14
D52V4, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  T1             0               6
  T2             1              24
  T3             2               5
  T4             1              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"
D52V5, binary
                 cls
clus               0  1
  RREB1 MUTATED    2  2
  RREB1 WILD-TYPE 45  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      2    2
  RREB1 WILD-TYPE   45    4
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             2              45
  1             2               4
[1] 2 2
[1] FALSE
D52V6, binary
                 cls
clus               0  1
  RREB1 MUTATED    2  2
  RREB1 WILD-TYPE 35 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      2    2
  RREB1 WILD-TYPE   35   17
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             2              35
  MALE               2              17
[1] 2 2
[1] FALSE
D52V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    1  0
  RREB1 WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      1    0
  RREB1 WILD-TYPE    6   21
                        clus
vv                       RREB1 MUTATED RREB1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             0              21
[1] 2 2
[1] FALSE

Clustering(53) Variable = RNF39 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2              0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 32 18
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              50 
  RNF39 MUTATED RNF39 WILD-TYPE 
              2              18 
$`RNF39 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JA TCGA-OR-A5JP TCGA-OR-A5KW TCGA-PK-A5HB 
       55.13        30.31         4.90        50.14        42.51 

$`RNF39 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26        22.03        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  RNF39 MUTATED RNF39 WILD-TYPE 
           4.90            4.11 
  RNF39 MUTATED RNF39 WILD-TYPE 
          55.13          153.63 
  RNF39 MUTATED RNF39 WILD-TYPE 
          42.51           36.10 
[1] "4.9 - 55.1 (42.5)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.2"
D53V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RNF39 MUTATED         0        1         1        2
  RNF39 WILD-TYPE       6       20        13       10
D53V3, multiclass
           clus
vv          RNF39 MUTATED RNF39 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              2              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              T1 T2 T3 T4
  RNF39 MUTATED    0  2  1  1
  RNF39 WILD-TYPE  6 23  6 14
D53V4, multiclass
    clus
vv   RNF39 MUTATED RNF39 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             1               6
  T4             1              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"
D53V5, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  1
  RNF39 WILD-TYPE 44  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    1
  RNF39 WILD-TYPE   44    5
   clus
vv  RNF39 MUTATED RNF39 WILD-TYPE
  0             3              44
  1             1               5
[1] 2 2
[1] FALSE
D53V6, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 34 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    2
  RNF39 WILD-TYPE   34   17
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  FEMALE             3              34
  MALE               2              17
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  1
  RNF39 WILD-TYPE  6 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    1
  RNF39 WILD-TYPE    6   20
                        clus
vv                       RNF39 MUTATED RNF39 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(54) Variable = SEMA5B MUTATION ANALYSIS
D54V1, survival
                  sevent
clus2               0  1
  SEMA5B MUTATED    3  3
  SEMA5B WILD-TYPE 32 17
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               6               49 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               3               17 
$`SEMA5B MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JR TCGA-OR-A5KV TCGA-OR-A5LD TCGA-OR-A5LK 
       55.13        18.12       121.25       120.30        39.35        73.05 

$`SEMA5B WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        30.31        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT 
       46.82        41.26        22.03         4.90        22.16        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL 
       21.21        16.01        39.58         5.23        36.33        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  SEMA5B MUTATED SEMA5B WILD-TYPE 
           18.12             4.11 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
          121.25           153.63 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
           64.09            32.68 
[1] "18.1 - 121.2 (64.1)" "4.1 - 153.6 (32.7)" 
[1] "hr=" "1.1"
D54V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEMA5B MUTATED         1        1         2        2
  SEMA5B WILD-TYPE       5       20        12       10
D54V3, multiclass
           clus
vv          SEMA5B MUTATED SEMA5B WILD-TYPE
  STAGE I                1                5
  STAGE II               1               20
  STAGE III              2               12
  STAGE IV               2               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               T1 T2 T3 T4
  SEMA5B MUTATED    1  2  1  2
  SEMA5B WILD-TYPE  5 23  6 13
D54V4, multiclass
    clus
vv   SEMA5B MUTATED SEMA5B WILD-TYPE
  T1              1                5
  T2              2               23
  T3              1                6
  T4              2               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"
D54V5, binary
                  cls
clus                0  1
  SEMA5B MUTATED    5  1
  SEMA5B WILD-TYPE 42  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      5    1
  SEMA5B WILD-TYPE   42    5
   clus
vv  SEMA5B MUTATED SEMA5B WILD-TYPE
  0              5               42
  1              1                5
[1] 2 2
[1] FALSE
D54V6, binary
                  cls
clus                0  1
  SEMA5B MUTATED    2  4
  SEMA5B WILD-TYPE 35 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      2    4
  SEMA5B WILD-TYPE   35   15
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  FEMALE              2               35
  MALE                4               15
[1] 2 2
[1] FALSE
D54V7, binary
                  cls
clus                0  1
  SEMA5B MUTATED    1  2
  SEMA5B WILD-TYPE  6 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      1    2
  SEMA5B WILD-TYPE    6   19
                        clus
vv                       SEMA5B MUTATED SEMA5B WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               19
[1] 2 2
[1] FALSE

Clustering(55) Variable = TAF5 MUTATION ANALYSIS
D55V1, survival
                sevent
clus2             0  1
  TAF5 MUTATED    1  2
  TAF5 WILD-TYPE 34 18
  TAF5 MUTATED TAF5 WILD-TYPE 
             3             52 
  TAF5 MUTATED TAF5 WILD-TYPE 
             2             18 
$`TAF5 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JY TCGA-OR-A5LR 
       55.13        18.15        21.01 

$`TAF5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 
      121.25        16.04        50.66        63.25        31.23        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  TAF5 MUTATED TAF5 WILD-TYPE 
         18.15           4.11 
  TAF5 MUTATED TAF5 WILD-TYPE 
         55.13         153.63 
  TAF5 MUTATED TAF5 WILD-TYPE 
         21.01          37.84 
[1] "18.1 - 55.1 (21.0)" "4.1 - 153.6 (37.8)"
[1] "hr=" "2"  
D55V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TAF5 MUTATED         0        1         0        2
  TAF5 WILD-TYPE       6       20        14       10
D55V3, multiclass
           clus
vv          TAF5 MUTATED TAF5 WILD-TYPE
  STAGE I              0              6
  STAGE II             1             20
  STAGE III            0             14
  STAGE IV             2             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             T1 T2 T3 T4
  TAF5 MUTATED    0  1  1  1
  TAF5 WILD-TYPE  6 24  6 14
D55V4, multiclass
    clus
vv   TAF5 MUTATED TAF5 WILD-TYPE
  T1            0              6
  T2            1             24
  T3            1              6
  T4            1             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"
D55V5, binary
                cls
clus              0  1
  TAF5 MUTATED    2  1
  TAF5 WILD-TYPE 45  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      2    1
  TAF5 WILD-TYPE   45    5
   clus
vv  TAF5 MUTATED TAF5 WILD-TYPE
  0            2             45
  1            1              5
[1] 2 2
[1] FALSE
D55V6, binary
                cls
clus              0  1
  TAF5 MUTATED    3  0
  TAF5 WILD-TYPE 34 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      3    0
  TAF5 WILD-TYPE   34   19
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  FEMALE            3             34
  MALE              0             19
[1] 2 2
[1] FALSE
D55V7, binary
                cls
clus              0  1
  TAF5 MUTATED    1  0
  TAF5 WILD-TYPE  6 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      1    0
  TAF5 WILD-TYPE    6   21
                        clus
vv                       TAF5 MUTATED TAF5 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            0             21
[1] 2 2
[1] FALSE

Clustering(56) Variable = SARM1 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  SARM1 MUTATED    1  5
  SARM1 WILD-TYPE 34 15
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              49 
  SARM1 MUTATED SARM1 WILD-TYPE 
              5              15 
$`SARM1 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JW TCGA-P6-A5OG 
       55.13        19.04        30.31        57.53        63.25        12.59 

$`SARM1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        91.46        41.39        40.34        46.82        41.26 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       31.23        18.15        32.68        17.36         8.32        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01         6.81       106.52 
TCGA-PK-A5HB 
       42.51 

  SARM1 MUTATED SARM1 WILD-TYPE 
          12.59            4.11 
  SARM1 MUTATED SARM1 WILD-TYPE 
          63.25          153.63 
  SARM1 MUTATED SARM1 WILD-TYPE 
          42.72           36.33 
[1] "12.6 - 63.2 (42.7)" "4.1 - 153.6 (36.3)"
[1] "hr=" "2.3"
D56V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SARM1 MUTATED         0        1         1        3
  SARM1 WILD-TYPE       6       20        13        9
D56V3, multiclass
           clus
vv          SARM1 MUTATED SARM1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              3               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  SARM1 MUTATED    0  1  2  2
  SARM1 WILD-TYPE  6 24  5 13
D56V4, multiclass
    clus
vv   SARM1 MUTATED SARM1 WILD-TYPE
  T1             0               6
  T2             1              24
  T3             2               5
  T4             2              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"
D56V5, binary
                 cls
clus               0  1
  SARM1 MUTATED    5  0
  SARM1 WILD-TYPE 42  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      5    0
  SARM1 WILD-TYPE   42    6
   clus
vv  SARM1 MUTATED SARM1 WILD-TYPE
  0             5              42
  1             0               6
[1] 2 2
[1] FALSE
D56V6, binary
                 cls
clus               0  1
  SARM1 MUTATED    3  3
  SARM1 WILD-TYPE 34 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      3    3
  SARM1 WILD-TYPE   34   16
        clus
vv       SARM1 MUTATED SARM1 WILD-TYPE
  FEMALE             3              34
  MALE               3              16
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus               0  1
  SARM1 MUTATED    2  1
  SARM1 WILD-TYPE  5 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      2    1
  SARM1 WILD-TYPE    5   20
                        clus
vv                       SARM1 MUTATED SARM1 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(57) Variable = PRSS27 MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2               0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 34 18
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               52 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               2               18 
$`PRSS27 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JF 
       12.00        19.04        41.39 

$`PRSS27 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       30.31        18.12        57.53        91.46        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        22.03         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PRSS27 MUTATED PRSS27 WILD-TYPE 
           12.00             4.11 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
           41.39           153.63 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
           19.04            37.84 
[1] "12.0 - 41.4 (19.0)" "4.1 - 153.6 (37.8)"
[1] "hr=" "2.9"
D57V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PRSS27 MUTATED         0        1         2        0
  PRSS27 WILD-TYPE       6       20        12       12
D57V3, multiclass
           clus
vv          PRSS27 MUTATED PRSS27 WILD-TYPE
  STAGE I                0                6
  STAGE II               1               20
  STAGE III              2               12
  STAGE IV               0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  PRSS27 MUTATED    0  1  1  1
  PRSS27 WILD-TYPE  6 24  6 14
D57V4, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  T1              0                6
  T2              1               24
  T3              1                6
  T4              1               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"
D57V5, binary
                  cls
clus                0  1
  PRSS27 MUTATED    3  0
  PRSS27 WILD-TYPE 44  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      3    0
  PRSS27 WILD-TYPE   44    6
   clus
vv  PRSS27 MUTATED PRSS27 WILD-TYPE
  0              3               44
  1              0                6
[1] 2 2
[1] FALSE
D57V6, binary
                  cls
clus                0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 36 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      1    2
  PRSS27 WILD-TYPE   36   17
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  FEMALE              1               36
  MALE                2               17
[1] 2 2
[1] FALSE
D57V7, binary
                  cls
clus                0  1
  PRSS27 MUTATED    2  0
  PRSS27 WILD-TYPE  5 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      2    0
  PRSS27 WILD-TYPE    5   21
                        clus
vv                       PRSS27 MUTATED PRSS27 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              0               21
[1] 2 2
[1] FALSE

Clustering(58) Variable = TMEM189 MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  TMEM189 MUTATED    1  1
  TMEM189 WILD-TYPE 34 19
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                53 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                1                19 
$`TMEM189 MUTATED`
TCGA-OR-A5J2 TCGA-PK-A5HB 
       55.13        42.51 

$`TMEM189 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        20.65        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        73.05        53.03        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       52.04        21.01         6.81        12.59       106.52 

  TMEM189 MUTATED TMEM189 WILD-TYPE 
            42.51              4.11 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
            55.13            153.63 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
            48.82             35.87 
[1] "42.5 - 55.1 (48.8)" "4.1 - 153.6 (35.9)"
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TMEM189 MUTATED         0        0         0        2
  TMEM189 WILD-TYPE       6       21        14       10
D58V3, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                51 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JD        TCGA-OR-A5JF        TCGA-OR-A5JH 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K9        TCGA-OR-A5KO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-P6-A5OG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  TMEM189 MUTATED    0  0  1  1
  TMEM189 WILD-TYPE  6 25  6 14
D58V4, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                51 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JD        TCGA-OR-A5JF        TCGA-OR-A5JH 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K9        TCGA-OR-A5KO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-P6-A5OG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
D58V5, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  0
  TMEM189 WILD-TYPE 45  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    0
  TMEM189 WILD-TYPE   45    6
   clus
vv  TMEM189 MUTATED TMEM189 WILD-TYPE
  0               2                45
  1               0                 6
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  1
  TMEM189 WILD-TYPE 35 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    1
  TMEM189 WILD-TYPE   35   18
        clus
vv       TMEM189 MUTATED TMEM189 WILD-TYPE
  FEMALE               2                35
  MALE                 1                18
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    1  1
  TMEM189 WILD-TYPE  6 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      1    1
  TMEM189 WILD-TYPE    6   20
                        clus
vv                       TMEM189 MUTATED TMEM189 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(59) Variable = NOXA1 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  NOXA1 MUTATED    2  1
  NOXA1 WILD-TYPE 33 19
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              3              52 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              1              19 
$`NOXA1 MUTATED`
TCGA-OR-A5K2 TCGA-OR-A5KX TCGA-OR-A5LO 
       32.68        35.87        64.08 

$`NOXA1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       18.15        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        50.14         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        36.33        73.05        53.03        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  NOXA1 MUTATED NOXA1 WILD-TYPE 
          32.68            4.11 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          64.08          153.63 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          35.87           37.84 
[1] "32.7 - 64.1 (35.9)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.3"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NOXA1 MUTATED         0        1         2        1
  NOXA1 WILD-TYPE       6       20        12       11
D59V3, multiclass
           clus
vv          NOXA1 MUTATED NOXA1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             2              12
  STAGE IV              1              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              T1 T2 T3 T4
  NOXA1 MUTATED    0  2  0  2
  NOXA1 WILD-TYPE  6 23  7 13
D59V4, multiclass
    clus
vv   NOXA1 MUTATED NOXA1 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             0               7
  T4             2              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"
D59V5, binary
                 cls
clus               0  1
  NOXA1 MUTATED    3  1
  NOXA1 WILD-TYPE 44  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      3    1
  NOXA1 WILD-TYPE   44    5
   clus
vv  NOXA1 MUTATED NOXA1 WILD-TYPE
  0             3              44
  1             1               5
[1] 2 2
[1] FALSE
D59V6, binary
                 cls
clus               0  1
  NOXA1 MUTATED    4  0
  NOXA1 WILD-TYPE 33 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      4    0
  NOXA1 WILD-TYPE   33   19
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  FEMALE             4              33
  MALE               0              19
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus               0  1
  NOXA1 MUTATED    0  2
  NOXA1 WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      0    2
  NOXA1 WILD-TYPE    7   19
                        clus
vv                       NOXA1 MUTATED NOXA1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(60) Variable = LRP11 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2              0  1
  LRP11 MUTATED    2  2
  LRP11 WILD-TYPE 33 18
  LRP11 MUTATED LRP11 WILD-TYPE 
              4              51 
  LRP11 MUTATED LRP11 WILD-TYPE 
              2              18 
$`LRP11 MUTATED`
TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-P6-A5OF TCGA-PK-A5HB 
       11.31        20.65         6.81        42.51 

$`LRP11 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       18.15        32.68        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       23.80        27.62        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01        12.59       106.52 

  LRP11 MUTATED LRP11 WILD-TYPE 
           6.81            4.11 
  LRP11 MUTATED LRP11 WILD-TYPE 
          42.51          153.63 
  LRP11 MUTATED LRP11 WILD-TYPE 
          15.98           39.35 
[1] "6.8 - 42.5 (16.0)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "2.8"
D60V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRP11 MUTATED         0        2         1        0
  LRP11 WILD-TYPE       6       19        13       12
D60V3, multiclass
           clus
vv          LRP11 MUTATED LRP11 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              19
  STAGE III             1              13
  STAGE IV              0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  LRP11 MUTATED    0  2  0  1
  LRP11 WILD-TYPE  6 23  7 14
D60V4, multiclass
    clus
vv   LRP11 MUTATED LRP11 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             0               7
  T4             1              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"
D60V5, binary
                 cls
clus               0  1
  LRP11 MUTATED    3  0
  LRP11 WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      3    0
  LRP11 WILD-TYPE   44    6
   clus
vv  LRP11 MUTATED LRP11 WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D60V6, binary
                 cls
clus               0  1
  LRP11 MUTATED    2  2
  LRP11 WILD-TYPE 35 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      2    2
  LRP11 WILD-TYPE   35   17
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  FEMALE             2              35
  MALE               2              17
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus               0  1
  LRP11 MUTATED    0  2
  LRP11 WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      0    2
  LRP11 WILD-TYPE    7   19
                        clus
vv                       LRP11 MUTATED LRP11 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(61) Variable = RNF149 MUTATION ANALYSIS
D61V1, survival
                  sevent
clus2               0  1
  RNF149 MUTATED    3  0
  RNF149 WILD-TYPE 32 20
  RNF149 MUTATED RNF149 WILD-TYPE 
               3               52 
  RNF149 MUTATED RNF149 WILD-TYPE 
               0               20 
$`RNF149 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5KU TCGA-OR-A5LP 
       22.03       153.63        52.04 

$`RNF149 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        46.82        41.26         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
       39.35        36.33        73.05        53.03        64.08        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  RNF149 MUTATED RNF149 WILD-TYPE 
           22.03             4.11 
  RNF149 MUTATED RNF149 WILD-TYPE 
          153.63           128.12 
  RNF149 MUTATED RNF149 WILD-TYPE 
           52.04            36.10 
[1] "22.0 - 153.6 (52.0)" "4.1 - 128.1 (36.1)" 
[1] "hr="     "7.4e+07"
D61V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF149 MUTATED         1        2         0        0
  RNF149 WILD-TYPE       5       19        14       12
D61V3, multiclass
           clus
vv          RNF149 MUTATED RNF149 WILD-TYPE
  STAGE I                1                5
  STAGE II               2               19
  STAGE III              0               14
  STAGE IV               0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  RNF149 MUTATED    1  2  0  0
  RNF149 WILD-TYPE  5 23  7 15
D61V4, multiclass
    clus
vv   RNF149 MUTATED RNF149 WILD-TYPE
  T1              1                5
  T2              2               23
  T3              0                7
  T4              0               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"
D61V5, binary
                  cls
clus                0  1
  RNF149 MUTATED    3  0
  RNF149 WILD-TYPE 44  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      3    0
  RNF149 WILD-TYPE   44    6
   clus
vv  RNF149 MUTATED RNF149 WILD-TYPE
  0              3               44
  1              0                6
[1] 2 2
[1] FALSE
D61V6, binary
                  cls
clus                0  1
  RNF149 MUTATED    3  0
  RNF149 WILD-TYPE 34 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      3    0
  RNF149 WILD-TYPE   34   19
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  FEMALE              3               34
  MALE                0               19
[1] 2 2
[1] FALSE
D61V7, binary
                  cls
clus                0  1
  RNF149 MUTATED    0  1
  RNF149 WILD-TYPE  7 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      0    1
  RNF149 WILD-TYPE    7   20
                        clus
vv                       RNF149 MUTATED RNF149 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              1               20
[1] 2 2
[1] FALSE

Clustering(62) Variable = DMKN MUTATION ANALYSIS
D62V1, survival
                sevent
clus2             0  1
  DMKN MUTATED    3  0
  DMKN WILD-TYPE 32 20
  DMKN MUTATED DMKN WILD-TYPE 
             3             52 
  DMKN MUTATED DMKN WILD-TYPE 
             0             20 
$`DMKN MUTATED`
TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-PK-A5HB 
      153.63       128.12        42.51 

$`DMKN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 
       87.88       120.30        50.14        35.87         4.11        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  DMKN MUTATED DMKN WILD-TYPE 
         42.51           4.11 
  DMKN MUTATED DMKN WILD-TYPE 
        153.63         121.25 
  DMKN MUTATED DMKN WILD-TYPE 
       128.120         34.275 
[1] "42.5 - 153.6 (128.1)" "4.1 - 121.2 (34.3)"  
[1] "hr="     "7.8e+07"
D62V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DMKN MUTATED         1        1         0        0
  DMKN WILD-TYPE       5       20        14       12
D62V3, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             51 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JH     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KV     TCGA-OR-A5KW 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L4     TCGA-OR-A5L5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-P6-A5OG     TCGA-P6-A5OH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
                vv
clus             T1 T2 T3 T4
  DMKN MUTATED    1  1  0  0
  DMKN WILD-TYPE  5 24  7 15
D62V4, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             51 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JH     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KV     TCGA-OR-A5KW 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L4     TCGA-OR-A5L5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-P6-A5OG     TCGA-P6-A5OH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
D62V5, binary
                cls
clus              0  1
  DMKN MUTATED    2  0
  DMKN WILD-TYPE 45  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    0
  DMKN WILD-TYPE   45    6
   clus
vv  DMKN MUTATED DMKN WILD-TYPE
  0            2             45
  1            0              6
[1] 2 2
[1] FALSE
D62V6, binary
                cls
clus              0  1
  DMKN MUTATED    2  1
  DMKN WILD-TYPE 35 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    1
  DMKN WILD-TYPE   35   18
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  FEMALE            2             35
  MALE              1             18
[1] 2 2
[1] FALSE
D62V7, binary
                cls
clus              0  1
  DMKN MUTATED    0  2
  DMKN WILD-TYPE  7 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      0    2
  DMKN WILD-TYPE    7   19
                        clus
vv                       DMKN MUTATED DMKN WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(63) Variable = FANK1 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  FANK1 MUTATED    2  1
  FANK1 WILD-TYPE 33 19
  FANK1 MUTATED FANK1 WILD-TYPE 
              3              52 
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              19 
$`FANK1 MUTATED`
TCGA-OR-A5KT TCGA-OR-A5L5 TCGA-OR-A5LJ 
       87.88        27.62        36.33 

$`FANK1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        17.36         8.32        11.31        46.49 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       23.80        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  FANK1 MUTATED FANK1 WILD-TYPE 
          27.62            4.11 
  FANK1 MUTATED FANK1 WILD-TYPE 
          87.88          153.63 
  FANK1 MUTATED FANK1 WILD-TYPE 
          36.33           37.61 
[1] "27.6 - 87.9 (36.3)" "4.1 - 153.6 (37.6)"
[1] "hr=" "1.3"
D63V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FANK1 MUTATED         2        0         0        1
  FANK1 WILD-TYPE       4       21        14       11
D63V3, multiclass
           clus
vv          FANK1 MUTATED FANK1 WILD-TYPE
  STAGE I               2               4
  STAGE II              0              21
  STAGE III             0              14
  STAGE IV              1              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              T1 T2 T3 T4
  FANK1 MUTATED    2  1  0  0
  FANK1 WILD-TYPE  4 24  7 15
D63V4, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  T1             2               4
  T2             1              24
  T3             0               7
  T4             0              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"
D63V5, binary
                 cls
clus               0  1
  FANK1 MUTATED    2  1
  FANK1 WILD-TYPE 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      2    1
  FANK1 WILD-TYPE   45    5
   clus
vv  FANK1 MUTATED FANK1 WILD-TYPE
  0             2              45
  1             1               5
[1] 2 2
[1] FALSE
D63V6, binary
                 cls
clus               0  1
  FANK1 MUTATED    3  0
  FANK1 WILD-TYPE 34 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      3    0
  FANK1 WILD-TYPE   34   19
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  FEMALE             3              34
  MALE               0              19
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus               0  1
  FANK1 MUTATED    0  3
  FANK1 WILD-TYPE  7 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      0    3
  FANK1 WILD-TYPE    7   18
                        clus
vv                       FANK1 MUTATED FANK1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(64) Variable = MUC5B MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  MUC5B MUTATED   12  7
  MUC5B WILD-TYPE 23 13
  MUC5B MUTATED MUC5B WILD-TYPE 
             19              36 
  MUC5B MUTATED MUC5B WILD-TYPE 
              7              13 
$`MUC5B MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JQ TCGA-OR-A5JV 
       63.85        12.00        19.04        18.12        22.16        50.66 
TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5L5 
       63.25        32.68        11.31        46.49       153.63        27.62 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LP TCGA-PK-A5H8 
       16.01         5.23        36.33        64.08        52.04       106.52 
TCGA-PK-A5HB 
       42.51 

$`MUC5B WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       44.55        55.13        15.45        79.82        16.11        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        91.46        41.39        40.34        46.82        41.26 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JY 
       22.03         4.90       121.25        16.04        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       17.36         8.32        87.88       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB 
        4.11       128.12        23.80        20.65        21.21        39.58 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       39.35        73.05        53.03        21.01         6.81        12.59 

  MUC5B MUTATED MUC5B WILD-TYPE 
           5.23            4.11 
  MUC5B MUTATED MUC5B WILD-TYPE 
         153.63          128.12 
  MUC5B MUTATED MUC5B WILD-TYPE 
          36.33           37.61 
[1] "5.2 - 153.6 (36.3)" "4.1 - 128.1 (37.6)"
[1] "hr=" "1"  
D64V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED         1        8         4        4
  MUC5B WILD-TYPE       5       13        10        8
D64V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I               1               5
  STAGE II              8              13
  STAGE III             4              10
  STAGE IV              4               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  MUC5B MUTATED    1  9  2  5
  MUC5B WILD-TYPE  5 16  5 10
D64V4, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  T1             1               5
  T2             9              16
  T3             2               5
  T4             5              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"
D64V5, binary
                 cls
clus               0  1
  MUC5B MUTATED   16  1
  MUC5B WILD-TYPE 31  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     16    1
  MUC5B WILD-TYPE   31    5
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0            16              31
  1             1               5
[1] 2 2
[1] FALSE
D64V6, binary
                 cls
clus               0  1
  MUC5B MUTATED   12  7
  MUC5B WILD-TYPE 25 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     12    7
  MUC5B WILD-TYPE   25   12
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE            12              25
  MALE               7              12
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus               0  1
  MUC5B MUTATED    3  7
  MUC5B WILD-TYPE  4 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      3    7
  MUC5B WILD-TYPE    4   14
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO             7              14
[1] 2 2
[1] FALSE

Clustering(65) Variable = GLTPD2 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2               0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 32 17
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               49 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               3               17 
$`GLTPD2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5K9 TCGA-PK-A5HB 
       19.04        30.31        91.46        41.26        11.31        42.51 

$`GLTPD2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       16.11        18.12        57.53        41.39        40.34        46.82 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       63.25        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 
      106.52 

  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
           11.31             4.11 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
           91.46           153.63 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
          35.785           36.330 
[1] "11.3 - 91.5 (35.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.5"
D65V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GLTPD2 MUTATED         0        2         1        2
  GLTPD2 WILD-TYPE       6       19        13       10
D65V3, multiclass
           clus
vv          GLTPD2 MUTATED GLTPD2 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               19
  STAGE III              1               13
  STAGE IV               2               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               T1 T2 T3 T4
  GLTPD2 MUTATED    0  2  1  2
  GLTPD2 WILD-TYPE  6 23  6 13
D65V4, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  T1              0                6
  T2              2               23
  T3              1                6
  T4              2               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"
D65V5, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    5  0
  GLTPD2 WILD-TYPE 42  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      5    0
  GLTPD2 WILD-TYPE   42    6
   clus
vv  GLTPD2 MUTATED GLTPD2 WILD-TYPE
  0              5               42
  1              0                6
[1] 2 2
[1] FALSE
D65V6, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 34 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      3    3
  GLTPD2 WILD-TYPE   34   16
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  FEMALE              3               34
  MALE                3               16
[1] 2 2
[1] FALSE
D65V7, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    1  0
  GLTPD2 WILD-TYPE  6 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      1    0
  GLTPD2 WILD-TYPE    6   21
                        clus
vv                       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              0               21
[1] 2 2
[1] FALSE

Clustering(66) Variable = MEN1 MUTATION ANALYSIS
D66V1, survival
                sevent
clus2             0  1
  MEN1 MUTATED    2  3
  MEN1 WILD-TYPE 33 17
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             50 
  MEN1 MUTATED MEN1 WILD-TYPE 
             3             17 
$`MEN1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5KW TCGA-P6-A5OF TCGA-PK-A5HB 
       12.00        30.31        50.14         6.81        42.51 

$`MEN1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OG TCGA-PK-A5H8 
       12.59       106.52 

  MEN1 MUTATED MEN1 WILD-TYPE 
          6.81           4.11 
  MEN1 MUTATED MEN1 WILD-TYPE 
         50.14         153.63 
  MEN1 MUTATED MEN1 WILD-TYPE 
         30.31          37.84 
[1] "6.8 - 50.1 (30.3)"  "4.1 - 153.6 (37.8)"
[1] "hr=" "2.6"
D66V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MEN1 MUTATED         0        0         3        1
  MEN1 WILD-TYPE       6       21        11       11
D66V3, multiclass
           clus
vv          MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             21
  STAGE III            3             11
  STAGE IV             1             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             T1 T2 T3 T4
  MEN1 MUTATED    0  1  0  3
  MEN1 WILD-TYPE  6 24  7 12
D66V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            0              6
  T2            1             24
  T3            0              7
  T4            3             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                cls
clus              0  1
  MEN1 MUTATED    3  1
  MEN1 WILD-TYPE 44  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    1
  MEN1 WILD-TYPE   44    5
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0            3             44
  1            1              5
[1] 2 2
[1] FALSE
D66V6, binary
                cls
clus              0  1
  MEN1 MUTATED    3  2
  MEN1 WILD-TYPE 34 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    2
  MEN1 WILD-TYPE   34   17
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE            3             34
  MALE              2             17
[1] 2 2
[1] FALSE
D66V7, binary
                cls
clus              0  1
  MEN1 MUTATED    1  2
  MEN1 WILD-TYPE  6 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      1    2
  MEN1 WILD-TYPE    6   19
                        clus
vv                       MEN1 MUTATED MEN1 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(67) Variable = SRPX MUTATION ANALYSIS
D67V1, survival
                sevent
clus2             0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 33 19
  SRPX MUTATED SRPX WILD-TYPE 
             3             52 
  SRPX MUTATED SRPX WILD-TYPE 
             1             19 
$`SRPX MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5KW TCGA-OR-A5L9 
       55.13        50.14        21.21 

$`SRPX WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  SRPX MUTATED SRPX WILD-TYPE 
         21.21           4.11 
  SRPX MUTATED SRPX WILD-TYPE 
         55.13         153.63 
  SRPX MUTATED SRPX WILD-TYPE 
         50.14          36.10 
[1] "21.2 - 55.1 (50.1)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.3"
D67V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SRPX MUTATED         0        1         1        1
  SRPX WILD-TYPE       6       20        13       11
D67V3, multiclass
           clus
vv          SRPX MUTATED SRPX WILD-TYPE
  STAGE I              0              6
  STAGE II             1             20
  STAGE III            1             13
  STAGE IV             1             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             T1 T2 T3 T4
  SRPX MUTATED    0  2  1  0
  SRPX WILD-TYPE  6 23  6 15
D67V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            0              6
  T2            2             23
  T3            1              6
  T4            0             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"
D67V5, binary
                cls
clus              0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 45  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      2    1
  SRPX WILD-TYPE   45    5
   clus
vv  SRPX MUTATED SRPX WILD-TYPE
  0            2             45
  1            1              5
[1] 2 2
[1] FALSE
D67V6, binary
                cls
clus              0  1
  SRPX MUTATED    3  0
  SRPX WILD-TYPE 34 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      3    0
  SRPX WILD-TYPE   34   19
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE            3             34
  MALE              0             19
[1] 2 2
[1] FALSE
D67V7, binary
                cls
clus              0  1
  SRPX MUTATED    1  2
  SRPX WILD-TYPE  6 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    2
  SRPX WILD-TYPE    6   19
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(68) Variable = MAP1S MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  MAP1S MUTATED    3  2
  MAP1S WILD-TYPE 32 18
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              50 
  MAP1S MUTATED MAP1S WILD-TYPE 
              2              18 
$`MAP1S MUTATED`
TCGA-OR-A5JK TCGA-OR-A5JT TCGA-OR-A5KZ TCGA-OR-A5LJ TCGA-OR-A5LK 
       41.26        16.04         4.11        36.33        73.05 

$`MAP1S WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        46.82        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  MAP1S MUTATED MAP1S WILD-TYPE 
           4.11            4.90 
  MAP1S MUTATED MAP1S WILD-TYPE 
          73.05          153.63 
  MAP1S MUTATED MAP1S WILD-TYPE 
          36.33           37.61 
[1] "4.1 - 73.0 (36.3)"  "4.9 - 153.6 (37.6)"
[1] "hr=" "1.3"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MAP1S MUTATED         0        3         0        2
  MAP1S WILD-TYPE       6       18        14       10
D68V3, multiclass
           clus
vv          MAP1S MUTATED MAP1S WILD-TYPE
  STAGE I               0               6
  STAGE II              3              18
  STAGE III             0              14
  STAGE IV              2              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              T1 T2 T3 T4
  MAP1S MUTATED    0  4  0  1
  MAP1S WILD-TYPE  6 21  7 14
D68V4, multiclass
    clus
vv   MAP1S MUTATED MAP1S WILD-TYPE
  T1             0               6
  T2             4              21
  T3             0               7
  T4             1              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"
D68V5, binary
                 cls
clus               0  1
  MAP1S MUTATED    4  1
  MAP1S WILD-TYPE 43  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      4    1
  MAP1S WILD-TYPE   43    5
   clus
vv  MAP1S MUTATED MAP1S WILD-TYPE
  0             4              43
  1             1               5
[1] 2 2
[1] FALSE
D68V6, binary
                 cls
clus               0  1
  MAP1S MUTATED    2  3
  MAP1S WILD-TYPE 35 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      2    3
  MAP1S WILD-TYPE   35   16
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  FEMALE             2              35
  MALE               3              16
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus               0  1
  MAP1S MUTATED    0  2
  MAP1S WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      0    2
  MAP1S WILD-TYPE    7   19
                        clus
vv                       MAP1S MUTATED MAP1S WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(69) Variable = SCRT1 MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2              0  1
  SCRT1 MUTATED    1  2
  SCRT1 WILD-TYPE 34 18
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              52 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              2              18 
$`SCRT1 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K9 TCGA-OR-A5L4 
       18.15        11.31        23.80 

$`SCRT1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 
      120.30        50.14        35.87         4.11       128.12        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  SCRT1 MUTATED SCRT1 WILD-TYPE 
          11.31            4.11 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
          23.80          153.63 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
         18.150          39.465 
[1] "11.3 - 23.8 (18.1)" "4.1 - 153.6 (39.5)"
[1] "hr=" "4.5"
D69V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SCRT1 MUTATED         0        1         1        1
  SCRT1 WILD-TYPE       6       20        13       11
D69V3, multiclass
           clus
vv          SCRT1 MUTATED SCRT1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              20
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  SCRT1 MUTATED    0  1  0  2
  SCRT1 WILD-TYPE  6 24  7 13
D69V4, multiclass
    clus
vv   SCRT1 MUTATED SCRT1 WILD-TYPE
  T1             0               6
  T2             1              24
  T3             0               7
  T4             2              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"
D69V5, binary
                 cls
clus               0  1
  SCRT1 MUTATED    2  1
  SCRT1 WILD-TYPE 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      2    1
  SCRT1 WILD-TYPE   45    5
   clus
vv  SCRT1 MUTATED SCRT1 WILD-TYPE
  0             2              45
  1             1               5
[1] 2 2
[1] FALSE
D69V6, binary
                 cls
clus               0  1
  SCRT1 MUTATED    3  0
  SCRT1 WILD-TYPE 34 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      3    0
  SCRT1 WILD-TYPE   34   19
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  FEMALE             3              34
  MALE               0              19
[1] 2 2
[1] FALSE
D69V7, binary
                 cls
clus               0  1
  SCRT1 MUTATED    0  1
  SCRT1 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      0    1
  SCRT1 WILD-TYPE    7   20
                        clus
vv                       SCRT1 MUTATED SCRT1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(70) Variable = OBSCN MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2              0  1
  OBSCN MUTATED   11  7
  OBSCN WILD-TYPE 24 13
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              37 
  OBSCN MUTATED OBSCN WILD-TYPE 
              7              13 
$`OBSCN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JV 
       63.85        19.04        18.12        41.39        46.82        50.66 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KV TCGA-OR-A5KW 
       18.15        17.36        11.31        46.49       120.30        50.14 
TCGA-OR-A5L5 TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-P6-A5OG TCGA-PK-A5HB 
       27.62         5.23        36.33        52.04        12.59        42.51 

$`OBSCN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        57.53        91.46        40.34        41.26        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX 
        4.90        22.16       121.25        16.04        63.25        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KZ 
       32.68         8.32        87.88       153.63        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
      128.12        23.80        20.65        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF 
       39.35        73.05        53.03        64.08        21.01         6.81 
TCGA-PK-A5H8 
      106.52 

  OBSCN MUTATED OBSCN WILD-TYPE 
           5.23            4.11 
  OBSCN MUTATED OBSCN WILD-TYPE 
         120.30          153.63 
  OBSCN MUTATED OBSCN WILD-TYPE 
          38.86           35.87 
[1] "5.2 - 120.3 (38.9)" "4.1 - 153.6 (35.9)"
[1] "hr=" "1.2"
D70V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OBSCN MUTATED         2        4         5        6
  OBSCN WILD-TYPE       4       17         9        6
D70V3, multiclass
           clus
vv          OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I               2               4
  STAGE II              4              17
  STAGE III             5               9
  STAGE IV              6               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              T1 T2 T3 T4
  OBSCN MUTATED    2  7  2  6
  OBSCN WILD-TYPE  4 18  5  9
D70V4, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  T1             2               4
  T2             7              18
  T3             2               5
  T4             6               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                 cls
clus               0  1
  OBSCN MUTATED   13  4
  OBSCN WILD-TYPE 34  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     13    4
  OBSCN WILD-TYPE   34    2
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0            13              34
  1             4               2
[1] 2 2
[1] FALSE
D70V6, binary
                 cls
clus               0  1
  OBSCN MUTATED   13  5
  OBSCN WILD-TYPE 24 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     13    5
  OBSCN WILD-TYPE   24   14
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  FEMALE            13              24
  MALE               5              14
[1] 2 2
[1] FALSE
D70V7, binary
                 cls
clus               0  1
  OBSCN MUTATED    2  7
  OBSCN WILD-TYPE  5 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      2    7
  OBSCN WILD-TYPE    5   14
                        clus
vv                       OBSCN MUTATED OBSCN WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             7              14
[1] 2 2
[1] FALSE

Clustering(71) Variable = IER5 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2             0  1
  IER5 MUTATED    0  2
  IER5 WILD-TYPE 35 18
  IER5 MUTATED IER5 WILD-TYPE 
             2             53 
  IER5 MUTATED IER5 WILD-TYPE 
             2             18 
$`IER5 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K2 
       18.15        32.68 

$`IER5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       21.01         6.81        12.59       106.52        42.51 

  IER5 MUTATED IER5 WILD-TYPE 
         18.15           4.11 
  IER5 MUTATED IER5 WILD-TYPE 
         32.68         153.63 
  IER5 MUTATED IER5 WILD-TYPE 
        25.415         39.350 
[1] "18.1 - 32.7 (25.4)" "4.1 - 153.6 (39.4)"
[1] "Remove cluster labels:" "IER5 MUTATED"          
D71V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IER5 MUTATED         0        0         1        2
  IER5 WILD-TYPE       6       21        13       10
D71V3, multiclass
           clus
vv          IER5 MUTATED IER5 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             21
  STAGE III            1             13
  STAGE IV             2             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             T1 T2 T3 T4
  IER5 MUTATED    0  0  0  3
  IER5 WILD-TYPE  6 25  7 12
D71V4, multiclass
    clus
vv   IER5 MUTATED IER5 WILD-TYPE
  T1            0              6
  T2            0             25
  T3            0              7
  T4            3             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                cls
clus              0  1
  IER5 MUTATED    2  1
  IER5 WILD-TYPE 45  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      2    1
  IER5 WILD-TYPE   45    5
   clus
vv  IER5 MUTATED IER5 WILD-TYPE
  0            2             45
  1            1              5
[1] 2 2
[1] FALSE
D71V6, binary
                cls
clus              0  1
  IER5 MUTATED    3  0
  IER5 WILD-TYPE 34 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      3    0
  IER5 WILD-TYPE   34   19
        clus
vv       IER5 MUTATED IER5 WILD-TYPE
  FEMALE            3             34
  MALE              0             19
[1] 2 2
[1] FALSE
D71V7, binary
                cls
clus              0  1
  IER5 MUTATED    0  1
  IER5 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      0    1
  IER5 WILD-TYPE    7   20
                        clus
vv                       IER5 MUTATED IER5 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(72) Variable = TNIP2 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2              0  1
  TNIP2 MUTATED    4  0
  TNIP2 WILD-TYPE 31 20
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              4              51 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              0              20 
$`TNIP2 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5KV TCGA-OR-A5KW TCGA-PK-A5HB 
       46.82       120.30        50.14        42.51 

$`TNIP2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      153.63        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
        6.81        12.59       106.52 

  TNIP2 MUTATED TNIP2 WILD-TYPE 
          42.51            4.11 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
         120.30          153.63 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
          48.48           32.68 
[1] "42.5 - 120.3 (48.5)" "4.1 - 153.6 (32.7)" 
[1] "hr="     "7.9e+07"
D72V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TNIP2 MUTATED         1        0         2        1
  TNIP2 WILD-TYPE       5       21        12       11
D72V3, multiclass
           clus
vv          TNIP2 MUTATED TNIP2 WILD-TYPE
  STAGE I               1               5
  STAGE II              0              21
  STAGE III             2              12
  STAGE IV              1              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              T1 T2 T3 T4
  TNIP2 MUTATED    1  2  0  1
  TNIP2 WILD-TYPE  5 23  7 14
D72V4, multiclass
    clus
vv   TNIP2 MUTATED TNIP2 WILD-TYPE
  T1             1               5
  T2             2              23
  T3             0               7
  T4             1              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"
D72V5, binary
                 cls
clus               0  1
  TNIP2 MUTATED    2  2
  TNIP2 WILD-TYPE 45  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      2    2
  TNIP2 WILD-TYPE   45    4
   clus
vv  TNIP2 MUTATED TNIP2 WILD-TYPE
  0             2              45
  1             2               4
[1] 2 2
[1] FALSE
D72V6, binary
                 cls
clus               0  1
  TNIP2 MUTATED    3  2
  TNIP2 WILD-TYPE 34 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      3    2
  TNIP2 WILD-TYPE   34   17
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  FEMALE             3              34
  MALE               2              17
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus               0  1
  TNIP2 MUTATED    0  3
  TNIP2 WILD-TYPE  7 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      0    3
  TNIP2 WILD-TYPE    7   18
                        clus
vv                       TNIP2 MUTATED TNIP2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(73) Variable = NOTCH2 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2               0  1
  NOTCH2 MUTATED    3  2
  NOTCH2 WILD-TYPE 32 18
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               50 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               2               18 
$`NOTCH2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-P6-A5OG TCGA-PK-A5HB 
       19.04       153.63       120.30        12.59        42.51 

$`NOTCH2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-PK-A5H8 
        6.81       106.52 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           12.59             4.11 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          153.63           128.12 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           42.51            36.10 
[1] "12.6 - 153.6 (42.5)" "4.1 - 128.1 (36.1)" 
[1] "hr=" "1.1"
D73V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NOTCH2 MUTATED         0        1         2        1
  NOTCH2 WILD-TYPE       6       20        12       11
D73V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                0                6
  STAGE II               1               20
  STAGE III              2               12
  STAGE IV               1               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               T1 T2 T3 T4
  NOTCH2 MUTATED    0  2  1  1
  NOTCH2 WILD-TYPE  6 23  6 14
D73V4, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T1              0                6
  T2              2               23
  T3              1                6
  T4              1               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"
D73V5, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    3  1
  NOTCH2 WILD-TYPE 44  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    1
  NOTCH2 WILD-TYPE   44    5
   clus
vv  NOTCH2 MUTATED NOTCH2 WILD-TYPE
  0              3               44
  1              1                5
[1] 2 2
[1] FALSE
D73V6, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    3  2
  NOTCH2 WILD-TYPE 34 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    2
  NOTCH2 WILD-TYPE   34   17
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE              3               34
  MALE                2               17
[1] 2 2
[1] FALSE
D73V7, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    1  3
  NOTCH2 WILD-TYPE  6 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      1    3
  NOTCH2 WILD-TYPE    6   18
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(74) Variable = RASIP1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2               0  1
  RASIP1 MUTATED    2  5
  RASIP1 WILD-TYPE 33 15
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               7               48 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               5               15 
$`RASIP1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5K2 TCGA-OR-A5KU TCGA-OR-A5LC TCGA-OR-A5LJ 
       12.00        41.39        32.68       153.63         5.23        36.33 
TCGA-P6-A5OG 
       12.59 

$`RASIP1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       19.04        30.31        18.12        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        18.15        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       21.21        16.01        39.58        39.35        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       64.08        52.04        21.01         6.81       106.52        42.51 

  RASIP1 MUTATED RASIP1 WILD-TYPE 
            5.23             4.11 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          153.63           128.12 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          32.680           39.465 
[1] "5.2 - 153.6 (32.7)" "4.1 - 128.1 (39.5)"
[1] "hr=" "3.1"
D74V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RASIP1 MUTATED         0        2         2        3
  RASIP1 WILD-TYPE       6       19        12        9
D74V3, multiclass
           clus
vv          RASIP1 MUTATED RASIP1 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               19
  STAGE III              2               12
  STAGE IV               3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  RASIP1 MUTATED    0  3  0  4
  RASIP1 WILD-TYPE  6 22  7 11
D74V4, multiclass
    clus
vv   RASIP1 MUTATED RASIP1 WILD-TYPE
  T1              0                6
  T2              3               22
  T3              0                7
  T4              4               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"
D74V5, binary
                  cls
clus                0  1
  RASIP1 MUTATED    6  1
  RASIP1 WILD-TYPE 41  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      6    1
  RASIP1 WILD-TYPE   41    5
   clus
vv  RASIP1 MUTATED RASIP1 WILD-TYPE
  0              6               41
  1              1                5
[1] 2 2
[1] FALSE
D74V6, binary
                  cls
clus                0  1
  RASIP1 MUTATED    6  1
  RASIP1 WILD-TYPE 31 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      6    1
  RASIP1 WILD-TYPE   31   18
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  FEMALE              6               31
  MALE                1               18
[1] 2 2
[1] FALSE
D74V7, binary
                  cls
clus                0  1
  RASIP1 MUTATED    1  4
  RASIP1 WILD-TYPE  6 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      1    4
  RASIP1 WILD-TYPE    6   17
                        clus
vv                       RASIP1 MUTATED RASIP1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              4               17
[1] 2 2
[1] FALSE

Clustering(75) Variable = NMU MUTATION ANALYSIS
D75V1, survival
               sevent
clus2            0  1
  NMU MUTATED    2  2
  NMU WILD-TYPE 33 18
  NMU MUTATED NMU WILD-TYPE 
            4            51 
  NMU MUTATED NMU WILD-TYPE 
            2            18 
$`NMU MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JF TCGA-OR-A5JT TCGA-P6-A5OF 
       15.45        41.39        16.04         6.81 

$`NMU WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       19.04        30.31        18.12        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  NMU MUTATED NMU WILD-TYPE 
         6.81          4.11 
  NMU MUTATED NMU WILD-TYPE 
        41.39        153.63 
  NMU MUTATED NMU WILD-TYPE 
       15.745        39.350 
[1] "6.8 - 41.4 (15.7)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "3"  
D75V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NMU MUTATED         0        2         1        1
  NMU WILD-TYPE       6       19        13       11
D75V3, multiclass
           clus
vv          NMU MUTATED NMU WILD-TYPE
  STAGE I             0             6
  STAGE II            2            19
  STAGE III           1            13
  STAGE IV            1            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            T1 T2 T3 T4
  NMU MUTATED    0  2  1  1
  NMU WILD-TYPE  6 23  6 14
D75V4, multiclass
    clus
vv   NMU MUTATED NMU WILD-TYPE
  T1           0             6
  T2           2            23
  T3           1             6
  T4           1            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"
D75V5, binary
               cls
clus             0  1
  NMU MUTATED    3  1
  NMU WILD-TYPE 44  5
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      3    1
  NMU WILD-TYPE   44    5
   clus
vv  NMU MUTATED NMU WILD-TYPE
  0           3            44
  1           1             5
[1] 2 2
[1] FALSE
D75V6, binary
               cls
clus             0  1
  NMU MUTATED    4  0
  NMU WILD-TYPE 33 19
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      4    0
  NMU WILD-TYPE   33   19
        clus
vv       NMU MUTATED NMU WILD-TYPE
  FEMALE           4            33
  MALE             0            19
[1] 2 2
[1] FALSE
D75V7, binary
               cls
clus             0  1
  NMU MUTATED    1  1
  NMU WILD-TYPE  6 20
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      1    1
  NMU WILD-TYPE    6   20
                        clus
vv                       NMU MUTATED NMU WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           1            20
[1] 2 2
[1] FALSE

Clustering(76) Variable = VARS MUTATION ANALYSIS
D76V1, survival
                sevent
clus2             0  1
  VARS MUTATED    4  2
  VARS WILD-TYPE 31 18
  VARS MUTATED VARS WILD-TYPE 
             6             49 
  VARS MUTATED VARS WILD-TYPE 
             2             18 
$`VARS MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JW TCGA-OR-A5L9 TCGA-PK-A5HB 
       63.85        12.00        19.04        63.25        21.21        42.51 

$`VARS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       44.55        55.13        15.45        79.82        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        91.46        41.39        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        22.03         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 
      106.52 

  VARS MUTATED VARS WILD-TYPE 
         12.00           4.11 
  VARS MUTATED VARS WILD-TYPE 
         63.85         153.63 
  VARS MUTATED VARS WILD-TYPE 
         31.86          36.33 
[1] "12.0 - 63.9 (31.9)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.2"
D76V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  VARS MUTATED         0        2         3        0
  VARS WILD-TYPE       6       19        11       12
D76V3, multiclass
           clus
vv          VARS MUTATED VARS WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            3             11
  STAGE IV             0             12
[1] 4 2
[1] TRUE
[1] "dimension of 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    0  2  2  1
  VARS WILD-TYPE  6 23  5 14
D76V4, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  T1            0              6
  T2            2             23
  T3            2              5
  T4            1             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"
D76V5, binary
                cls
clus              0  1
  VARS MUTATED    5  0
  VARS WILD-TYPE 42  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      5    0
  VARS WILD-TYPE   42    6
   clus
vv  VARS MUTATED VARS WILD-TYPE
  0            5             42
  1            0              6
[1] 2 2
[1] FALSE
D76V6, binary
                cls
clus              0  1
  VARS MUTATED    2  4
  VARS WILD-TYPE 35 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      2    4
  VARS WILD-TYPE   35   15
        clus
vv       VARS MUTATED VARS WILD-TYPE
  FEMALE            2             35
  MALE              4             15
[1] 2 2
[1] FALSE
D76V7, binary
                cls
clus              0  1
  VARS MUTATED    3  1
  VARS WILD-TYPE  4 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      3    1
  VARS WILD-TYPE    4   20
                        clus
vv                       VARS MUTATED VARS WILD-TYPE
  HISPANIC OR LATINO                3              4
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(77) Variable = HSD17B1 MUTATION ANALYSIS
D77V1, survival
                   sevent
clus2                0  1
  HSD17B1 MUTATED    3  1
  HSD17B1 WILD-TYPE 32 19
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                51 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                1                19 
$`HSD17B1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K4 TCGA-OR-A5KT TCGA-OR-A5LP 
       19.04        17.36        87.88        52.04 

$`HSD17B1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV 
       32.68         8.32        11.31        46.49       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        73.05        53.03        64.08        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            17.36              4.11 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            87.88            153.63 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            35.54             36.33 
[1] "17.4 - 87.9 (35.5)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.6"
D77V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  HSD17B1 MUTATED         1        1         2        0
  HSD17B1 WILD-TYPE       5       20        12       12
D77V3, multiclass
           clus
vv          HSD17B1 MUTATED HSD17B1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                20
  STAGE III               2                12
  STAGE IV                0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  HSD17B1 MUTATED    1  1  1  1
  HSD17B1 WILD-TYPE  5 24  6 14
D77V4, multiclass
    clus
vv   HSD17B1 MUTATED HSD17B1 WILD-TYPE
  T1               1                 5
  T2               1                24
  T3               1                 6
  T4               1                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"
D77V5, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    4  0
  HSD17B1 WILD-TYPE 43  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      4    0
  HSD17B1 WILD-TYPE   43    6
   clus
vv  HSD17B1 MUTATED HSD17B1 WILD-TYPE
  0               4                43
  1               0                 6
[1] 2 2
[1] FALSE
D77V6, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    3  1
  HSD17B1 WILD-TYPE 34 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      3    1
  HSD17B1 WILD-TYPE   34   18
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  FEMALE               3                34
  MALE                 1                18
[1] 2 2
[1] FALSE
D77V7, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    1  1
  HSD17B1 WILD-TYPE  6 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      1    1
  HSD17B1 WILD-TYPE    6   20
                        clus
vv                       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(78) Variable = COQ2 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2             0  1
  COQ2 MUTATED    3  1
  COQ2 WILD-TYPE 32 19
  COQ2 MUTATED COQ2 WILD-TYPE 
             4             51 
  COQ2 MUTATED COQ2 WILD-TYPE 
             1             19 
$`COQ2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5LK 
       30.31        41.39        22.03        73.05 

$`COQ2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       16.11        19.04        18.12        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  COQ2 MUTATED COQ2 WILD-TYPE 
         22.03           4.11 
  COQ2 MUTATED COQ2 WILD-TYPE 
         73.05         153.63 
  COQ2 MUTATED COQ2 WILD-TYPE 
         35.85          36.33 
[1] "22.0 - 73.0 (35.9)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.6"
D78V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  COQ2 MUTATED         1        2         0        1
  COQ2 WILD-TYPE       5       19        14       11
D78V3, multiclass
           clus
vv          COQ2 MUTATED COQ2 WILD-TYPE
  STAGE I              1              5
  STAGE II             2             19
  STAGE III            0             14
  STAGE IV             1             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             T1 T2 T3 T4
  COQ2 MUTATED    1  2  0  1
  COQ2 WILD-TYPE  5 23  7 14
D78V4, multiclass
    clus
vv   COQ2 MUTATED COQ2 WILD-TYPE
  T1            1              5
  T2            2             23
  T3            0              7
  T4            1             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"
D78V5, binary
                cls
clus              0  1
  COQ2 MUTATED    4  0
  COQ2 WILD-TYPE 43  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      4    0
  COQ2 WILD-TYPE   43    6
   clus
vv  COQ2 MUTATED COQ2 WILD-TYPE
  0            4             43
  1            0              6
[1] 2 2
[1] FALSE
D78V6, binary
                cls
clus              0  1
  COQ2 MUTATED    3  1
  COQ2 WILD-TYPE 34 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      3    1
  COQ2 WILD-TYPE   34   18
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  FEMALE            3             34
  MALE              1             18
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus              0  1
  COQ2 MUTATED    0  0
  COQ2 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      0    0
  COQ2 WILD-TYPE    7   21

Clustering(79) Variable = KNDC1 MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2              0  1
  KNDC1 MUTATED    7  2
  KNDC1 WILD-TYPE 28 18
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              46 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              2              18 
$`KNDC1 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JT TCGA-OR-A5LA TCGA-OR-A5LJ 
       41.39        46.82        22.03        16.04        16.01        36.33 
TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OG 
       64.08        21.01        12.59 

$`KNDC1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       40.34        41.26         4.90        22.16       121.25        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       63.25        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       21.21        39.58         5.23        39.35        73.05        53.03 
TCGA-OR-A5LP TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       52.04         6.81       106.52        42.51 

  KNDC1 MUTATED KNDC1 WILD-TYPE 
          12.59            4.11 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
          64.08          153.63 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
         22.030          39.465 
[1] "12.6 - 64.1 (22.0)" "4.1 - 153.6 (39.5)"
[1] "hr=" "1.4"
D79V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KNDC1 MUTATED         2        5         0        2
  KNDC1 WILD-TYPE       4       16        14       10
D79V3, multiclass
           clus
vv          KNDC1 MUTATED KNDC1 WILD-TYPE
  STAGE I               2               4
  STAGE II              5              16
  STAGE III             0              14
  STAGE IV              2              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              T1 T2 T3 T4
  KNDC1 MUTATED    2  6  0  1
  KNDC1 WILD-TYPE  4 19  7 14
D79V4, multiclass
    clus
vv   KNDC1 MUTATED KNDC1 WILD-TYPE
  T1             2               4
  T2             6              19
  T3             0               7
  T4             1              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"
D79V5, binary
                 cls
clus               0  1
  KNDC1 MUTATED    8  1
  KNDC1 WILD-TYPE 39  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      8    1
  KNDC1 WILD-TYPE   39    5
   clus
vv  KNDC1 MUTATED KNDC1 WILD-TYPE
  0             8              39
  1             1               5
[1] 2 2
[1] FALSE
D79V6, binary
                 cls
clus               0  1
  KNDC1 MUTATED    8  1
  KNDC1 WILD-TYPE 29 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      8    1
  KNDC1 WILD-TYPE   29   18
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  FEMALE             8              29
  MALE               1              18
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus               0  1
  KNDC1 MUTATED    0  3
  KNDC1 WILD-TYPE  7 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      0    3
  KNDC1 WILD-TYPE    7   18
                        clus
vv                       KNDC1 MUTATED KNDC1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(80) Variable = AR MUTATION ANALYSIS
D80V1, survival
              sevent
clus2           0  1
  AR MUTATED    1  3
  AR WILD-TYPE 34 17
  AR MUTATED AR WILD-TYPE 
           4           51 
  AR MUTATED AR WILD-TYPE 
           3           17 
$`AR MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JH TCGA-OR-A5JY TCGA-OR-A5LD 
       30.31        40.34        18.15        39.35 

$`AR WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        18.12        57.53        91.46        41.39 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       20.65        21.21        16.01        39.58         5.23        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  AR MUTATED AR WILD-TYPE 
       18.15         4.11 
  AR MUTATED AR WILD-TYPE 
       40.34       153.63 
  AR MUTATED AR WILD-TYPE 
       34.83        36.33 
[1] "18.1 - 40.3 (34.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "2.7"
D80V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV
  AR MUTATED         0        1         1        2
  AR WILD-TYPE       6       20        13       10
D80V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            0            6
  STAGE II           1           20
  STAGE III          1           13
  STAGE IV           2           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           T1 T2 T3 T4
  AR MUTATED    0  1  0  3
  AR WILD-TYPE  6 24  7 12
D80V4, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  T1          0            6
  T2          1           24
  T3          0            7
  T4          3           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V5, binary
              cls
clus            0  1
  AR MUTATED    3  1
  AR WILD-TYPE 44  5
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   44    5
   clus
vv  AR MUTATED AR WILD-TYPE
  0          3           44
  1          1            5
[1] 2 2
[1] FALSE
D80V6, binary
              cls
clus            0  1
  AR MUTATED    3  1
  AR WILD-TYPE 34 18
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   34   18
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          3           34
  MALE            1           18
[1] 2 2
[1] FALSE
D80V7, binary
              cls
clus            0  1
  AR MUTATED    0  1
  AR WILD-TYPE  7 20
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      0    1
  AR WILD-TYPE    7   20
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              0            7
  NOT HISPANIC OR LATINO          1           20
[1] 2 2
[1] FALSE

Clustering(81) Variable = KCTD3 MUTATION ANALYSIS
D81V1, survival
                 sevent
clus2              0  1
  KCTD3 MUTATED    2  0
  KCTD3 WILD-TYPE 33 20
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              2              53 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              0              20 
$`KCTD3 MUTATED`
TCGA-OR-A5LP TCGA-PK-A5HB 
       52.04        42.51 

$`KCTD3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.58         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        21.01         6.81        12.59       106.52 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
          42.51            4.11 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          52.04          153.63 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         47.275          35.870 
[1] "42.5 - 52.0 (47.3)" "4.1 - 153.6 (35.9)"
[1] "Remove cluster labels:" "KCTD3 MUTATED"         
D81V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KCTD3 MUTATED         0        1         0        1
  KCTD3 WILD-TYPE       6       20        14       11
D81V3, multiclass
[1] "Remove cluster labels:" "KCTD3 MUTATED"         
clus
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JD      TCGA-OR-A5JF 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JH      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-P6-A5OG 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
                 vv
clus              T1 T2 T3 T4
  KCTD3 MUTATED    0  1  0  1
  KCTD3 WILD-TYPE  6 24  7 14
D81V4, multiclass
[1] "Remove cluster labels:" "KCTD3 MUTATED"         
clus
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JD      TCGA-OR-A5JF 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JH      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-P6-A5OG 
"KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" "KCTD3 WILD-TYPE" 
D81V5, binary
                 cls
clus               0  1
  KCTD3 MUTATED    2  0
  KCTD3 WILD-TYPE 45  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      2    0
  KCTD3 WILD-TYPE   45    6
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0             2              45
  1             0               6
[1] 2 2
[1] FALSE
D81V6, binary
                 cls
clus               0  1
  KCTD3 MUTATED    2  1
  KCTD3 WILD-TYPE 35 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      2    1
  KCTD3 WILD-TYPE   35   18
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             2              35
  MALE               1              18
[1] 2 2
[1] FALSE
D81V7, binary
                 cls
clus               0  1
  KCTD3 MUTATED    0  1
  KCTD3 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0    1
  KCTD3 WILD-TYPE    7   20
                        clus
vv                       KCTD3 MUTATED KCTD3 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(82) Variable = KRTAP5-5 MUTATION ANALYSIS
D82V1, survival
                    sevent
clus2                 0  1
  KRTAP5-5 MUTATED    0  3
  KRTAP5-5 WILD-TYPE 35 17
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 52 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 17 
$`KRTAP5-5 MUTATED`
TCGA-OR-A5K9 TCGA-OR-A5LB TCGA-P6-A5OG 
       11.31        39.58        12.59 

$`KRTAP5-5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       18.15        32.68        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       23.80        27.62        20.65        21.21        16.01         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       21.01         6.81       106.52        42.51 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             11.31               4.11 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             39.58             153.63 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             12.59              37.84 
[1] "11.3 - 39.6 (12.6)" "4.1 - 153.6 (37.8)"
[1] "hr=" "6"  
D82V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP5-5 MUTATED         0        1         0        2
  KRTAP5-5 WILD-TYPE       6       20        14       10
D82V3, multiclass
           clus
vv          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 1                 20
  STAGE III                0                 14
  STAGE IV                 2                 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                 T1 T2 T3 T4
  KRTAP5-5 MUTATED    0  1  0  2
  KRTAP5-5 WILD-TYPE  6 24  7 13
D82V4, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  T1                0                  6
  T2                1                 24
  T3                0                  7
  T4                2                 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"
D82V5, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    3  0
  KRTAP5-5 WILD-TYPE 44  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      3    0
  KRTAP5-5 WILD-TYPE   44    6
   clus
vv  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  0                3                 44
  1                0                  6
[1] 2 2
[1] FALSE
D82V6, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    2  1
  KRTAP5-5 WILD-TYPE 35 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      2    1
  KRTAP5-5 WILD-TYPE   35   18
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                2                 35
  MALE                  1                 18
[1] 2 2
[1] FALSE
D82V7, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    0  2
  KRTAP5-5 WILD-TYPE  7 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      0    2
  KRTAP5-5 WILD-TYPE    7   19
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                2                 19
[1] 2 2
[1] FALSE

Clustering(83) Variable = AKAP2 MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2              0  1
  AKAP2 MUTATED    2  2
  AKAP2 WILD-TYPE 33 18
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              51 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              2              18 
$`AKAP2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5LK 
       30.31        18.12        63.25        73.05 

$`AKAP2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        19.04        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  AKAP2 MUTATED AKAP2 WILD-TYPE 
          18.12            4.11 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
          73.05          153.63 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
          46.78           36.33 
[1] "18.1 - 73.0 (46.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.1"
D83V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  AKAP2 MUTATED         0        2         0        2
  AKAP2 WILD-TYPE       6       19        14       10
D83V3, multiclass
           clus
vv          AKAP2 MUTATED AKAP2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              19
  STAGE III             0              14
  STAGE IV              2              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              T1 T2 T3 T4
  AKAP2 MUTATED    0  2  0  2
  AKAP2 WILD-TYPE  6 23  7 13
D83V4, multiclass
    clus
vv   AKAP2 MUTATED AKAP2 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             0               7
  T4             2              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"
D83V5, binary
                 cls
clus               0  1
  AKAP2 MUTATED    4  0
  AKAP2 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      4    0
  AKAP2 WILD-TYPE   43    6
   clus
vv  AKAP2 MUTATED AKAP2 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D83V6, binary
                 cls
clus               0  1
  AKAP2 MUTATED    1  3
  AKAP2 WILD-TYPE 36 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      1    3
  AKAP2 WILD-TYPE   36   16
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  FEMALE             1              36
  MALE               3              16
[1] 2 2
[1] FALSE
D83V7, binary
                 cls
clus               0  1
  AKAP2 MUTATED    0  0
  AKAP2 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      0    0
  AKAP2 WILD-TYPE    7   21

Clustering(84) Variable = KBTBD13 MUTATION ANALYSIS
D84V1, survival
                   sevent
clus2                0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 28 18
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                46 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                2                18 
$`KBTBD13 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5KV 
       55.13        22.03         4.90        18.15        87.88       120.30 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LP 
       27.62        21.21        52.04 

$`KBTBD13 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       40.34        46.82        41.26        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        63.25        31.23        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       11.31        46.49       153.63        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
      128.12        23.80        20.65        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
       39.35        36.33        73.05        53.03        64.08        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
             4.90              4.11 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
           120.30            153.63 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
            27.62             37.84 
[1] "4.9 - 120.3 (27.6)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.8"
D84V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  KBTBD13 MUTATED         3        3         1        2
  KBTBD13 WILD-TYPE       3       18        13       10
D84V3, multiclass
           clus
vv          KBTBD13 MUTATED KBTBD13 WILD-TYPE
  STAGE I                 3                 3
  STAGE II                3                18
  STAGE III               1                13
  STAGE IV                2                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                T1 T2 T3 T4
  KBTBD13 MUTATED    3  4  1  1
  KBTBD13 WILD-TYPE  3 21  6 14
D84V4, multiclass
    clus
vv   KBTBD13 MUTATED KBTBD13 WILD-TYPE
  T1               3                 3
  T2               4                21
  T3               1                 6
  T4               1                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"
D84V5, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 40  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      7    2
  KBTBD13 WILD-TYPE   40    4
   clus
vv  KBTBD13 MUTATED KBTBD13 WILD-TYPE
  0               7                40
  1               2                 4
[1] 2 2
[1] FALSE
D84V6, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    8  1
  KBTBD13 WILD-TYPE 29 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      8    1
  KBTBD13 WILD-TYPE   29   18
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  FEMALE               8                29
  MALE                 1                18
[1] 2 2
[1] FALSE
D84V7, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    1  4
  KBTBD13 WILD-TYPE  6 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      1    4
  KBTBD13 WILD-TYPE    6   17
                        clus
vv                       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               4                17
[1] 2 2
[1] FALSE

Clustering(85) Variable = SPIRE2 MUTATION ANALYSIS
D85V1, survival
                  sevent
clus2               0  1
  SPIRE2 MUTATED    2  1
  SPIRE2 WILD-TYPE 33 19
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               52 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               1               19 
$`SPIRE2 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JL TCGA-OR-A5LP 
       16.11        22.03        52.04 

$`SPIRE2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
       39.35        36.33        73.05        53.03        64.08        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           16.11             4.11 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           52.04           153.63 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           22.03            37.84 
[1] "16.1 - 52.0 (22.0)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.2"
D85V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SPIRE2 MUTATED         1        1         1        0
  SPIRE2 WILD-TYPE       5       20        13       12
D85V3, multiclass
           clus
vv          SPIRE2 MUTATED SPIRE2 WILD-TYPE
  STAGE I                1                5
  STAGE II               1               20
  STAGE III              1               13
  STAGE IV               0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  SPIRE2 MUTATED    1  1  1  0
  SPIRE2 WILD-TYPE  5 24  6 15
D85V4, multiclass
    clus
vv   SPIRE2 MUTATED SPIRE2 WILD-TYPE
  T1              1                5
  T2              1               24
  T3              1                6
  T4              0               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"
D85V5, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 44  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   44    6
   clus
vv  SPIRE2 MUTATED SPIRE2 WILD-TYPE
  0              3               44
  1              0                6
[1] 2 2
[1] FALSE
D85V6, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 34 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   34   19
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  FEMALE              3               34
  MALE                0               19
[1] 2 2
[1] FALSE
D85V7, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    1  0
  SPIRE2 WILD-TYPE  6 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      1    0
  SPIRE2 WILD-TYPE    6   21
                        clus
vv                       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              0               21
[1] 2 2
[1] FALSE

Clustering(86) Variable = NPTX1 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2              0  1
  NPTX1 MUTATED    2  1
  NPTX1 WILD-TYPE 33 19
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              52 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              1              19 
$`NPTX1 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JV TCGA-OR-A5LC 
       46.82        50.66         5.23 

$`NPTX1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        16.04        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           5.23            4.11 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          50.66          153.63 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          46.82           36.10 
[1] "5.2 - 50.7 (46.8)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.1"
D86V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NPTX1 MUTATED         1        1         0        1
  NPTX1 WILD-TYPE       5       20        14       11
D86V3, multiclass
           clus
vv          NPTX1 MUTATED NPTX1 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              20
  STAGE III             0              14
  STAGE IV              1              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              T1 T2 T3 T4
  NPTX1 MUTATED    1  1  0  1
  NPTX1 WILD-TYPE  5 24  7 14
D86V4, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  T1             1               5
  T2             1              24
  T3             0               7
  T4             1              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"
D86V5, binary
                 cls
clus               0  1
  NPTX1 MUTATED    3  0
  NPTX1 WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      3    0
  NPTX1 WILD-TYPE   44    6
   clus
vv  NPTX1 MUTATED NPTX1 WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D86V6, binary
                 cls
clus               0  1
  NPTX1 MUTATED    1  2
  NPTX1 WILD-TYPE 36 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      1    2
  NPTX1 WILD-TYPE   36   17
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  FEMALE             1              36
  MALE               2              17
[1] 2 2
[1] FALSE
D86V7, binary
                 cls
clus               0  1
  NPTX1 MUTATED    0  1
  NPTX1 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    1
  NPTX1 WILD-TYPE    7   20
                        clus
vv                       NPTX1 MUTATED NPTX1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(87) Variable = ADAD2 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2              0  1
  ADAD2 MUTATED    2  1
  ADAD2 WILD-TYPE 33 19
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              3              52 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              1              19 
$`ADAD2 MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JQ TCGA-PK-A5HB 
       18.12        22.16        42.51 

$`ADAD2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        30.31        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR 
       40.34        46.82        41.26        22.03         4.90       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  ADAD2 MUTATED ADAD2 WILD-TYPE 
          18.12            4.11 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
          42.51          153.63 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
          22.16           37.84 
[1] "18.1 - 42.5 (22.2)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.2"
D87V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ADAD2 MUTATED         0        1         0        1
  ADAD2 WILD-TYPE       6       20        14       11
D87V3, multiclass
[1] "Remove cluster labels:" "ADAD2 MUTATED"         
clus
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JH 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-P6-A5OG      TCGA-P6-A5OH 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
                 vv
clus              T1 T2 T3 T4
  ADAD2 MUTATED    0  1  0  1
  ADAD2 WILD-TYPE  6 24  7 14
D87V4, multiclass
[1] "Remove cluster labels:" "ADAD2 MUTATED"         
clus
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JH 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-P6-A5OG      TCGA-P6-A5OH 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
D87V5, binary
                 cls
clus               0  1
  ADAD2 MUTATED    2  0
  ADAD2 WILD-TYPE 45  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      2    0
  ADAD2 WILD-TYPE   45    6
   clus
vv  ADAD2 MUTATED ADAD2 WILD-TYPE
  0             2              45
  1             0               6
[1] 2 2
[1] FALSE
D87V6, binary
                 cls
clus               0  1
  ADAD2 MUTATED    1  2
  ADAD2 WILD-TYPE 36 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      1    2
  ADAD2 WILD-TYPE   36   17
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  FEMALE             1              36
  MALE               2              17
[1] 2 2
[1] FALSE
D87V7, binary
                 cls
clus               0  1
  ADAD2 MUTATED    0  0
  ADAD2 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      0    0
  ADAD2 WILD-TYPE    7   21

Clustering(88) Variable = SEZ6L2 MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2               0  1
  SEZ6L2 MUTATED    3  2
  SEZ6L2 WILD-TYPE 32 18
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               5               50 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               2               18 
$`SEZ6L2 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5LC 
       46.82        32.68        46.49        50.14         5.23 

$`SEZ6L2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        11.31        87.88       153.63       120.30 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.21        16.01        39.58        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       53.03        64.08        52.04        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
            5.23             4.11 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
           50.14           153.63 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
           46.49            36.10 
[1] "5.2 - 50.1 (46.5)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.2"
D88V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEZ6L2 MUTATED         1        0         2        2
  SEZ6L2 WILD-TYPE       5       21        12       10
D88V3, multiclass
           clus
vv          SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  STAGE I                1                5
  STAGE II               0               21
  STAGE III              2               12
  STAGE IV               2               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               T1 T2 T3 T4
  SEZ6L2 MUTATED    1  1  0  3
  SEZ6L2 WILD-TYPE  5 24  7 12
D88V4, multiclass
    clus
vv   SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  T1              1                5
  T2              1               24
  T3              0                7
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V5, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    4  1
  SEZ6L2 WILD-TYPE 43  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      4    1
  SEZ6L2 WILD-TYPE   43    5
   clus
vv  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  0              4               43
  1              1                5
[1] 2 2
[1] FALSE
D88V6, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    4  1
  SEZ6L2 WILD-TYPE 33 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      4    1
  SEZ6L2 WILD-TYPE   33   18
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  FEMALE              4               33
  MALE                1               18
[1] 2 2
[1] FALSE
D88V7, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    0  3
  SEZ6L2 WILD-TYPE  7 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      0    3
  SEZ6L2 WILD-TYPE    7   18
                        clus
vv                       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(89) Variable = NEFH MUTATION ANALYSIS
D89V1, survival
                sevent
clus2             0  1
  NEFH MUTATED    1  4
  NEFH WILD-TYPE 34 16
  NEFH MUTATED NEFH WILD-TYPE 
             5             50 
  NEFH MUTATED NEFH WILD-TYPE 
             4             16 
$`NEFH MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5JP TCGA-OR-A5K2 TCGA-P6-A5OG 
       15.45        19.04         4.90        32.68        12.59 

$`NEFH WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26        22.03        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        63.25        31.23        18.15        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  NEFH MUTATED NEFH WILD-TYPE 
          4.90           4.11 
  NEFH MUTATED NEFH WILD-TYPE 
         32.68         153.63 
  NEFH MUTATED NEFH WILD-TYPE 
         15.45          39.96 
[1] "4.9 - 32.7 (15.4)"  "4.1 - 153.6 (40.0)"
[1] "hr=" "6.9"
D89V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         0        1         2        2
  NEFH WILD-TYPE       6       20        12       10
D89V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              0              6
  STAGE II             1             20
  STAGE III            2             12
  STAGE IV             2             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             T1 T2 T3 T4
  NEFH MUTATED    0  1  2  2
  NEFH WILD-TYPE  6 24  5 13
D89V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0              6
  T2            1             24
  T3            2              5
  T4            2             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"
D89V5, binary
                cls
clus              0  1
  NEFH MUTATED    4  1
  NEFH WILD-TYPE 43  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    1
  NEFH WILD-TYPE   43    5
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            4             43
  1            1              5
[1] 2 2
[1] FALSE
D89V6, binary
                cls
clus              0  1
  NEFH MUTATED    3  2
  NEFH WILD-TYPE 34 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      3    2
  NEFH WILD-TYPE   34   17
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            3             34
  MALE              2             17
[1] 2 2
[1] FALSE
D89V7, binary
                cls
clus              0  1
  NEFH MUTATED    2  1
  NEFH WILD-TYPE  5 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    1
  NEFH WILD-TYPE    5   20
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(90) Variable = AMDHD1 MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2               0  1
  AMDHD1 MUTATED    6  3
  AMDHD1 WILD-TYPE 29 17
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               9               46 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               3               17 
$`AMDHD1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JW TCGA-OR-A5K9 
       19.04        18.12        41.39        22.03        63.25        11.31 
TCGA-OR-A5L6 TCGA-OR-A5LO TCGA-PK-A5HB 
       20.65        64.08        42.51 

$`AMDHD1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       16.11        30.31        57.53        91.46        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       41.26         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
       31.23        18.15        32.68        17.36         8.32        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
      128.12        23.80        27.62        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
        5.23        39.35        36.33        73.05        53.03        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           11.31             4.11 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           64.08           153.63 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           22.03            37.84 
[1] "11.3 - 64.1 (22.0)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.1"
D90V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AMDHD1 MUTATED         1        5         1        2
  AMDHD1 WILD-TYPE       5       16        13       10
D90V3, multiclass
           clus
vv          AMDHD1 MUTATED AMDHD1 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               16
  STAGE III              1               13
  STAGE IV               2               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               T1 T2 T3 T4
  AMDHD1 MUTATED    1  5  1  2
  AMDHD1 WILD-TYPE  5 20  6 13
D90V4, multiclass
    clus
vv   AMDHD1 MUTATED AMDHD1 WILD-TYPE
  T1              1                5
  T2              5               20
  T3              1                6
  T4              2               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"
D90V5, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    9  0
  AMDHD1 WILD-TYPE 38  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      9    0
  AMDHD1 WILD-TYPE   38    6
   clus
vv  AMDHD1 MUTATED AMDHD1 WILD-TYPE
  0              9               38
  1              0                6
[1] 2 2
[1] FALSE
D90V6, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    5  5
  AMDHD1 WILD-TYPE 32 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      5    5
  AMDHD1 WILD-TYPE   32   14
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  FEMALE              5               32
  MALE                5               14
[1] 2 2
[1] FALSE
D90V7, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    1  2
  AMDHD1 WILD-TYPE  6 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      1    2
  AMDHD1 WILD-TYPE    6   19
                        clus
vv                       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               19
[1] 2 2
[1] FALSE

Clustering(91) Variable = GLTSCR2 MUTATION ANALYSIS
D91V1, survival
                   sevent
clus2                0  1
  GLTSCR2 MUTATED    3  1
  GLTSCR2 WILD-TYPE 32 19
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
                4                51 
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
                1                19 
$`GLTSCR2 MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5KV 
       18.12         4.90        63.25       120.30 

$`GLTSCR2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        30.31        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26        22.03        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
        8.32        11.31        46.49        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
             4.90              4.11 
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
           120.30            153.63 
  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE 
           40.685            36.330 
[1] "4.9 - 120.3 (40.7)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.6"
D91V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  GLTSCR2 MUTATED         0        2         1        1
  GLTSCR2 WILD-TYPE       6       19        13       11
D91V3, multiclass
           clus
vv          GLTSCR2 MUTATED GLTSCR2 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                19
  STAGE III               1                13
  STAGE IV                1                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                T1 T2 T3 T4
  GLTSCR2 MUTATED    0  3  0  1
  GLTSCR2 WILD-TYPE  6 22  7 14
D91V4, multiclass
    clus
vv   GLTSCR2 MUTATED GLTSCR2 WILD-TYPE
  T1               0                 6
  T2               3                22
  T3               0                 7
  T4               1                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"
D91V5, binary
                   cls
clus                 0  1
  GLTSCR2 MUTATED    3  1
  GLTSCR2 WILD-TYPE 44  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR2 MUTATED      3    1
  GLTSCR2 WILD-TYPE   44    5
   clus
vv  GLTSCR2 MUTATED GLTSCR2 WILD-TYPE
  0               3                44
  1               1                 5
[1] 2 2
[1] FALSE
D91V6, binary
                   cls
clus                 0  1
  GLTSCR2 MUTATED    1  3
  GLTSCR2 WILD-TYPE 36 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR2 MUTATED      1    3
  GLTSCR2 WILD-TYPE   36   16
        clus
vv       GLTSCR2 MUTATED GLTSCR2 WILD-TYPE
  FEMALE               1                36
  MALE                 3                16
[1] 2 2
[1] FALSE
D91V7, binary
                   cls
clus                 0  1
  GLTSCR2 MUTATED    0  1
  GLTSCR2 WILD-TYPE  7 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR2 MUTATED      0    1
  GLTSCR2 WILD-TYPE    7   20
                        clus
vv                       GLTSCR2 MUTATED GLTSCR2 WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(92) Variable = PLEC MUTATION ANALYSIS
D92V1, survival
                sevent
clus2             0  1
  PLEC MUTATED    8  1
  PLEC WILD-TYPE 27 19
  PLEC MUTATED PLEC WILD-TYPE 
             9             46 
  PLEC MUTATED PLEC WILD-TYPE 
             1             19 
$`PLEC MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KW 
       63.85        41.26        22.03        17.36         8.32        50.14 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       21.21        16.01         5.23 

$`PLEC WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       40.34        46.82         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K9 
       50.66        63.25        31.23        18.15        32.68        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ 
       46.49        87.88       153.63       120.30        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LD 
      128.12        23.80        27.62        20.65        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PLEC MUTATED PLEC WILD-TYPE 
          5.23           4.11 
  PLEC MUTATED PLEC WILD-TYPE 
         63.85         153.63 
  PLEC MUTATED PLEC WILD-TYPE 
        21.210         39.465 
[1] "5.2 - 63.9 (21.2)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2.6"
D92V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PLEC MUTATED         1        2         4        3
  PLEC WILD-TYPE       5       19        10        9
D92V3, multiclass
           clus
vv          PLEC MUTATED PLEC WILD-TYPE
  STAGE I              1              5
  STAGE II             2             19
  STAGE III            4             10
  STAGE IV             3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PLEC MUTATED    1  3  2  4
  PLEC WILD-TYPE  5 22  5 11
D92V4, multiclass
    clus
vv   PLEC MUTATED PLEC WILD-TYPE
  T1            1              5
  T2            3             22
  T3            2              5
  T4            4             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"
D92V5, binary
                cls
clus              0  1
  PLEC MUTATED    9  1
  PLEC WILD-TYPE 38  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      9    1
  PLEC WILD-TYPE   38    5
   clus
vv  PLEC MUTATED PLEC WILD-TYPE
  0            9             38
  1            1              5
[1] 2 2
[1] FALSE
D92V6, binary
                cls
clus              0  1
  PLEC MUTATED    9  1
  PLEC WILD-TYPE 28 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      9    1
  PLEC WILD-TYPE   28   18
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  FEMALE            9             28
  MALE              1             18
[1] 2 2
[1] FALSE
D92V7, binary
                cls
clus              0  1
  PLEC MUTATED    1  5
  PLEC WILD-TYPE  6 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      1    5
  PLEC WILD-TYPE    6   16
                        clus
vv                       PLEC MUTATED PLEC WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            5             16
[1] 2 2
[1] FALSE

Clustering(93) Variable = MAP7 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 33 19
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             52 
  MAP7 MUTATED MAP7 WILD-TYPE 
             1             19 
$`MAP7 MUTATED`
TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5LA 
       50.66        32.68        16.01 

$`MAP7 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        16.04        63.25        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  MAP7 MUTATED MAP7 WILD-TYPE 
         16.01           4.11 
  MAP7 MUTATED MAP7 WILD-TYPE 
         50.66         153.63 
  MAP7 MUTATED MAP7 WILD-TYPE 
         32.68          37.84 
[1] "16.0 - 50.7 (32.7)" "4.1 - 153.6 (37.8)"
[1] "hr=" "1.1"
D93V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAP7 MUTATED         0        2         1        0
  MAP7 WILD-TYPE       6       19        13       12
D93V3, multiclass
           clus
vv          MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            1             13
  STAGE IV             0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MAP7 MUTATED    0  2  0  1
  MAP7 WILD-TYPE  6 23  7 14
D93V4, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            0              6
  T2            2             23
  T3            0              7
  T4            1             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"
D93V5, binary
                cls
clus              0  1
  MAP7 MUTATED    3  0
  MAP7 WILD-TYPE 44  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      3    0
  MAP7 WILD-TYPE   44    6
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0            3             44
  1            0              6
[1] 2 2
[1] FALSE
D93V6, binary
                cls
clus              0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 35 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      2    1
  MAP7 WILD-TYPE   35   18
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  FEMALE            2             35
  MALE              1             18
[1] 2 2
[1] FALSE
D93V7, binary
                cls
clus              0  1
  MAP7 MUTATED    0  1
  MAP7 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      0    1
  MAP7 WILD-TYPE    7   20
                        clus
vv                       MAP7 MUTATED MAP7 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(94) Variable = DSPP MUTATION ANALYSIS
D94V1, survival
                sevent
clus2             0  1
  DSPP MUTATED    6  3
  DSPP WILD-TYPE 29 17
  DSPP MUTATED DSPP WILD-TYPE 
             9             46 
  DSPP MUTATED DSPP WILD-TYPE 
             3             17 
$`DSPP MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 
       55.13        18.12        50.14        35.87       128.12        23.80 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LL 
       20.65        21.21        53.03 

$`DSPP WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        30.31        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
      120.30         4.11        27.62        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        36.33        73.05        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  DSPP MUTATED DSPP WILD-TYPE 
         18.12           4.11 
  DSPP MUTATED DSPP WILD-TYPE 
        128.12         153.63 
  DSPP MUTATED DSPP WILD-TYPE 
         35.87          37.84 
[1] "18.1 - 128.1 (35.9)" "4.1 - 153.6 (37.8)" 
[1] "hr=" "1.2"
D94V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DSPP MUTATED         1        3         3        2
  DSPP WILD-TYPE       5       18        11       10
D94V3, multiclass
           clus
vv          DSPP MUTATED DSPP WILD-TYPE
  STAGE I              1              5
  STAGE II             3             18
  STAGE III            3             11
  STAGE IV             2             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             T1 T2 T3 T4
  DSPP MUTATED    1  5  1  2
  DSPP WILD-TYPE  5 20  6 13
D94V4, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  T1            1              5
  T2            5             20
  T3            1              6
  T4            2             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"
D94V5, binary
                cls
clus              0  1
  DSPP MUTATED    7  2
  DSPP WILD-TYPE 40  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    2
  DSPP WILD-TYPE   40    4
   clus
vv  DSPP MUTATED DSPP WILD-TYPE
  0            7             40
  1            2              4
[1] 2 2
[1] FALSE
D94V6, binary
                cls
clus              0  1
  DSPP MUTATED    7  2
  DSPP WILD-TYPE 30 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    2
  DSPP WILD-TYPE   30   17
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  FEMALE            7             30
  MALE              2             17
[1] 2 2
[1] FALSE
D94V7, binary
                cls
clus              0  1
  DSPP MUTATED    1  6
  DSPP WILD-TYPE  6 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      1    6
  DSPP WILD-TYPE    6   15
                        clus
vv                       DSPP MUTATED DSPP WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            6             15
[1] 2 2
[1] FALSE

Clustering(95) Variable = CRIPAK MUTATION ANALYSIS
D95V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED    6  2
  CRIPAK WILD-TYPE 29 18
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               8               47 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               2               18 
$`CRIPAK MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5L6 
       79.82        22.03        11.31        46.49         4.11        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LR 
       21.21        21.01 

$`CRIPAK WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       17.36         8.32        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LB 
       35.87       128.12        23.80        27.62        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        73.05        53.03        64.08 
TCGA-OR-A5LP TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       52.04         6.81        12.59       106.52        42.51 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            4.11             4.90 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           79.82           153.63 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           21.11            39.58 
[1] "4.1 - 79.8 (21.1)"  "4.9 - 153.6 (39.6)"
[1] "hr=" "1.1"
D95V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CRIPAK MUTATED         1        6         0        1
  CRIPAK WILD-TYPE       5       15        14       11
D95V3, multiclass
           clus
vv          CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                1                5
  STAGE II               6               15
  STAGE III              0               14
  STAGE IV               1               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               T1 T2 T3 T4
  CRIPAK MUTATED    1  6  0  1
  CRIPAK WILD-TYPE  5 19  7 14
D95V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              1                5
  T2              6               19
  T3              0                7
  T4              1               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"
D95V5, binary
                  cls
clus                0  1
  CRIPAK MUTATED    8  0
  CRIPAK WILD-TYPE 39  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      8    0
  CRIPAK WILD-TYPE   39    6
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0              8               39
  1              0                6
[1] 2 2
[1] FALSE
D95V6, binary
                  cls
clus                0  1
  CRIPAK MUTATED    6  2
  CRIPAK WILD-TYPE 31 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      6    2
  CRIPAK WILD-TYPE   31   17
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE              6               31
  MALE                2               17
[1] 2 2
[1] FALSE
D95V7, binary
                  cls
clus                0  1
  CRIPAK MUTATED    1  4
  CRIPAK WILD-TYPE  6 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      1    4
  CRIPAK WILD-TYPE    6   17
                        clus
vv                       CRIPAK MUTATED CRIPAK WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              4               17
[1] 2 2
[1] FALSE

Clustering(96) Variable = PRKAR1A MUTATION ANALYSIS
D96V1, survival
                   sevent
clus2                0  1
  PRKAR1A MUTATED    4  2
  PRKAR1A WILD-TYPE 31 18
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                49 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                2                18 
$`PRKAR1A MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JL TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5LO 
       63.85        30.31        22.03        18.15        87.88        64.08 

$`PRKAR1A WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        63.25        31.23        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        46.49       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       53.03        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            18.15              4.11 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            87.88            153.63 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            47.08             36.33 
[1] "18.1 - 87.9 (47.1)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.4"
D96V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PRKAR1A MUTATED         2        1         1        2
  PRKAR1A WILD-TYPE       4       20        13       10
D96V3, multiclass
           clus
vv          PRKAR1A MUTATED PRKAR1A WILD-TYPE
  STAGE I                 2                 4
  STAGE II                1                20
  STAGE III               1                13
  STAGE IV                2                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                T1 T2 T3 T4
  PRKAR1A MUTATED    2  1  1  2
  PRKAR1A WILD-TYPE  4 24  6 13
D96V4, multiclass
    clus
vv   PRKAR1A MUTATED PRKAR1A WILD-TYPE
  T1               2                 4
  T2               1                24
  T3               1                 6
  T4               2                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"
D96V5, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    5  1
  PRKAR1A WILD-TYPE 42  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      5    1
  PRKAR1A WILD-TYPE   42    5
   clus
vv  PRKAR1A MUTATED PRKAR1A WILD-TYPE
  0               5                42
  1               1                 5
[1] 2 2
[1] FALSE
D96V6, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    6  0
  PRKAR1A WILD-TYPE 31 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      6    0
  PRKAR1A WILD-TYPE   31   19
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  FEMALE               6                31
  MALE                 0                19
[1] 2 2
[1] FALSE
D96V7, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    1  1
  PRKAR1A WILD-TYPE  6 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      1    1
  PRKAR1A WILD-TYPE    6   20
                        clus
vv                       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(97) Variable = CYP4A22 MUTATION ANALYSIS
D97V1, survival
                   sevent
clus2                0  1
  CYP4A22 MUTATED    0  3
  CYP4A22 WILD-TYPE 35 17
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                3                52 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                3                17 
$`CYP4A22 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5K9 TCGA-OR-A5LB 
       55.13        11.31        39.58 

$`CYP4A22 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            11.31              4.11 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            55.13            153.63 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            39.58             36.10 
[1] "11.3 - 55.1 (39.6)" "4.1 - 153.6 (36.1)"
[1] "hr=" "3.1"
D97V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CYP4A22 MUTATED         0        1         0        2
  CYP4A22 WILD-TYPE       6       20        14       10
D97V3, multiclass
           clus
vv          CYP4A22 MUTATED CYP4A22 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                1                20
  STAGE III               0                14
  STAGE IV                2                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                T1 T2 T3 T4
  CYP4A22 MUTATED    0  1  1  1
  CYP4A22 WILD-TYPE  6 24  6 14
D97V4, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  T1               0                 6
  T2               1                24
  T3               1                 6
  T4               1                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"
D97V5, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    3  0
  CYP4A22 WILD-TYPE 44  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      3    0
  CYP4A22 WILD-TYPE   44    6
   clus
vv  CYP4A22 MUTATED CYP4A22 WILD-TYPE
  0               3                44
  1               0                 6
[1] 2 2
[1] FALSE
D97V6, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    2  1
  CYP4A22 WILD-TYPE 35 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      2    1
  CYP4A22 WILD-TYPE   35   18
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  FEMALE               2                35
  MALE                 1                18
[1] 2 2
[1] FALSE
D97V7, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    1  1
  CYP4A22 WILD-TYPE  6 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      1    1
  CYP4A22 WILD-TYPE    6   20
                        clus
vv                       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(98) Variable = NOM1 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2             0  1
  NOM1 MUTATED    3  2
  NOM1 WILD-TYPE 32 18
  NOM1 MUTATED NOM1 WILD-TYPE 
             5             50 
  NOM1 MUTATED NOM1 WILD-TYPE 
             2             18 
$`NOM1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5LP 
       12.00         4.11       128.12        27.62        52.04 

$`NOM1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L4 TCGA-OR-A5L6 
      153.63       120.30        50.14        35.87        23.80        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG 
       73.05        53.03        64.08        21.01         6.81        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  NOM1 MUTATED NOM1 WILD-TYPE 
          4.11           4.90 
  NOM1 MUTATED NOM1 WILD-TYPE 
        128.12         153.63 
  NOM1 MUTATED NOM1 WILD-TYPE 
         27.62          37.84 
[1] "4.1 - 128.1 (27.6)" "4.9 - 153.6 (37.8)"
[1] "hr=" "1.4"
D98V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NOM1 MUTATED         2        2         1        0
  NOM1 WILD-TYPE       4       19        13       12
D98V3, multiclass
           clus
vv          NOM1 MUTATED NOM1 WILD-TYPE
  STAGE I              2              4
  STAGE II             2             19
  STAGE III            1             13
  STAGE IV             0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  NOM1 MUTATED    2  2  0  1
  NOM1 WILD-TYPE  4 23  7 14
D98V4, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  T1            2              4
  T2            2             23
  T3            0              7
  T4            1             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"
D98V5, binary
                cls
clus              0  1
  NOM1 MUTATED    5  0
  NOM1 WILD-TYPE 42  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      5    0
  NOM1 WILD-TYPE   42    6
   clus
vv  NOM1 MUTATED NOM1 WILD-TYPE
  0            5             42
  1            0              6
[1] 2 2
[1] FALSE
D98V6, binary
                cls
clus              0  1
  NOM1 MUTATED    3  2
  NOM1 WILD-TYPE 34 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      3    2
  NOM1 WILD-TYPE   34   17
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  FEMALE            3             34
  MALE              2             17
[1] 2 2
[1] FALSE
D98V7, binary
                cls
clus              0  1
  NOM1 MUTATED    1  3
  NOM1 WILD-TYPE  6 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      1    3
  NOM1 WILD-TYPE    6   18
                        clus
vv                       NOM1 MUTATED NOM1 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(99) Variable = C12ORF65 MUTATION ANALYSIS
D99V1, survival
                    sevent
clus2                 0  1
  C12ORF65 MUTATED    0  3
  C12ORF65 WILD-TYPE 35 17
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
                 3                 52 
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
                 3                 17 
$`C12ORF65 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5LC 
       18.15        32.68         5.23 

$`C12ORF65 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
              5.23               4.11 
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
             32.68             153.63 
  C12ORF65 MUTATED C12ORF65 WILD-TYPE 
            18.150             39.465 
[1] "5.2 - 32.7 (18.1)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "6.9"
D99V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C12ORF65 MUTATED         0        0         1        2
  C12ORF65 WILD-TYPE       6       21        13       10
D99V3, multiclass
           clus
vv          C12ORF65 MUTATED C12ORF65 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 0                 21
  STAGE III                1                 13
  STAGE IV                 2                 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                 T1 T2 T3 T4
  C12ORF65 MUTATED    0  0  0  3
  C12ORF65 WILD-TYPE  6 25  7 12
D99V4, multiclass
    clus
vv   C12ORF65 MUTATED C12ORF65 WILD-TYPE
  T1                0                  6
  T2                0                 25
  T3                0                  7
  T4                3                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V5, binary
                    cls
clus                  0  1
  C12ORF65 MUTATED    2  1
  C12ORF65 WILD-TYPE 45  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF65 MUTATED      2    1
  C12ORF65 WILD-TYPE   45    5
   clus
vv  C12ORF65 MUTATED C12ORF65 WILD-TYPE
  0                2                 45
  1                1                  5
[1] 2 2
[1] FALSE
D99V6, binary
                    cls
clus                  0  1
  C12ORF65 MUTATED    3  0
  C12ORF65 WILD-TYPE 34 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF65 MUTATED      3    0
  C12ORF65 WILD-TYPE   34   19
        clus
vv       C12ORF65 MUTATED C12ORF65 WILD-TYPE
  FEMALE                3                 34
  MALE                  0                 19
[1] 2 2
[1] FALSE
D99V7, binary
                    cls
clus                  0  1
  C12ORF65 MUTATED    0  1
  C12ORF65 WILD-TYPE  7 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF65 MUTATED      0    1
  C12ORF65 WILD-TYPE    7   20
                        clus
vv                       C12ORF65 MUTATED C12ORF65 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                1                 20
[1] 2 2
[1] FALSE

Clustering(100) Variable = HLA-B MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2              0  1
  HLA-B MUTATED    2  4
  HLA-B WILD-TYPE 33 16
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              49 
  HLA-B MUTATED HLA-B WILD-TYPE 
              4              16 
$`HLA-B MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JC TCGA-OR-A5JY TCGA-OR-A5KZ TCGA-OR-A5L9 TCGA-OR-A5LK 
       12.00        57.53        18.15         4.11        21.21        73.05 

$`HLA-B WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        30.31        18.12        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14        35.87       128.12        23.80        27.62        20.65 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL 
       16.01        39.58         5.23        39.35        36.33        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  HLA-B MUTATED HLA-B WILD-TYPE 
           4.11            4.90 
  HLA-B MUTATED HLA-B WILD-TYPE 
          73.05          153.63 
  HLA-B MUTATED HLA-B WILD-TYPE 
          19.68           39.35 
[1] "4.1 - 73.0 (19.7)"  "4.9 - 153.6 (39.4)"
[1] "hr=" "2.4"
D100V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-B MUTATED         0        3         1        1
  HLA-B WILD-TYPE       6       18        13       11
D100V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               0               6
  STAGE II              3              18
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  HLA-B MUTATED    0  3  0  2
  HLA-B WILD-TYPE  6 22  7 13
D100V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             0               6
  T2             3              22
  T3             0               7
  T4             2              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"
D100V5, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  1
  HLA-B WILD-TYPE 43  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    1
  HLA-B WILD-TYPE   43    5
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             4              43
  1             1               5
[1] 2 2
[1] FALSE
D100V6, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  4
  HLA-B WILD-TYPE 35 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    4
  HLA-B WILD-TYPE   35   15
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             2              35
  MALE               4              15
[1] 2 2
[1] FALSE
D100V7, binary
                 cls
clus               0  1
  HLA-B MUTATED    1  2
  HLA-B WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      1    2
  HLA-B WILD-TYPE    6   19
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(101) Variable = CSGALNACT2 MUTATION ANALYSIS
D101V1, survival
                      sevent
clus2                   0  1
  CSGALNACT2 MUTATED    2  1
  CSGALNACT2 WILD-TYPE 33 19
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   52 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   19 
$`CSGALNACT2 MUTATED`
TCGA-OR-A5LC TCGA-OR-A5LP TCGA-OR-A5LR 
        5.23        52.04        21.01 

$`CSGALNACT2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        20.65        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       39.58        39.35        36.33        73.05        53.03        64.08 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                5.23                 4.11 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               52.04               153.63 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               21.01                37.84 
[1] "5.2 - 52.0 (21.0)"  "4.1 - 153.6 (37.8)"
[1] "hr=" "1.4"
D101V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         0        2         0        1
  CSGALNACT2 WILD-TYPE       6       19        14       11
D101V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    0                    6
  STAGE II                   2                   19
  STAGE III                  0                   14
  STAGE IV                   1                   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                   T1 T2 T3 T4
  CSGALNACT2 MUTATED    0  2  0  1
  CSGALNACT2 WILD-TYPE  6 23  7 14
D101V4, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                  0                    6
  T2                  2                   23
  T3                  0                    7
  T4                  1                   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"
D101V5, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 44  6
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   44    6
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  3                   44
  1                  0                    6
[1] 2 2
[1] FALSE
D101V6, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 34 19
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   34   19
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  3                   34
  MALE                    0                   19
[1] 2 2
[1] FALSE
D101V7, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    0  1
  CSGALNACT2 WILD-TYPE  7 20
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    1
  CSGALNACT2 WILD-TYPE    7   20
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                    7
  NOT HISPANIC OR LATINO                  1                   20
[1] 2 2
[1] FALSE

Clustering(102) Variable = UQCRFS1 MUTATION ANALYSIS
D102V1, survival
                   sevent
clus2                0  1
  UQCRFS1 MUTATED    2  3
  UQCRFS1 WILD-TYPE 33 17
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                50 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                3                17 
$`UQCRFS1 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5JI TCGA-OR-A5LD TCGA-P6-A5OF 
       63.85        15.45        46.82        39.35         6.81 

$`UQCRFS1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        12.00        79.82        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       30.31        18.12        57.53        91.46        41.39        40.34 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        22.03         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       20.65        21.21        16.01        39.58         5.23        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG 
       73.05        53.03        64.08        52.04        21.01        12.59 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
             6.81              4.11 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            63.85            153.63 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            39.35             36.10 
[1] "6.8 - 63.9 (39.4)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.9"
D102V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  UQCRFS1 MUTATED         1        0         3        1
  UQCRFS1 WILD-TYPE       5       21        11       11
D102V3, multiclass
           clus
vv          UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                0                21
  STAGE III               3                11
  STAGE IV                1                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                T1 T2 T3 T4
  UQCRFS1 MUTATED    1  0  2  2
  UQCRFS1 WILD-TYPE  5 25  5 13
D102V4, multiclass
    clus
vv   UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  T1               1                 5
  T2               0                25
  T3               2                 5
  T4               2                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"
D102V5, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    4  1
  UQCRFS1 WILD-TYPE 43  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      4    1
  UQCRFS1 WILD-TYPE   43    5
   clus
vv  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  0               4                43
  1               1                 5
[1] 2 2
[1] FALSE
D102V6, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    3  2
  UQCRFS1 WILD-TYPE 34 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      3    2
  UQCRFS1 WILD-TYPE   34   17
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  FEMALE               3                34
  MALE                 2                17
[1] 2 2
[1] FALSE
D102V7, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    2  2
  UQCRFS1 WILD-TYPE  5 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      2    2
  UQCRFS1 WILD-TYPE    5   19
                        clus
vv                       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               2                19
[1] 2 2
[1] FALSE

Clustering(103) Variable = PDCD6 MUTATION ANALYSIS
D103V1, survival
                 sevent
clus2              0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 33 19
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              52 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              1              19 
$`PDCD6 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JL TCGA-OR-A5JR 
       15.45        22.03       121.25 

$`PDCD6 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT 
       40.34        46.82        41.26         4.90        22.16        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       50.66        63.25        31.23        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PDCD6 MUTATED PDCD6 WILD-TYPE 
          15.45            4.11 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
         121.25          153.63 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
          22.03           37.84 
[1] "15.4 - 121.2 (22.0)" "4.1 - 153.6 (37.8)" 
[1] "hr=" "1"  
D103V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PDCD6 MUTATED         2        0         0        1
  PDCD6 WILD-TYPE       4       21        14       11
D103V3, multiclass
           clus
vv          PDCD6 MUTATED PDCD6 WILD-TYPE
  STAGE I               2               4
  STAGE II              0              21
  STAGE III             0              14
  STAGE IV              1              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              T1 T2 T3 T4
  PDCD6 MUTATED    2  0  1  0
  PDCD6 WILD-TYPE  4 25  6 15
D103V4, multiclass
    clus
vv   PDCD6 MUTATED PDCD6 WILD-TYPE
  T1             2               4
  T2             0              25
  T3             1               6
  T4             0              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"
D103V5, binary
                 cls
clus               0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      2    1
  PDCD6 WILD-TYPE   45    5
   clus
vv  PDCD6 MUTATED PDCD6 WILD-TYPE
  0             2              45
  1             1               5
[1] 2 2
[1] FALSE
D103V6, binary
                 cls
clus               0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 35 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      2    1
  PDCD6 WILD-TYPE   35   18
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  FEMALE             2              35
  MALE               1              18
[1] 2 2
[1] FALSE
D103V7, binary
                 cls
clus               0  1
  PDCD6 MUTATED    1  0
  PDCD6 WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      1    0
  PDCD6 WILD-TYPE    6   21
                        clus
vv                       PDCD6 MUTATED PDCD6 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             0              21
[1] 2 2
[1] FALSE

Clustering(104) Variable = PTX4 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2             0  1
  PTX4 MUTATED    0  3
  PTX4 WILD-TYPE 35 17
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             52 
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             17 
$`PTX4 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5LC 
       30.31        18.12         5.23 

$`PTX4 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        19.04        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        41.26        22.03         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  PTX4 MUTATED PTX4 WILD-TYPE 
          5.23           4.11 
  PTX4 MUTATED PTX4 WILD-TYPE 
         30.31         153.63 
  PTX4 MUTATED PTX4 WILD-TYPE 
        18.120         39.465 
[1] "5.2 - 30.3 (18.1)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "8"  
D104V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTX4 MUTATED         0        0         0        3
  PTX4 WILD-TYPE       6       21        14        9
D104V3, multiclass
           clus
vv          PTX4 MUTATED PTX4 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             21
  STAGE III            0             14
  STAGE IV             3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PTX4 MUTATED    0  0  0  3
  PTX4 WILD-TYPE  6 25  7 12
D104V4, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  T1            0              6
  T2            0             25
  T3            0              7
  T4            3             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V5, binary
                cls
clus              0  1
  PTX4 MUTATED    3  0
  PTX4 WILD-TYPE 44  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      3    0
  PTX4 WILD-TYPE   44    6
   clus
vv  PTX4 MUTATED PTX4 WILD-TYPE
  0            3             44
  1            0              6
[1] 2 2
[1] FALSE
D104V6, binary
                cls
clus              0  1
  PTX4 MUTATED    2  1
  PTX4 WILD-TYPE 35 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      2    1
  PTX4 WILD-TYPE   35   18
        clus
vv       PTX4 MUTATED PTX4 WILD-TYPE
  FEMALE            2             35
  MALE              1             18
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus              0  1
  PTX4 MUTATED    0  1
  PTX4 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      0    1
  PTX4 WILD-TYPE    7   20
                        clus
vv                       PTX4 MUTATED PTX4 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(105) Variable = POLRMT MUTATION ANALYSIS
D105V1, survival
                  sevent
clus2               0  1
  POLRMT MUTATED    4  0
  POLRMT WILD-TYPE 31 20
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               51 
  POLRMT MUTATED POLRMT WILD-TYPE 
               0               20 
$`POLRMT MUTATED`
TCGA-OR-A5JL TCGA-OR-A5JV TCGA-OR-A5LK TCGA-OR-A5LP 
       22.03        50.66        73.05        52.04 

$`POLRMT WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.39        40.34        46.82        41.26         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        16.04        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF 
       39.35        36.33        53.03        64.08        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  POLRMT MUTATED POLRMT WILD-TYPE 
           22.03             4.11 
  POLRMT MUTATED POLRMT WILD-TYPE 
           73.05           153.63 
  POLRMT MUTATED POLRMT WILD-TYPE 
           51.35            35.87 
[1] "22.0 - 73.0 (51.3)" "4.1 - 153.6 (35.9)"
[1] "hr="     "7.7e+07"
D105V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  POLRMT MUTATED         1        3         0        0
  POLRMT WILD-TYPE       5       18        14       12
D105V3, multiclass
           clus
vv          POLRMT MUTATED POLRMT WILD-TYPE
  STAGE I                1                5
  STAGE II               3               18
  STAGE III              0               14
  STAGE IV               0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  POLRMT MUTATED    1  3  0  0
  POLRMT WILD-TYPE  5 22  7 15
D105V4, multiclass
    clus
vv   POLRMT MUTATED POLRMT WILD-TYPE
  T1              1                5
  T2              3               22
  T3              0                7
  T4              0               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"
D105V5, binary
                  cls
clus                0  1
  POLRMT MUTATED    4  0
  POLRMT WILD-TYPE 43  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      4    0
  POLRMT WILD-TYPE   43    6
   clus
vv  POLRMT MUTATED POLRMT WILD-TYPE
  0              4               43
  1              0                6
[1] 2 2
[1] FALSE
D105V6, binary
                  cls
clus                0  1
  POLRMT MUTATED    2  2
  POLRMT WILD-TYPE 35 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      2    2
  POLRMT WILD-TYPE   35   17
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  FEMALE              2               35
  MALE                2               17
[1] 2 2
[1] FALSE
D105V7, binary
                  cls
clus                0  1
  POLRMT MUTATED    0  0
  POLRMT WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      0    0
  POLRMT WILD-TYPE    7   21

Clustering(106) Variable = NF1 MUTATION ANALYSIS
D106V1, survival
               sevent
clus2            0  1
  NF1 MUTATED    4  3
  NF1 WILD-TYPE 31 17
  NF1 MUTATED NF1 WILD-TYPE 
            7            48 
  NF1 MUTATED NF1 WILD-TYPE 
            3            17 
$`NF1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5KZ TCGA-OR-A5LA 
       19.04        18.12         4.90        63.25         4.11        16.01 
TCGA-PK-A5HB 
       42.51 

$`NF1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       16.11        30.31        57.53        91.46        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        41.26        22.03        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       50.66        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       35.87       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.58         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 

  NF1 MUTATED NF1 WILD-TYPE 
         4.11          5.23 
  NF1 MUTATED NF1 WILD-TYPE 
        63.25        153.63 
  NF1 MUTATED NF1 WILD-TYPE 
       18.120        39.465 
[1] "4.1 - 63.2 (18.1)"  "5.2 - 153.6 (39.5)"
[1] "hr=" "1.9"
D106V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF1 MUTATED         0        4         1        1
  NF1 WILD-TYPE       6       17        13       11
D106V3, multiclass
           clus
vv          NF1 MUTATED NF1 WILD-TYPE
  STAGE I             0             6
  STAGE II            4            17
  STAGE III           1            13
  STAGE IV            1            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            T1 T2 T3 T4
  NF1 MUTATED    0  4  1  1
  NF1 WILD-TYPE  6 21  6 14
D106V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           0             6
  T2           4            21
  T3           1             6
  T4           1            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"
D106V5, binary
               cls
clus             0  1
  NF1 MUTATED    6  0
  NF1 WILD-TYPE 41  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6    0
  NF1 WILD-TYPE   41    6
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0           6            41
  1           0             6
[1] 2 2
[1] FALSE
D106V6, binary
               cls
clus             0  1
  NF1 MUTATED    1  6
  NF1 WILD-TYPE 36 13
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    6
  NF1 WILD-TYPE   36   13
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           1            36
  MALE             6            13
[1] 2 2
[1] FALSE
D106V7, binary
               cls
clus             0  1
  NF1 MUTATED    1  2
  NF1 WILD-TYPE  6 19
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    2
  NF1 WILD-TYPE    6   19
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           2            19
[1] 2 2
[1] FALSE

Clustering(107) Variable = ADAMTS7 MUTATION ANALYSIS
D107V1, survival
                   sevent
clus2                0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 31 20
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                51 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                0                20 
$`ADAMTS7 MUTATED`
TCGA-OR-A5JT TCGA-OR-A5KU TCGA-OR-A5L5 TCGA-OR-A5LK 
       16.04       153.63        27.62        73.05 

$`ADAMTS7 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
            16.04              4.11 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           153.63            128.12 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           50.335            36.330 
[1] "16.0 - 153.6 (50.3)" "4.1 - 128.1 (36.3)" 
[1] "hr="     "7.7e+07"
D107V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ADAMTS7 MUTATED         1        3         0        0
  ADAMTS7 WILD-TYPE       5       18        14       12
D107V3, multiclass
           clus
vv          ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                3                18
  STAGE III               0                14
  STAGE IV                0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  ADAMTS7 MUTATED    1  3  0  0
  ADAMTS7 WILD-TYPE  5 22  7 15
D107V4, multiclass
    clus
vv   ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  T1               1                 5
  T2               3                22
  T3               0                 7
  T4               0                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"
D107V5, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 43  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      4    0
  ADAMTS7 WILD-TYPE   43    6
   clus
vv  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  0               4                43
  1               0                 6
[1] 2 2
[1] FALSE
D107V6, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    3  1
  ADAMTS7 WILD-TYPE 34 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      3    1
  ADAMTS7 WILD-TYPE   34   18
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  FEMALE               3                34
  MALE                 1                18
[1] 2 2
[1] FALSE
D107V7, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    0  2
  ADAMTS7 WILD-TYPE  7 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      0    2
  ADAMTS7 WILD-TYPE    7   19
                        clus
vv                       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO               2                19
[1] 2 2
[1] FALSE

Clustering(108) Variable = CLIC6 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2              0  1
  CLIC6 MUTATED    3  1
  CLIC6 WILD-TYPE 32 19
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              4              51 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              1              19 
$`CLIC6 MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-OR-A5LC 
       79.82       153.63       128.12         5.23 

$`CLIC6 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87         4.11        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ 
       20.65        21.21        16.01        39.58        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  CLIC6 MUTATED CLIC6 WILD-TYPE 
           5.23            4.11 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
         153.63          121.25 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
         103.97           35.87 
[1] "5.2 - 153.6 (104.0)" "4.1 - 121.2 (35.9)" 
[1] "hr=" "2.2"
D108V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CLIC6 MUTATED         1        2         0        1
  CLIC6 WILD-TYPE       5       19        14       11
D108V3, multiclass
           clus
vv          CLIC6 MUTATED CLIC6 WILD-TYPE
  STAGE I               1               5
  STAGE II              2              19
  STAGE III             0              14
  STAGE IV              1              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              T1 T2 T3 T4
  CLIC6 MUTATED    1  2  0  1
  CLIC6 WILD-TYPE  5 23  7 14
D108V4, multiclass
    clus
vv   CLIC6 MUTATED CLIC6 WILD-TYPE
  T1             1               5
  T2             2              23
  T3             0               7
  T4             1              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"
D108V5, binary
                 cls
clus               0  1
  CLIC6 MUTATED    4  0
  CLIC6 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      4    0
  CLIC6 WILD-TYPE   43    6
   clus
vv  CLIC6 MUTATED CLIC6 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D108V6, binary
                 cls
clus               0  1
  CLIC6 MUTATED    4  0
  CLIC6 WILD-TYPE 33 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      4    0
  CLIC6 WILD-TYPE   33   19
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  FEMALE             4              33
  MALE               0              19
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus               0  1
  CLIC6 MUTATED    1  3
  CLIC6 WILD-TYPE  6 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      1    3
  CLIC6 WILD-TYPE    6   18
                        clus
vv                       CLIC6 MUTATED CLIC6 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             3              18
[1] 2 2
[1] FALSE

Clustering(109) Variable = EMR2 MUTATION ANALYSIS
D109V1, survival
                sevent
clus2             0  1
  EMR2 MUTATED    3  1
  EMR2 WILD-TYPE 32 19
  EMR2 MUTATED EMR2 WILD-TYPE 
             4             51 
  EMR2 MUTATED EMR2 WILD-TYPE 
             1             19 
$`EMR2 MUTATED`
TCGA-OR-A5JT TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-PK-A5HB 
       16.04        20.65        39.58        42.51 

$`EMR2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       23.80        27.62        21.21        16.01         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
        6.81        12.59       106.52 

  EMR2 MUTATED EMR2 WILD-TYPE 
         16.04           4.11 
  EMR2 MUTATED EMR2 WILD-TYPE 
         42.51         153.63 
  EMR2 MUTATED EMR2 WILD-TYPE 
        30.115         36.330 
[1] "16.0 - 42.5 (30.1)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.2"
D109V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EMR2 MUTATED         0        2         0        1
  EMR2 WILD-TYPE       6       19        14       11
D109V3, multiclass
           clus
vv          EMR2 MUTATED EMR2 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            0             14
  STAGE IV             1             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             T1 T2 T3 T4
  EMR2 MUTATED    0  2  0  1
  EMR2 WILD-TYPE  6 23  7 14
D109V4, multiclass
    clus
vv   EMR2 MUTATED EMR2 WILD-TYPE
  T1            0              6
  T2            2             23
  T3            0              7
  T4            1             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"
D109V5, binary
                cls
clus              0  1
  EMR2 MUTATED    3  0
  EMR2 WILD-TYPE 44  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR2 MUTATED      3    0
  EMR2 WILD-TYPE   44    6
   clus
vv  EMR2 MUTATED EMR2 WILD-TYPE
  0            3             44
  1            0              6
[1] 2 2
[1] FALSE
D109V6, binary
                cls
clus              0  1
  EMR2 MUTATED    1  3
  EMR2 WILD-TYPE 36 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR2 MUTATED      1    3
  EMR2 WILD-TYPE   36   16
        clus
vv       EMR2 MUTATED EMR2 WILD-TYPE
  FEMALE            1             36
  MALE              3             16
[1] 2 2
[1] FALSE
D109V7, binary
                cls
clus              0  1
  EMR2 MUTATED    0  2
  EMR2 WILD-TYPE  7 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR2 MUTATED      0    2
  EMR2 WILD-TYPE    7   19
                        clus
vv                       EMR2 MUTATED EMR2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(110) Variable = PCDHB13 MUTATION ANALYSIS
D110V1, survival
                   sevent
clus2                0  1
  PCDHB13 MUTATED    2  2
  PCDHB13 WILD-TYPE 33 18
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                4                51 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                2                18 
$`PCDHB13 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JI 
       63.85        12.00        30.31        46.82 

$`PCDHB13 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        15.45        79.82        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        91.46        41.39        40.34        41.26 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       63.25        31.23        18.15        32.68        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       21.21        16.01        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            12.00              4.11 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            63.85            153.63 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
           38.565            36.330 
[1] "12.0 - 63.9 (38.6)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.4"
D110V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PCDHB13 MUTATED         1        0         2        1
  PCDHB13 WILD-TYPE       5       21        12       11
D110V3, multiclass
           clus
vv          PCDHB13 MUTATED PCDHB13 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                0                21
  STAGE III               2                12
  STAGE IV                1                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                T1 T2 T3 T4
  PCDHB13 MUTATED    1  0  1  2
  PCDHB13 WILD-TYPE  5 25  6 13
D110V4, multiclass
    clus
vv   PCDHB13 MUTATED PCDHB13 WILD-TYPE
  T1               1                 5
  T2               0                25
  T3               1                 6
  T4               2                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"
D110V5, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    4  0
  PCDHB13 WILD-TYPE 43  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      4    0
  PCDHB13 WILD-TYPE   43    6
   clus
vv  PCDHB13 MUTATED PCDHB13 WILD-TYPE
  0               4                43
  1               0                 6
[1] 2 2
[1] FALSE
D110V6, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    2  2
  PCDHB13 WILD-TYPE 35 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      2    2
  PCDHB13 WILD-TYPE   35   17
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  FEMALE               2                35
  MALE                 2                17
[1] 2 2
[1] FALSE
D110V7, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    2  0
  PCDHB13 WILD-TYPE  5 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      2    0
  PCDHB13 WILD-TYPE    5   21
                        clus
vv                       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               0                21
[1] 2 2
[1] FALSE

Clustering(111) Variable = HLA-A MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2              0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 32 20
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              52 
  HLA-A MUTATED HLA-A WILD-TYPE 
              0              20 
$`HLA-A MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JP TCGA-OR-A5JX 
       79.82         4.90        31.23 

$`HLA-A WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26        22.03        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       16.04        50.66        63.25        18.15        32.68        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  HLA-A MUTATED HLA-A WILD-TYPE 
           4.90            4.11 
  HLA-A MUTATED HLA-A WILD-TYPE 
          79.82          153.63 
  HLA-A MUTATED HLA-A WILD-TYPE 
          31.23           37.84 
[1] "4.9 - 79.8 (31.2)"  "4.1 - 153.6 (37.8)"
[1] "hr="     "2.6e+07"
D111V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-A MUTATED         0        2         1        0
  HLA-A WILD-TYPE       6       19        13       12
D111V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0               6
  STAGE II              2              19
  STAGE III             1              13
  STAGE IV              0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  HLA-A MUTATED    0  2  1  0
  HLA-A WILD-TYPE  6 23  6 15
D111V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0               6
  T2             2              23
  T3             1               6
  T4             0              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"
D111V5, binary
                 cls
clus               0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3    0
  HLA-A WILD-TYPE   44    6
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D111V6, binary
                 cls
clus               0  1
  HLA-A MUTATED    1  2
  HLA-A WILD-TYPE 36 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    2
  HLA-A WILD-TYPE   36   17
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             1              36
  MALE               2              17
[1] 2 2
[1] FALSE
D111V7, binary
                 cls
clus               0  1
  HLA-A MUTATED    1  0
  HLA-A WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    0
  HLA-A WILD-TYPE    6   21
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             0              21
[1] 2 2
[1] FALSE

Clustering(112) Variable = ASB16 MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2              0  1
  ASB16 MUTATED    3  1
  ASB16 WILD-TYPE 32 19
  ASB16 MUTATED ASB16 WILD-TYPE 
              4              51 
  ASB16 MUTATED ASB16 WILD-TYPE 
              1              19 
$`ASB16 MUTATED`
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5K2 TCGA-OR-A5LO 
       41.26        22.16        32.68        64.08 

$`ASB16 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR 
       41.39        40.34        46.82        22.03         4.90       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        18.15        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        73.05        53.03        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  ASB16 MUTATED ASB16 WILD-TYPE 
          22.16            4.11 
  ASB16 MUTATED ASB16 WILD-TYPE 
          64.08          153.63 
  ASB16 MUTATED ASB16 WILD-TYPE 
          36.97           36.33 
[1] "22.2 - 64.1 (37.0)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.7"
D112V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASB16 MUTATED         0        2         1        1
  ASB16 WILD-TYPE       6       19        13       11
D112V3, multiclass
           clus
vv          ASB16 MUTATED ASB16 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              19
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  ASB16 MUTATED    0  2  0  2
  ASB16 WILD-TYPE  6 23  7 13
D112V4, multiclass
    clus
vv   ASB16 MUTATED ASB16 WILD-TYPE
  T1             0               6
  T2             2              23
  T3             0               7
  T4             2              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"
D112V5, binary
                 cls
clus               0  1
  ASB16 MUTATED    4  0
  ASB16 WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB16 MUTATED      4    0
  ASB16 WILD-TYPE   43    6
   clus
vv  ASB16 MUTATED ASB16 WILD-TYPE
  0             4              43
  1             0               6
[1] 2 2
[1] FALSE
D112V6, binary
                 cls
clus               0  1
  ASB16 MUTATED    3  1
  ASB16 WILD-TYPE 34 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB16 MUTATED      3    1
  ASB16 WILD-TYPE   34   18
        clus
vv       ASB16 MUTATED ASB16 WILD-TYPE
  FEMALE             3              34
  MALE               1              18
[1] 2 2
[1] FALSE
D112V7, binary
                 cls
clus               0  1
  ASB16 MUTATED    0  0
  ASB16 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB16 MUTATED      0    0
  ASB16 WILD-TYPE    7   21

Clustering(113) Variable = GPRIN2 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2               0  1
  GPRIN2 MUTATED    4  2
  GPRIN2 WILD-TYPE 31 18
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               6               49 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               2               18 
$`GPRIN2 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5KU TCGA-OR-A5LA 
       12.00        16.04        63.25        32.68       153.63        16.01 

$`GPRIN2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
      121.25        50.66        31.23        18.15        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        46.49        87.88       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        20.65        21.21 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.58         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       64.08        52.04        21.01         6.81        12.59       106.52 
TCGA-PK-A5HB 
       42.51 

  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
           12.00             4.11 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          153.63           128.12 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
           24.36            39.35 
[1] "12.0 - 153.6 (24.4)" "4.1 - 128.1 (39.4)" 
[1] "hr=" "1"  
D113V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GPRIN2 MUTATED         0        4         2        1
  GPRIN2 WILD-TYPE       6       17        12       11
D113V3, multiclass
           clus
vv          GPRIN2 MUTATED GPRIN2 WILD-TYPE
  STAGE I                0                6
  STAGE II               4               17
  STAGE III              2               12
  STAGE IV               1               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               T1 T2 T3 T4
  GPRIN2 MUTATED    0  4  0  3
  GPRIN2 WILD-TYPE  6 21  7 12
D113V4, multiclass
    clus
vv   GPRIN2 MUTATED GPRIN2 WILD-TYPE
  T1              0                6
  T2              4               21
  T3              0                7
  T4              3               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V5, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    7  0
  GPRIN2 WILD-TYPE 40  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      7    0
  GPRIN2 WILD-TYPE   40    6
   clus
vv  GPRIN2 MUTATED GPRIN2 WILD-TYPE
  0              7               40
  1              0                6
[1] 2 2
[1] FALSE
D113V6, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    5  2
  GPRIN2 WILD-TYPE 32 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      5    2
  GPRIN2 WILD-TYPE   32   17
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  FEMALE              5               32
  MALE                2               17
[1] 2 2
[1] FALSE
D113V7, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    1  3
  GPRIN2 WILD-TYPE  6 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      1    3
  GPRIN2 WILD-TYPE    6   18
                        clus
vv                       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(114) Variable = HNRNPCL1 MUTATION ANALYSIS
D114V1, survival
                    sevent
clus2                 0  1
  HNRNPCL1 MUTATED    1  1
  HNRNPCL1 WILD-TYPE 34 19
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 2                 53 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 1                 19 
$`HNRNPCL1 MUTATED`
TCGA-OR-A5K2 TCGA-OR-A5LK 
       32.68        73.05 

$`HNRNPCL1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       18.15        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        20.65        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        36.33        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       21.01         6.81        12.59       106.52        42.51 

  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             32.68               4.11 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             73.05             153.63 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
            52.865             36.330 
[1] "32.7 - 73.0 (52.9)" "4.1 - 153.6 (36.3)"
[1] "Remove cluster labels:" "HNRNPCL1 MUTATED"      
D114V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  HNRNPCL1 MUTATED         0        1         1        1
  HNRNPCL1 WILD-TYPE       6       20        13       11
D114V3, multiclass
           clus
vv          HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 1                 20
  STAGE III                1                 13
  STAGE IV                 1                 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                 T1 T2 T3 T4
  HNRNPCL1 MUTATED    0  1  0  2
  HNRNPCL1 WILD-TYPE  6 24  7 13
D114V4, multiclass
    clus
vv   HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  T1                0                  6
  T2                1                 24
  T3                0                  7
  T4                2                 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"
D114V5, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    3  0
  HNRNPCL1 WILD-TYPE 44  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      3    0
  HNRNPCL1 WILD-TYPE   44    6
   clus
vv  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  0                3                 44
  1                0                  6
[1] 2 2
[1] FALSE
D114V6, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    2  1
  HNRNPCL1 WILD-TYPE 35 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      2    1
  HNRNPCL1 WILD-TYPE   35   18
        clus
vv       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  FEMALE                2                 35
  MALE                  1                 18
[1] 2 2
[1] FALSE
D114V7, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    0  1
  HNRNPCL1 WILD-TYPE  7 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      0    1
  HNRNPCL1 WILD-TYPE    7   20
                        clus
vv                       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                1                 20
[1] 2 2
[1] FALSE

Clustering(115) Variable = BTNL9 MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2              0  1
  BTNL9 MUTATED    2  1
  BTNL9 WILD-TYPE 33 19
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              3              52 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              1              19 
$`BTNL9 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5KU TCGA-PK-A5HB 
       30.31       153.63        42.51 

$`BTNL9 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        73.05        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  BTNL9 MUTATED BTNL9 WILD-TYPE 
          30.31            4.11 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
         153.63          128.12 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
          42.51           36.10 
[1] "30.3 - 153.6 (42.5)" "4.1 - 128.1 (36.1)" 
[1] "hr=" "1.4"
D115V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  BTNL9 MUTATED         0        1         0        1
  BTNL9 WILD-TYPE       6       20        14       11
D115V3, multiclass
[1] "Remove cluster labels:" "BTNL9 MUTATED"         
clus
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JH 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-P6-A5OG      TCGA-P6-A5OH 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
                 vv
clus              T1 T2 T3 T4
  BTNL9 MUTATED    0  1  0  1
  BTNL9 WILD-TYPE  6 24  7 14
D115V4, multiclass
[1] "Remove cluster labels:" "BTNL9 MUTATED"         
clus
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              2              51 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JH 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-P6-A5OG      TCGA-P6-A5OH 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
D115V5, binary
                 cls
clus               0  1
  BTNL9 MUTATED    2  0
  BTNL9 WILD-TYPE 45  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      2    0
  BTNL9 WILD-TYPE   45    6
   clus
vv  BTNL9 MUTATED BTNL9 WILD-TYPE
  0             2              45
  1             0               6
[1] 2 2
[1] FALSE
D115V6, binary
                 cls
clus               0  1
  BTNL9 MUTATED    2  1
  BTNL9 WILD-TYPE 35 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      2    1
  BTNL9 WILD-TYPE   35   18
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  FEMALE             2              35
  MALE               1              18
[1] 2 2
[1] FALSE
D115V7, binary
                 cls
clus               0  1
  BTNL9 MUTATED    0  1
  BTNL9 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      0    1
  BTNL9 WILD-TYPE    7   20
                        clus
vv                       BTNL9 MUTATED BTNL9 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              20
[1] 2 2
[1] FALSE

Clustering(116) Variable = KCNJ11 MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2               0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 33 18
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               51 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               2               18 
$`KCNJ11 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5LB 
       12.00        50.14        35.87        39.58 

$`KCNJ11 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      153.63       120.30         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       20.65        21.21        16.01         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
           12.00             4.11 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
           50.14           153.63 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
          37.725           36.330 
[1] "12.0 - 50.1 (37.7)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.7"
D116V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KCNJ11 MUTATED         0        0         3        1
  KCNJ11 WILD-TYPE       6       21        11       11
D116V3, multiclass
           clus
vv          KCNJ11 MUTATED KCNJ11 WILD-TYPE
  STAGE I                0                6
  STAGE II               0               21
  STAGE III              3               11
  STAGE IV               1               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               T1 T2 T3 T4
  KCNJ11 MUTATED    0  2  0  2
  KCNJ11 WILD-TYPE  6 23  7 13
D116V4, multiclass
    clus
vv   KCNJ11 MUTATED KCNJ11 WILD-TYPE
  T1              0                6
  T2              2               23
  T3              0                7
  T4              2               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"
D116V5, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 45  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      2    2
  KCNJ11 WILD-TYPE   45    4
   clus
vv  KCNJ11 MUTATED KCNJ11 WILD-TYPE
  0              2               45
  1              2                4
[1] 2 2
[1] FALSE
D116V6, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 35 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      2    2
  KCNJ11 WILD-TYPE   35   17
        clus
vv       KCNJ11 MUTATED KCNJ11 WILD-TYPE
  FEMALE              2               35
  MALE                2               17
[1] 2 2
[1] FALSE
D116V7, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    1  3
  KCNJ11 WILD-TYPE  6 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      1    3
  KCNJ11 WILD-TYPE    6   18
                        clus
vv                       KCNJ11 MUTATED KCNJ11 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               18
[1] 2 2
[1] FALSE

Clustering(117) Variable = LRRC4B MUTATION ANALYSIS
D117V1, survival
                  sevent
clus2               0  1
  LRRC4B MUTATED    3  3
  LRRC4B WILD-TYPE 32 17
  LRRC4B MUTATED LRRC4B WILD-TYPE 
               6               49 
  LRRC4B MUTATED LRRC4B WILD-TYPE 
               3               17 
$`LRRC4B MUTATED`
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5LB TCGA-P6-A5OG 
        8.32        11.31       120.30        35.87        39.58        12.59 

$`LRRC4B WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       18.15        32.68        17.36        46.49        87.88       153.63 
TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.21        16.01         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 
       53.03        64.08        52.04        21.01         6.81       106.52 
TCGA-PK-A5HB 
       42.51 

  LRRC4B MUTATED LRRC4B WILD-TYPE 
            8.32             4.11 
  LRRC4B MUTATED LRRC4B WILD-TYPE 
          120.30           153.63 
  LRRC4B MUTATED LRRC4B WILD-TYPE 
           24.23            39.35 
[1] "8.3 - 120.3 (24.2)" "4.1 - 153.6 (39.4)"
[1] "hr=" "2"  
D117V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  LRRC4B MUTATED         0        1         3        2
  LRRC4B WILD-TYPE       6       20        11       10
D117V3, multiclass
           clus
vv          LRRC4B MUTATED LRRC4B WILD-TYPE
  STAGE I                0                6
  STAGE II               1               20
  STAGE III              3               11
  STAGE IV               2               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               T1 T2 T3 T4
  LRRC4B MUTATED    0  3  1  2
  LRRC4B WILD-TYPE  6 22  6 13
D117V4, multiclass
    clus
vv   LRRC4B MUTATED LRRC4B WILD-TYPE
  T1              0                6
  T2              3               22
  T3              1                6
  T4              2               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"
D117V5, binary
                  cls
clus                0  1
  LRRC4B MUTATED    4  2
  LRRC4B WILD-TYPE 43  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC4B MUTATED      4    2
  LRRC4B WILD-TYPE   43    4
   clus
vv  LRRC4B MUTATED LRRC4B WILD-TYPE
  0              4               43
  1              2                4
[1] 2 2
[1] FALSE
D117V6, binary
                  cls
clus                0  1
  LRRC4B MUTATED    5  1
  LRRC4B WILD-TYPE 32 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC4B MUTATED      5    1
  LRRC4B WILD-TYPE   32   18
        clus
vv       LRRC4B MUTATED LRRC4B WILD-TYPE
  FEMALE              5               32
  MALE                1               18
[1] 2 2
[1] FALSE
D117V7, binary
                  cls
clus                0  1
  LRRC4B MUTATED    0  4
  LRRC4B WILD-TYPE  7 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC4B MUTATED      0    4
  LRRC4B WILD-TYPE    7   17
                        clus
vv                       LRRC4B MUTATED LRRC4B WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               17
[1] 2 2
[1] FALSE

Clustering(118) Variable = OPLAH MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2              0  1
  OPLAH MUTATED    1  2
  OPLAH WILD-TYPE 34 18
  OPLAH MUTATED OPLAH WILD-TYPE 
              3              52 
  OPLAH MUTATED OPLAH WILD-TYPE 
              2              18 
$`OPLAH MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5L3 TCGA-OR-A5LC 
       12.00       128.12         5.23 

$`OPLAH WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 
      153.63       120.30        50.14        35.87         4.11        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  OPLAH MUTATED OPLAH WILD-TYPE 
           5.23            4.11 
  OPLAH MUTATED OPLAH WILD-TYPE 
         128.12          153.63 
  OPLAH MUTATED OPLAH WILD-TYPE 
          12.00           37.84 
[1] "5.2 - 128.1 (12.0)" "4.1 - 153.6 (37.8)"
[1] "hr=" "2.7"
D118V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OPLAH MUTATED         1        0         1        1
  OPLAH WILD-TYPE       5       21        13       11
D118V3, multiclass
           clus
vv          OPLAH MUTATED OPLAH WILD-TYPE
  STAGE I               1               5
  STAGE II              0              21
  STAGE III             1              13
  STAGE IV              1              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              T1 T2 T3 T4
  OPLAH MUTATED    1  0  0  2
  OPLAH WILD-TYPE  5 25  7 13
D118V4, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  T1             1               5
  T2             0              25
  T3             0               7
  T4             2              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"
D118V5, binary
                 cls
clus               0  1
  OPLAH MUTATED    3  0
  OPLAH WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      3    0
  OPLAH WILD-TYPE   44    6
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D118V6, binary
                 cls
clus               0  1
  OPLAH MUTATED    2  1
  OPLAH WILD-TYPE 35 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      2    1
  OPLAH WILD-TYPE   35   18
        clus
vv       OPLAH MUTATED OPLAH WILD-TYPE
  FEMALE             2              35
  MALE               1              18
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus               0  1
  OPLAH MUTATED    1  2
  OPLAH WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      1    2
  OPLAH WILD-TYPE    6   19
                        clus
vv                       OPLAH MUTATED OPLAH WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(119) Variable = MADCAM1 MUTATION ANALYSIS
D119V1, survival
                   sevent
clus2                0  1
  MADCAM1 MUTATED    2  1
  MADCAM1 WILD-TYPE 33 19
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
                3                52 
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
                1                19 
$`MADCAM1 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5K4 TCGA-OR-A5L5 
       15.45        17.36        27.62 

$`MADCAM1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        41.26        22.03         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       32.68         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
            15.45              4.11 
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
            27.62            153.63 
  MADCAM1 MUTATED MADCAM1 WILD-TYPE 
           17.360            39.465 
[1] "15.4 - 27.6 (17.4)" "4.1 - 153.6 (39.5)"
[1] "hr=" "2"  
D119V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  MADCAM1 MUTATED         1        0         1        1
  MADCAM1 WILD-TYPE       5       21        13       11
D119V3, multiclass
           clus
vv          MADCAM1 MUTATED MADCAM1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                0                21
  STAGE III               1                13
  STAGE IV                1                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                T1 T2 T3 T4
  MADCAM1 MUTATED    1  0  1  1
  MADCAM1 WILD-TYPE  5 25  6 14
D119V4, multiclass
    clus
vv   MADCAM1 MUTATED MADCAM1 WILD-TYPE
  T1               1                 5
  T2               0                25
  T3               1                 6
  T4               1                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"
D119V5, binary
                   cls
clus                 0  1
  MADCAM1 MUTATED    2  1
  MADCAM1 WILD-TYPE 45  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MADCAM1 MUTATED      2    1
  MADCAM1 WILD-TYPE   45    5
   clus
vv  MADCAM1 MUTATED MADCAM1 WILD-TYPE
  0               2                45
  1               1                 5
[1] 2 2
[1] FALSE
D119V6, binary
                   cls
clus                 0  1
  MADCAM1 MUTATED    3  0
  MADCAM1 WILD-TYPE 34 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MADCAM1 MUTATED      3    0
  MADCAM1 WILD-TYPE   34   19
        clus
vv       MADCAM1 MUTATED MADCAM1 WILD-TYPE
  FEMALE               3                34
  MALE                 0                19
[1] 2 2
[1] FALSE
D119V7, binary
                   cls
clus                 0  1
  MADCAM1 MUTATED    1  1
  MADCAM1 WILD-TYPE  6 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MADCAM1 MUTATED      1    1
  MADCAM1 WILD-TYPE    6   20
                        clus
vv                       MADCAM1 MUTATED MADCAM1 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                20
[1] 2 2
[1] FALSE

Clustering(120) Variable = MSH3 MUTATION ANALYSIS
D120V1, survival
                sevent
clus2             0  1
  MSH3 MUTATED    1  2
  MSH3 WILD-TYPE 34 18
  MSH3 MUTATED MSH3 WILD-TYPE 
             3             52 
  MSH3 MUTATED MSH3 WILD-TYPE 
             2             18 
$`MSH3 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JL TCGA-OR-A5LC 
       30.31        22.03         5.23 

$`MSH3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       16.11        19.04        18.12        57.53        91.46        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  MSH3 MUTATED MSH3 WILD-TYPE 
          5.23           4.11 
  MSH3 MUTATED MSH3 WILD-TYPE 
         30.31         153.63 
  MSH3 MUTATED MSH3 WILD-TYPE 
        22.030         39.465 
[1] "5.2 - 30.3 (22.0)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "4.3"
D120V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MSH3 MUTATED         1        0         0        2
  MSH3 WILD-TYPE       5       21        14       10
D120V3, multiclass
           clus
vv          MSH3 MUTATED MSH3 WILD-TYPE
  STAGE I              1              5
  STAGE II             0             21
  STAGE III            0             14
  STAGE IV             2             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             T1 T2 T3 T4
  MSH3 MUTATED    1  0  0  2
  MSH3 WILD-TYPE  5 25  7 13
D120V4, multiclass
    clus
vv   MSH3 MUTATED MSH3 WILD-TYPE
  T1            1              5
  T2            0             25
  T3            0              7
  T4            2             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"
D120V5, binary
                cls
clus              0  1
  MSH3 MUTATED    3  0
  MSH3 WILD-TYPE 44  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      3    0
  MSH3 WILD-TYPE   44    6
   clus
vv  MSH3 MUTATED MSH3 WILD-TYPE
  0            3             44
  1            0              6
[1] 2 2
[1] FALSE
D120V6, binary
                cls
clus              0  1
  MSH3 MUTATED    3  0
  MSH3 WILD-TYPE 34 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      3    0
  MSH3 WILD-TYPE   34   19
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  FEMALE            3             34
  MALE              0             19
[1] 2 2
[1] FALSE
D120V7, binary
                cls
clus              0  1
  MSH3 MUTATED    0  1
  MSH3 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      0    1
  MSH3 WILD-TYPE    7   20
                        clus
vv                       MSH3 MUTATED MSH3 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             20
[1] 2 2
[1] FALSE

Clustering(121) Variable = UTS2R MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2              0  1
  UTS2R MUTATED    2  1
  UTS2R WILD-TYPE 33 19
  UTS2R MUTATED UTS2R WILD-TYPE 
              3              52 
  UTS2R MUTATED UTS2R WILD-TYPE 
              1              19 
$`UTS2R MUTATED`
TCGA-OR-A5JQ TCGA-OR-A5KZ TCGA-OR-A5L9 
       22.16         4.11        21.21 

$`UTS2R WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        17.36         8.32        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        50.14        35.87       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        16.01        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  UTS2R MUTATED UTS2R WILD-TYPE 
           4.11            4.90 
  UTS2R MUTATED UTS2R WILD-TYPE 
          22.16          153.63 
  UTS2R MUTATED UTS2R WILD-TYPE 
         21.210          39.465 
[1] "4.1 - 22.2 (21.2)"  "4.9 - 153.6 (39.5)"
[1] "hr=" "2.2"
D121V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  UTS2R MUTATED         0        3         0        0
  UTS2R WILD-TYPE       6       18        14       12
D121V3, multiclass
           clus
vv          UTS2R MUTATED UTS2R WILD-TYPE
  STAGE I               0               6
  STAGE II              3              18
  STAGE III             0              14
  STAGE IV              0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  UTS2R MUTATED    0  3  0  0
  UTS2R WILD-TYPE  6 22  7 15
D121V4, multiclass
    clus
vv   UTS2R MUTATED UTS2R WILD-TYPE
  T1             0               6
  T2             3              22
  T3             0               7
  T4             0              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"
D121V5, binary
                 cls
clus               0  1
  UTS2R MUTATED    3  0
  UTS2R WILD-TYPE 44  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UTS2R MUTATED      3    0
  UTS2R WILD-TYPE   44    6
   clus
vv  UTS2R MUTATED UTS2R WILD-TYPE
  0             3              44
  1             0               6
[1] 2 2
[1] FALSE
D121V6, binary
                 cls
clus               0  1
  UTS2R MUTATED    2  1
  UTS2R WILD-TYPE 35 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UTS2R MUTATED      2    1
  UTS2R WILD-TYPE   35   18
        clus
vv       UTS2R MUTATED UTS2R WILD-TYPE
  FEMALE             2              35
  MALE               1              18
[1] 2 2
[1] FALSE
D121V7, binary
                 cls
clus               0  1
  UTS2R MUTATED    0  2
  UTS2R WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UTS2R MUTATED      0    2
  UTS2R WILD-TYPE    7   19
                        clus
vv                       UTS2R MUTATED UTS2R WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              19
[1] 2 2
[1] FALSE

Clustering(122) Variable = SMG1 MUTATION ANALYSIS
D122V1, survival
                sevent
clus2             0  1
  SMG1 MUTATED    2  1
  SMG1 WILD-TYPE 33 19
  SMG1 MUTATED SMG1 WILD-TYPE 
             3             52 
  SMG1 MUTATED SMG1 WILD-TYPE 
             1             19 
$`SMG1 MUTATED`
TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5LB 
       46.49        50.14        39.58 

$`SMG1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT 
       18.15        32.68        17.36         8.32        11.31        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       120.30        35.87         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  SMG1 MUTATED SMG1 WILD-TYPE 
         39.58           4.11 
  SMG1 MUTATED SMG1 WILD-TYPE 
         50.14         153.63 
  SMG1 MUTATED SMG1 WILD-TYPE 
        46.490         34.275 
[1] "39.6 - 50.1 (46.5)" "4.1 - 153.6 (34.3)"
[1] "hr=" "1.4"
D122V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SMG1 MUTATED         0        0         1        2
  SMG1 WILD-TYPE       6       21        13       10
D122V3, multiclass
           clus
vv          SMG1 MUTATED SMG1 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             21
  STAGE III            1             13
  STAGE IV             2             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             T1 T2 T3 T4
  SMG1 MUTATED    0  1  0  2
  SMG1 WILD-TYPE  6 24  7 13
D122V4, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  T1            0              6
  T2            1             24
  T3            0              7
  T4            2             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"
D122V5, binary
                cls
clus              0  1
  SMG1 MUTATED    2  1
  SMG1 WILD-TYPE 45  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED      2    1
  SMG1 WILD-TYPE   45    5
   clus
vv  SMG1 MUTATED SMG1 WILD-TYPE
  0            2             45
  1            1              5
[1] 2 2
[1] FALSE
D122V6, binary
                cls
clus              0  1
  SMG1 MUTATED    2  1
  SMG1 WILD-TYPE 35 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED      2    1
  SMG1 WILD-TYPE   35   18
        clus
vv       SMG1 MUTATED SMG1 WILD-TYPE
  FEMALE            2             35
  MALE              1             18
[1] 2 2
[1] FALSE
D122V7, binary
                cls
clus              0  1
  SMG1 MUTATED    0  3
  SMG1 WILD-TYPE  7 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED      0    3
  SMG1 WILD-TYPE    7   18
                        clus
vv                       SMG1 MUTATED SMG1 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(123) Variable = FEZ2 MUTATION ANALYSIS
D123V1, survival
                sevent
clus2             0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 33 19
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             52 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             1             19 
$`FEZ2 MUTATED`
TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LJ 
       20.65        16.01        36.33 

$`FEZ2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC 
      128.12        23.80        27.62        21.21        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        12.59       106.52        42.51 

  FEZ2 MUTATED FEZ2 WILD-TYPE 
         16.01           4.11 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
         36.33         153.63 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
        20.650         39.465 
[1] "16.0 - 36.3 (20.6)" "4.1 - 153.6 (39.5)"
[1] "hr=" "1.4"
D123V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FEZ2 MUTATED         0        2         0        1
  FEZ2 WILD-TYPE       6       19        14       11
D123V3, multiclass
           clus
vv          FEZ2 MUTATED FEZ2 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             19
  STAGE III            0             14
  STAGE IV             1             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             T1 T2 T3 T4
  FEZ2 MUTATED    0  3  0  0
  FEZ2 WILD-TYPE  6 22  7 15
D123V4, multiclass
    clus
vv   FEZ2 MUTATED FEZ2 WILD-TYPE
  T1            0              6
  T2            3             22
  T3            0              7
  T4            0             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"
D123V5, binary
                cls
clus              0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 45  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      2    1
  FEZ2 WILD-TYPE   45    5
   clus
vv  FEZ2 MUTATED FEZ2 WILD-TYPE
  0            2             45
  1            1              5
[1] 2 2
[1] FALSE
D123V6, binary
                cls
clus              0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 35 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      2    1
  FEZ2 WILD-TYPE   35   18
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  FEMALE            2             35
  MALE              1             18
[1] 2 2
[1] FALSE
D123V7, binary
                cls
clus              0  1
  FEZ2 MUTATED    0  3
  FEZ2 WILD-TYPE  7 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      0    3
  FEZ2 WILD-TYPE    7   18
                        clus
vv                       FEZ2 MUTATED FEZ2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             18
[1] 2 2
[1] FALSE

Clustering(124) Variable = GLI3 MUTATION ANALYSIS
D124V1, survival
                sevent
clus2             0  1
  GLI3 MUTATED    2  2
  GLI3 WILD-TYPE 33 18
  GLI3 MUTATED GLI3 WILD-TYPE 
             4             51 
  GLI3 MUTATED GLI3 WILD-TYPE 
             2             18 
$`GLI3 MUTATED`
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5LC 
       41.26        22.03        32.68         5.23 

$`GLI3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       41.39        40.34        46.82         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       16.04        50.66        63.25        31.23        18.15        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ 
       20.65        21.21        16.01        39.58        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       73.05        53.03        64.08        52.04        21.01         6.81 
TCGA-P6-A5OG TCGA-PK-A5H8 TCGA-PK-A5HB 
       12.59       106.52        42.51 

  GLI3 MUTATED GLI3 WILD-TYPE 
          5.23           4.11 
  GLI3 MUTATED GLI3 WILD-TYPE 
         41.26         153.63 
  GLI3 MUTATED GLI3 WILD-TYPE 
        27.355         39.350 
[1] "5.2 - 41.3 (27.4)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "2.2"
D124V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GLI3 MUTATED         1        0         1        3
  GLI3 WILD-TYPE       5       21        13        9
D124V3, multiclass
           clus
vv          GLI3 MUTATED GLI3 WILD-TYPE
  STAGE I              1              5
  STAGE II             0             21
  STAGE III            1             13
  STAGE IV             3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  GLI3 MUTATED    1  0  0  4
  GLI3 WILD-TYPE  5 25  7 11
D124V4, multiclass
    clus
vv   GLI3 MUTATED GLI3 WILD-TYPE
  T1            1              5
  T2            0             25
  T3            0              7
  T4            4             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"
D124V5, binary
                cls
clus              0  1
  GLI3 MUTATED    5  0
  GLI3 WILD-TYPE 42  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      5    0
  GLI3 WILD-TYPE   42    6
   clus
vv  GLI3 MUTATED GLI3 WILD-TYPE
  0            5             42
  1            0              6
[1] 2 2
[1] FALSE
D124V6, binary
                cls
clus              0  1
  GLI3 MUTATED    4  1
  GLI3 WILD-TYPE 33 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      4    1
  GLI3 WILD-TYPE   33   18
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  FEMALE            4             33
  MALE              1             18
[1] 2 2
[1] FALSE
D124V7, binary
                cls
clus              0  1
  GLI3 MUTATED    0  2
  GLI3 WILD-TYPE  7 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      0    2
  GLI3 WILD-TYPE    7   19
                        clus
vv                       GLI3 MUTATED GLI3 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             19
[1] 2 2
[1] FALSE

Clustering(125) Variable = NOL9 MUTATION ANALYSIS
D125V1, survival
                sevent
clus2             0  1
  NOL9 MUTATED    2  1
  NOL9 WILD-TYPE 33 19
  NOL9 MUTATED NOL9 WILD-TYPE 
             3             52 
  NOL9 MUTATED NOL9 WILD-TYPE 
             1             19 
$`NOL9 MUTATED`
TCGA-OR-A5K9 TCGA-OR-A5LK TCGA-PK-A5HB 
       11.31        73.05        42.51 

$`NOL9 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       41.39        40.34        46.82        41.26        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       18.15        32.68        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        50.14        35.87         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        20.65        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        36.33        53.03        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OG TCGA-PK-A5H8 
       21.01         6.81        12.59       106.52 

  NOL9 MUTATED NOL9 WILD-TYPE 
         11.31           4.11 
  NOL9 MUTATED NOL9 WILD-TYPE 
         73.05         153.63 
  NOL9 MUTATED NOL9 WILD-TYPE 
         42.51          36.10 
[1] "11.3 - 73.0 (42.5)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.2"
D125V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NOL9 MUTATED         0        2         0        0
  NOL9 WILD-TYPE       6       19        14       12
D125V3, multiclass
[1] "Remove cluster labels:" "NOL9 MUTATED"          
clus
  NOL9 MUTATED NOL9 WILD-TYPE 
             2             51 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JH     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5KO 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-P6-A5OG     TCGA-P6-A5OH 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
                vv
clus             T1 T2 T3 T4
  NOL9 MUTATED    0  2  0  0
  NOL9 WILD-TYPE  6 23  7 15
D125V4, multiclass
[1] "Remove cluster labels:" "NOL9 MUTATED"          
clus
  NOL9 MUTATED NOL9 WILD-TYPE 
             2             51 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JH     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5KO 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-P6-A5OG     TCGA-P6-A5OH 
"NOL9 WILD-TYPE" "NOL9 WILD-TYPE" "NOL9 WILD-TYPE" 
D125V5, binary
                cls
clus              0  1
  NOL9 MUTATED    2  0
  NOL9 WILD-TYPE 45  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      2    0
  NOL9 WILD-TYPE   45    6
   clus
vv  NOL9 MUTATED NOL9 WILD-TYPE
  0            2             45
  1            0              6
[1] 2 2
[1] FALSE
D125V6, binary
                cls
clus              0  1
  NOL9 MUTATED    1  2
  NOL9 WILD-TYPE 36 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      1    2
  NOL9 WILD-TYPE   36   17
        clus
vv       NOL9 MUTATED NOL9 WILD-TYPE
  FEMALE            1             36
  MALE              2             17
[1] 2 2
[1] FALSE
D125V7, binary
                cls
clus              0  1
  NOL9 MUTATED    0  0
  NOL9 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      0    0
  NOL9 WILD-TYPE    7   21
