[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/11541222/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/11561887/transformed.cor.cli.txt"

nPatients in clinical file=92, in cluster file=62, common to both=62
[1] "Reduce the number of clustering variables from 123 to 119."
[1] 119  62
[1] "ZFPM1 MUTATION ANALYSIS"
[1] 3
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             24              38 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             24              38 
[1] "LACTB MUTATION ANALYSIS"
[1] 3
  LACTB MUTATED LACTB WILD-TYPE 
             19              43 
  LACTB MUTATED LACTB WILD-TYPE 
             19              43 
[1] "CCDC102A MUTATION ANALYSIS"
[1] 3
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                17                 45 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                17                 45 
[1] "ZNF517 MUTATION ANALYSIS"
[1] 3
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              13               49 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              13               49 
[1] "MAL2 MUTATION ANALYSIS"
[1] 3
  MAL2 MUTATED MAL2 WILD-TYPE 
            11             51 
  MAL2 MUTATED MAL2 WILD-TYPE 
            11             51 
[1] "CLDN23 MUTATION ANALYSIS"
[1] 3
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               52 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               52 
[1] "TOR3A MUTATION ANALYSIS"
[1] 3
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              50 
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              50 
[1] "USP42 MUTATION ANALYSIS"
[1] 3
  USP42 MUTATED USP42 WILD-TYPE 
             15              47 
  USP42 MUTATED USP42 WILD-TYPE 
             15              47 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            12             50 
  TP53 MUTATED TP53 WILD-TYPE 
            12             50 
[1] "APOE MUTATION ANALYSIS"
[1] 3
  APOE MUTATED APOE WILD-TYPE 
             7             55 
  APOE MUTATED APOE WILD-TYPE 
             7             55 
[1] "ZAR1 MUTATION ANALYSIS"
[1] 3
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             51 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             51 
[1] "ASPDH MUTATION ANALYSIS"
[1] 3
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              54 
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              54 
[1] "KCNK17 MUTATION ANALYSIS"
[1] 3
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               53 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               53 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              56 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              56 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              52 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              52 
[1] "RINL MUTATION ANALYSIS"
[1] 3
  RINL MUTATED RINL WILD-TYPE 
             8             54 
  RINL MUTATED RINL WILD-TYPE 
             8             54 
[1] "SYT8 MUTATION ANALYSIS"
[1] 3
  SYT8 MUTATED SYT8 WILD-TYPE 
             8             54 
  SYT8 MUTATED SYT8 WILD-TYPE 
             8             54 
[1] "LRIG1 MUTATION ANALYSIS"
[1] 3
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             16              46 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             16              46 
[1] "C1ORF106 MUTATION ANALYSIS"
[1] 3
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 53 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 53 
[1] "GPRIN2 MUTATION ANALYSIS"
[1] 3
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               8               54 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               8               54 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               7               55 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               7               55 
[1] "C16ORF3 MUTATION ANALYSIS"
[1] 3
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                57 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                57 
[1] "CCDC105 MUTATION ANALYSIS"
[1] 3
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                56 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                56 
[1] "RGS9BP MUTATION ANALYSIS"
[1] 3
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8               54 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8               54 
[1] "HHIPL1 MUTATION ANALYSIS"
[1] 3
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               56 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               56 
[1] "C10ORF95 MUTATION ANALYSIS"
[1] 3
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 56 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 56 
[1] "TSC22D2 MUTATION ANALYSIS"
[1] 3
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                54 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                54 
[1] "NOXA1 MUTATION ANALYSIS"
[1] 3
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              5              57 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              5              57 
[1] "THEM4 MUTATION ANALYSIS"
[1] 3
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              57 
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              57 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              52 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              52 
[1] "PLIN5 MUTATION ANALYSIS"
[1] 3
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              57 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              57 
[1] "OPRD1 MUTATION ANALYSIS"
[1] 3
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             12              50 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             12              50 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                 57 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                 57 
[1] "C19ORF10 MUTATION ANALYSIS"
[1] 3
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 55 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 55 
[1] "AATK MUTATION ANALYSIS"
[1] 3
  AATK MUTATED AATK WILD-TYPE 
             6             56 
  AATK MUTATED AATK WILD-TYPE 
             6             56 
[1] "SARM1 MUTATION ANALYSIS"
[1] 3
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              56 
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              56 
[1] "TRIOBP MUTATION ANALYSIS"
[1] 3
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               52 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               52 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              12               50 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              12               50 
[1] "WDR34 MUTATION ANALYSIS"
[1] 3
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              57 
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              57 
[1] "ZNF628 MUTATION ANALYSIS"
[1] 3
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               7               55 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               7               55 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               56 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               56 
[1] "IRX3 MUTATION ANALYSIS"
[1] 3
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             57 
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             57 
[1] "FPGS MUTATION ANALYSIS"
[1] 3
  FPGS MUTATED FPGS WILD-TYPE 
             5             57 
  FPGS MUTATED FPGS WILD-TYPE 
             5             57 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             57 
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             57 
[1] "BHLHE22 MUTATION ANALYSIS"
[1] 3
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                57 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                57 
[1] "DMKN MUTATION ANALYSIS"
[1] 3
  DMKN MUTATED DMKN WILD-TYPE 
             3             59 
  DMKN MUTATED DMKN WILD-TYPE 
             3             59 
[1] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              44 
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              44 
[1] "PANK2 MUTATION ANALYSIS"
[1] 3
  PANK2 MUTATED PANK2 WILD-TYPE 
              5              57 
  PANK2 MUTATED PANK2 WILD-TYPE 
              5              57 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              57 
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              57 
[1] "RNF149 MUTATION ANALYSIS"
[1] 3
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               58 
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               58 
[1] "GLTPD2 MUTATION ANALYSIS"
[1] 3
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               56 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               56 
[1] "SNED1 MUTATION ANALYSIS"
[1] 3
  SNED1 MUTATED SNED1 WILD-TYPE 
              5              57 
  SNED1 MUTATED SNED1 WILD-TYPE 
              5              57 
[1] "TPO MUTATION ANALYSIS"
[1] 3
  TPO MUTATED TPO WILD-TYPE 
           12            50 
  TPO MUTATED TPO WILD-TYPE 
           12            50 
[1] "PTPLA MUTATION ANALYSIS"
[1] 3
  PTPLA MUTATED PTPLA WILD-TYPE 
              4              58 
  PTPLA MUTATED PTPLA WILD-TYPE 
              4              58 
[1] "PRSS27 MUTATION ANALYSIS"
[1] 3
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               59 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               59 
[1] "CD320 MUTATION ANALYSIS"
[1] 3
  CD320 MUTATED CD320 WILD-TYPE 
              4              58 
  CD320 MUTATED CD320 WILD-TYPE 
              4              58 
[1] "SEMA5B MUTATION ANALYSIS"
[1] 3
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               54 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               54 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                58 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                58 
[1] "TAF5 MUTATION ANALYSIS"
[1] 3
  TAF5 MUTATED TAF5 WILD-TYPE 
             4             58 
  TAF5 MUTATED TAF5 WILD-TYPE 
             4             58 
[1] "GARS MUTATION ANALYSIS"
[1] 3
  GARS MUTATED GARS WILD-TYPE 
            19             43 
  GARS MUTATED GARS WILD-TYPE 
            19             43 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              40 
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              40 
[1] "KIAA1984 MUTATION ANALYSIS"
[1] 3
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 58 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 58 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             3             59 
  SRPX MUTATED SRPX WILD-TYPE 
             3             59 
[1] "TNIP2 MUTATION ANALYSIS"
[1] 3
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              57 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              57 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             8             54 
  IDUA MUTATED IDUA WILD-TYPE 
             8             54 
[1] "RNF39 MUTATION ANALYSIS"
[1] 3
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              57 
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              57 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               58 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               58 
[1] "SCRT1 MUTATION ANALYSIS"
[1] 3
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              59 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              59 
[1] "MAP1S MUTATION ANALYSIS"
[1] 3
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              57 
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              57 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            7            55 
  NF1 MUTATED NF1 WILD-TYPE 
            7            55 
[1] "AKAP2 MUTATION ANALYSIS"
[1] 3
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              58 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              58 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               57 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               57 
[1] "FANK1 MUTATION ANALYSIS"
[1] 3
  FANK1 MUTATED FANK1 WILD-TYPE 
              4              58 
  FANK1 MUTATED FANK1 WILD-TYPE 
              4              58 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6             56 
  NEFH MUTATED NEFH WILD-TYPE 
             6             56 
[1] "NPTX1 MUTATION ANALYSIS"
[1] 3
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              59 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              59 
[1] "KBTBD13 MUTATION ANALYSIS"
[1] 3
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                53 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                53 
[1] "RASIP1 MUTATION ANALYSIS"
[1] 3
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               6               56 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               6               56 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
           4           58 
  AR MUTATED AR WILD-TYPE 
           4           58 
[1] "KNDC1 MUTATION ANALYSIS"
[1] 3
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              53 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              53 
[1] "SEZ6L2 MUTATION ANALYSIS"
[1] 3
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               54 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               54 
[1] "VARS MUTATION ANALYSIS"
[1] 3
  VARS MUTATED VARS WILD-TYPE 
             6             56 
  VARS MUTATED VARS WILD-TYPE 
             6             56 
[1] "IER5 MUTATION ANALYSIS"
[1] 3
  IER5 MUTATED IER5 WILD-TYPE 
             3             59 
  IER5 MUTATED IER5 WILD-TYPE 
             3             59 
[1] "NMU MUTATION ANALYSIS"
[1] 3
  NMU MUTATED NMU WILD-TYPE 
            5            57 
  NMU MUTATED NMU WILD-TYPE 
            5            57 
[1] "TMEM189 MUTATION ANALYSIS"
[1] 3
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                59 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                59 
[1] "ADAD2 MUTATION ANALYSIS"
[1] 3
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              58 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              58 
[1] "PLEC MUTATION ANALYSIS"
[1] 3
  PLEC MUTATED PLEC WILD-TYPE 
            13             49 
  PLEC MUTATED PLEC WILD-TYPE 
            13             49 
[1] "RGMB MUTATION ANALYSIS"
[1] 3
  RGMB MUTATED RGMB WILD-TYPE 
             6             56 
  RGMB MUTATED RGMB WILD-TYPE 
             6             56 
[1] "CLIC6 MUTATION ANALYSIS"
[1] 3
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              57 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              57 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               59 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               59 
[1] "DSPP MUTATION ANALYSIS"
[1] 3
  DSPP MUTATED DSPP WILD-TYPE 
             9             53 
  DSPP MUTATED DSPP WILD-TYPE 
             9             53 
[1] "AMDHD1 MUTATION ANALYSIS"
[1] 3
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               52 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               52 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               52 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               52 
[1] "NOM1 MUTATION ANALYSIS"
[1] 3
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             56 
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             56 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             59 
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             59 
[1] "PTX4 MUTATION ANALYSIS"
[1] 3
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             59 
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             59 
[1] "LRP11 MUTATION ANALYSIS"
[1] 3
  LRP11 MUTATED LRP11 WILD-TYPE 
              6              56 
  LRP11 MUTATED LRP11 WILD-TYPE 
              6              56 
[1] "PDCD6 MUTATION ANALYSIS"
[1] 3
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              59 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              59 
[1] "SHOX2 MUTATION ANALYSIS"
[1] 3
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              3              59 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              3              59 
[1] "UQCRFS1 MUTATION ANALYSIS"
[1] 3
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                57 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                57 
[1] "CTBP2 MUTATION ANALYSIS"
[1] 3
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              3              59 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              3              59 
[1] "PRKAR1A MUTATION ANALYSIS"
[1] 3
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                56 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                56 
[1] "JMJD4 MUTATION ANALYSIS"
[1] 3
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              3              59 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              3              59 
[1] "HSD17B1 MUTATION ANALYSIS"
[1] 3
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                58 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                58 
[1] "COQ2 MUTATION ANALYSIS"
[1] 3
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             57 
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             57 
[1] "FEZ2 MUTATION ANALYSIS"
[1] 3
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             59 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             59 
[1] "DLEU7 MUTATION ANALYSIS"
[1] 3
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              3              59 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              3              59 
[1] "RNF135 MUTATION ANALYSIS"
[1] 3
  RNF135 MUTATED RNF135 WILD-TYPE 
               3               59 
  RNF135 MUTATED RNF135 WILD-TYPE 
               3               59 
[1] "SPIRE2 MUTATION ANALYSIS"
[1] 3
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               59 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               59 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 59 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 59 
[1] "SGK223 MUTATION ANALYSIS"
[1] 3
  SGK223 MUTATED SGK223 WILD-TYPE 
               3               59 
  SGK223 MUTATED SGK223 WILD-TYPE 
               3               59 
[1] "C9ORF66 MUTATION ANALYSIS"
[1] 3
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                57 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                57 
[1] "AQP7 MUTATION ANALYSIS"
[1] 3
  AQP7 MUTATED AQP7 WILD-TYPE 
             3             59 
  AQP7 MUTATED AQP7 WILD-TYPE 
             3             59 
[1] "ADAMTS7 MUTATION ANALYSIS"
[1] 3
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                58 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                58 
[1] "PCDHB13 MUTATION ANALYSIS"
[1] 3
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                57 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                57 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   59 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   59 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              59 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              59 
[1] "MTFMT MUTATION ANALYSIS"
[1] 3
  MTFMT MUTATED MTFMT WILD-TYPE 
              3              59 
  MTFMT MUTATED MTFMT WILD-TYPE 
              3              59 
[1] "NLRP5 MUTATION ANALYSIS"
[1] 3
  NLRP5 MUTATED NLRP5 WILD-TYPE 
              4              58 
  NLRP5 MUTATED NLRP5 WILD-TYPE 
              4              58 
[1] "KCNJ11 MUTATION ANALYSIS"
[1] 3
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               58 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               58 
[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 62 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         2091           NA           NA         2703 
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         2110         1424         1497          670          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
        1103         3688          907         2023         2202          950 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
          NA           NA          699          253          749           NA 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
         741         1414         2777         2549         2895         4673 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
        3878         1525         1364           NA         1781           NA 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
        4628          967         1317          861          871          719 
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-A5OH TCGA-PA-A5YG 
        2102         1857          853           NA           NA          470 
TCGA-PK-A5H8 TCGA-PK-A5HB 
        3240         1293 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=41,	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=2,	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 62 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=42, 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 32  7 14 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 32  7 14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 6 32  7 14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 32  7 14 
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   14  9
  ZFPM1 WILD-TYPE 26 12
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             23              38 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
              9              12 
$`ZFPM1 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JH 
       55.13        68.75        16.11        30.31        18.12        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY 
       49.22        22.03       121.25        29.82        66.51        18.15 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ 
       24.62        11.31        24.36       127.50        50.14         4.11 
TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LL TCGA-PK-A5HB 
       28.31        23.64         5.23        53.03        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        88.87        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        36.26        72.39 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KP 
       31.23        32.68        22.98         8.32        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 
       83.80        95.18       153.63        44.84        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LD 
      152.15        31.79        43.30        28.64        39.58        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        73.05        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       106.52 

  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
           4.11            4.90 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
         127.50          153.63 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
         29.820          43.925 
[1] "4.1 - 127.5 (29.8)" "4.9 - 153.6 (43.9)"
[1] "hr=" "1.5"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ZFPM1 MUTATED         2       10         4        7
  ZFPM1 WILD-TYPE       4       18        10        4
D1V3, multiclass
           clus
vv          ZFPM1 MUTATED ZFPM1 WILD-TYPE
  STAGE I               2               4
  STAGE II             10              18
  STAGE III             4              10
  STAGE IV              7               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 12  3  6
  ZFPM1 WILD-TYPE  4 20  4  8
D1V4, multiclass
    clus
vv   ZFPM1 MUTATED ZFPM1 WILD-TYPE
  T1             2               4
  T2            12              20
  T3             3               4
  T4             6               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   20  3
  ZFPM1 WILD-TYPE 33  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     20    3
  ZFPM1 WILD-TYPE   33    3
   clus
vv  ZFPM1 MUTATED ZFPM1 WILD-TYPE
  0            20              33
  1             3               3
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus               0  1
  ZFPM1 MUTATED   16  8
  ZFPM1 WILD-TYPE 24 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     16    8
  ZFPM1 WILD-TYPE   24   14
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  FEMALE            16              24
  MALE               8              14
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus               0  1
  ZFPM1 MUTATED    3  9
  ZFPM1 WILD-TYPE  4 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED      3    9
  ZFPM1 WILD-TYPE    4   18
                        clus
vv                       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO             9              18
[1] 2 2
[1] FALSE

Clustering(2) Variable = LACTB MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  LACTB MUTATED   12  7
  LACTB WILD-TYPE 28 14
  LACTB MUTATED LACTB WILD-TYPE 
             19              42 
  LACTB MUTATED LACTB WILD-TYPE 
              7              14 
$`LACTB MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI 
       12.00        88.87        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-A5KB 
       22.03        36.26        29.82        72.39        11.31        24.36 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 
       83.80       153.63        50.14         4.11       152.15        43.30 
TCGA-OR-A5LJ 
       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        68.75        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        69.37        49.22         4.90       121.25 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       24.62        46.49        91.30        95.18       127.50        44.84 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
       58.55        60.89        31.79        28.31        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       39.58         5.23        39.35        73.05        53.03        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       61.05        28.04         6.81        15.45       106.52        42.51 

  LACTB MUTATED LACTB WILD-TYPE 
           4.11            4.90 
  LACTB MUTATED LACTB WILD-TYPE 
         153.63          127.50 
  LACTB MUTATED LACTB WILD-TYPE 
          36.33           41.95 
[1] "4.1 - 153.6 (36.3)" "4.9 - 127.5 (42.0)"
[1] "hr=" "1.2"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LACTB MUTATED         4        9         3        2
  LACTB WILD-TYPE       2       19        11        9
D2V3, multiclass
           clus
vv          LACTB MUTATED LACTB WILD-TYPE
  STAGE I               4               2
  STAGE II              9              19
  STAGE III             3              11
  STAGE IV              2               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
  LACTB MUTATED    4 11  1  2
  LACTB WILD-TYPE  2 21  6 12
D2V4, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  T1             4               2
  T2            11              21
  T3             1               6
  T4             2              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"
D2V5, binary
                 cls
clus               0  1
  LACTB MUTATED   16  2
  LACTB WILD-TYPE 37  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     16    2
  LACTB WILD-TYPE   37    4
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0            16              37
  1             2               4
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus               0  1
  LACTB MUTATED   11  8
  LACTB WILD-TYPE 29 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     11    8
  LACTB WILD-TYPE   29   14
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  FEMALE            11              29
  MALE               8              14
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus               0  1
  LACTB MUTATED    3  8
  LACTB WILD-TYPE  4 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    8
  LACTB WILD-TYPE    4   19
                        clus
vv                       LACTB MUTATED LACTB WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO             8              19
[1] 2 2
[1] FALSE

Clustering(3) Variable = CCDC102A MUTATION ANALYSIS
D3V1, survival
                    sevent
clus2                 0  1
  CCDC102A MUTATED   14  3
  CCDC102A WILD-TYPE 26 18
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                17                 44 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                 3                 18 
$`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        36.26       121.25 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS 
       72.39        31.23        22.98        11.31        46.49        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       95.18       153.63        28.64        23.64         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        68.75        15.45        12.00        88.87        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 
       69.37        49.22        29.82        66.51        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KV TCGA-OR-A5KW 
        8.32        24.62        24.36        91.30       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       43.30        28.31        39.58        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  CCDC102A MUTATED CCDC102A WILD-TYPE 
              4.90               4.11 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
            153.63             152.15 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
             36.26              41.95 
[1] "4.9 - 153.6 (36.3)" "4.1 - 152.2 (42.0)"
[1] "hr=" "2.2"
D3V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  CCDC102A MUTATED         4        8         2        3
  CCDC102A WILD-TYPE       2       20        12        8
D3V3, multiclass
           clus
vv          CCDC102A MUTATED CCDC102A WILD-TYPE
  STAGE I                  4                  2
  STAGE II                 8                 20
  STAGE III                2                 12
  STAGE IV                 3                  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
  CCDC102A MUTATED    4  8  2  3
  CCDC102A WILD-TYPE  2 24  5 11
D3V4, multiclass
    clus
vv   CCDC102A MUTATED CCDC102A WILD-TYPE
  T1                4                  2
  T2                8                 24
  T3                2                  5
  T4                3                 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"
D3V5, binary
                    cls
clus                  0  1
  CCDC102A MUTATED   17  0
  CCDC102A WILD-TYPE 36  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     17    0
  CCDC102A WILD-TYPE   36    6
   clus
vv  CCDC102A MUTATED CCDC102A WILD-TYPE
  0               17                 36
  1                0                  6
[1] 2 2
[1] FALSE
D3V6, binary
                    cls
clus                  0  1
  CCDC102A MUTATED   11  6
  CCDC102A WILD-TYPE 29 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     11    6
  CCDC102A WILD-TYPE   29   16
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  FEMALE               11                 29
  MALE                  6                 16
[1] 2 2
[1] FALSE
D3V7, binary
                    cls
clus                  0  1
  CCDC102A MUTATED    1  7
  CCDC102A WILD-TYPE  6 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED      1    7
  CCDC102A WILD-TYPE    6   20
                        clus
vv                       CCDC102A MUTATED CCDC102A WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                7                 20
[1] 2 2
[1] FALSE

Clustering(4) Variable = ZNF517 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  ZNF517 MUTATED    9  3
  ZNF517 WILD-TYPE 31 18
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              12               49 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
               3               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        69.37        22.98         8.32        11.31 
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KV TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-PK-A5HB 
       24.36        83.80       127.50        28.31        23.64        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        68.75        15.45        12.00        88.87 
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 
       49.22        22.03         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K8 
       66.51        72.39        31.23        18.15        32.68        24.62 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        91.30        95.18       153.63        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 
      106.52 

  ZNF517 MUTATED ZNF517 WILD-TYPE 
            8.32             4.11 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
          127.50           153.63 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
          26.335           44.550 
[1] "8.3 - 127.5 (26.3)" "4.1 - 153.6 (44.5)"
[1] "hr=" "1.2"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF517 MUTATED         0        7         3        2
  ZNF517 WILD-TYPE       6       21        11        9
D4V3, multiclass
           clus
vv          ZNF517 MUTATED ZNF517 WILD-TYPE
  STAGE I                0                6
  STAGE II               7               21
  STAGE III              3               11
  STAGE IV               2                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
  ZNF517 MUTATED    0  8  1  3
  ZNF517 WILD-TYPE  6 24  6 11
D4V4, multiclass
    clus
vv   ZNF517 MUTATED ZNF517 WILD-TYPE
  T1              0                6
  T2              8               24
  T3              1                6
  T4              3               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"
D4V5, binary
                  cls
clus                0  1
  ZNF517 MUTATED   11  1
  ZNF517 WILD-TYPE 42  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED     11    1
  ZNF517 WILD-TYPE   42    5
   clus
vv  ZNF517 MUTATED ZNF517 WILD-TYPE
  0             11               42
  1              1                5
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                0  1
  ZNF517 MUTATED    9  4
  ZNF517 WILD-TYPE 31 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      9    4
  ZNF517 WILD-TYPE   31   18
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  FEMALE              9               31
  MALE                4               18
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                0  1
  ZNF517 MUTATED    0  6
  ZNF517 WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      0    6
  ZNF517 WILD-TYPE    7   21
                        clus
vv                       ZNF517 MUTATED ZNF517 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              6               21
[1] 2 2
[1] FALSE

Clustering(5) Variable = MAL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  MAL2 MUTATED    8  3
  MAL2 WILD-TYPE 32 18
  MAL2 MUTATED MAL2 WILD-TYPE 
            11             50 
  MAL2 MUTATED MAL2 WILD-TYPE 
             3             18 
$`MAL2 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JT TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP 
       41.39        29.82         8.32        11.31        24.36        91.30 
TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LJ 
       83.80        44.84        28.64        23.64        36.33 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       22.98        24.62        46.49        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       43.30        28.31        39.58         5.23        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  MAL2 MUTATED MAL2 WILD-TYPE 
          8.32           4.11 
  MAL2 MUTATED MAL2 WILD-TYPE 
         91.30         153.63 
  MAL2 MUTATED MAL2 WILD-TYPE 
        29.820         43.925 
[1] "8.3 - 91.3 (29.8)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "1.1"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAL2 MUTATED         0        8         2        1
  MAL2 WILD-TYPE       6       20        12       10
D5V3, multiclass
           clus
vv          MAL2 MUTATED MAL2 WILD-TYPE
  STAGE I              0              6
  STAGE II             8             20
  STAGE III            2             12
  STAGE IV             1             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 10  1  0
  MAL2 WILD-TYPE  6 22  6 14
D5V4, multiclass
    clus
vv   MAL2 MUTATED MAL2 WILD-TYPE
  T1            0              6
  T2           10             22
  T3            1              6
  T4            0             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"
D5V5, binary
                cls
clus              0  1
  MAL2 MUTATED    9  2
  MAL2 WILD-TYPE 44  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      9    2
  MAL2 WILD-TYPE   44    4
   clus
vv  MAL2 MUTATED MAL2 WILD-TYPE
  0            9             44
  1            2              4
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus              0  1
  MAL2 MUTATED   10  1
  MAL2 WILD-TYPE 30 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED     10    1
  MAL2 WILD-TYPE   30   21
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  FEMALE           10             30
  MALE              1             21
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus              0  1
  MAL2 MUTATED    0  7
  MAL2 WILD-TYPE  7 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      0    7
  MAL2 WILD-TYPE    7   20
                        clus
vv                       MAL2 MUTATED MAL2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            7             20
[1] 2 2
[1] FALSE

Clustering(6) Variable = CLDN23 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2               0  1
  CLDN23 MUTATED    7  3
  CLDN23 WILD-TYPE 33 18
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               51 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
               3               18 
$`CLDN23 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JY TCGA-OR-A5L4 TCGA-OR-A5L9 
       46.82        49.22        36.26        18.15        31.79        28.64 
TCGA-OR-A5LA TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LR 
       23.64        36.33        53.03        28.04 

$`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        68.75        15.45        12.00        88.87 
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        69.37        22.03         4.90       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        72.39        31.23        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB 
       58.55        60.89       152.15        43.30        28.31        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        69.11        61.05         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  CLDN23 MUTATED CLDN23 WILD-TYPE 
           18.15             4.11 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
           53.03           153.63 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
          34.025           43.300 
[1] "18.1 - 53.0 (34.0)" "4.1 - 153.6 (43.3)"
[1] "hr=" "1.1"
D6V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CLDN23 MUTATED         1        5         1        3
  CLDN23 WILD-TYPE       5       23        13        8
D6V3, multiclass
           clus
vv          CLDN23 MUTATED CLDN23 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               23
  STAGE III              1               13
  STAGE IV               3                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
  CLDN23 MUTATED    1  6  0  3
  CLDN23 WILD-TYPE  5 26  7 11
D6V4, multiclass
    clus
vv   CLDN23 MUTATED CLDN23 WILD-TYPE
  T1              1                5
  T2              6               26
  T3              0                7
  T4              3               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
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 45  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   45    4
   clus
vv  CLDN23 MUTATED CLDN23 WILD-TYPE
  0              8               45
  1              2                4
[1] 2 2
[1] FALSE
D6V6, binary
                  cls
clus                0  1
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 32 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   32   20
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  FEMALE              8               32
  MALE                2               20
[1] 2 2
[1] FALSE
D6V7, binary
                  cls
clus                0  1
  CLDN23 MUTATED    0  4
  CLDN23 WILD-TYPE  7 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      0    4
  CLDN23 WILD-TYPE    7   23
                        clus
vv                       CLDN23 MUTATED CLDN23 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(7) Variable = TOR3A MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2              0  1
  TOR3A MUTATED    9  3
  TOR3A WILD-TYPE 31 18
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              49 
  TOR3A MUTATED TOR3A WILD-TYPE 
              3              18 
$`TOR3A MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT 
       88.87        30.31        18.12        22.03       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5L6 TCGA-P6-A5OF TCGA-PK-A5HB 
       66.51        24.36        95.18        28.31         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        68.75        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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       49.22         4.90        36.26        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        22.98         8.32        24.62        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        83.80       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       73.05        53.03        69.11        61.05        28.04        15.45 
TCGA-PK-A5H8 
      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 
         30.065          43.300 
[1] "6.8 - 121.2 (30.1)" "4.1 - 153.6 (43.3)"
[1] "hr=" "1.4"
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TOR3A MUTATED         3        5         1        2
  TOR3A WILD-TYPE       3       23        13        9
D7V3, multiclass
           clus
vv          TOR3A MUTATED TOR3A WILD-TYPE
  STAGE I               3               3
  STAGE II              5              23
  STAGE III             1              13
  STAGE IV              2               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
  TOR3A MUTATED    3  5  0  3
  TOR3A WILD-TYPE  3 27  7 11
D7V4, multiclass
    clus
vv   TOR3A MUTATED TOR3A WILD-TYPE
  T1             3               3
  T2             5              27
  T3             0               7
  T4             3              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"
D7V5, binary
                 cls
clus               0  1
  TOR3A MUTATED   11  0
  TOR3A WILD-TYPE 42  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED     11    0
  TOR3A WILD-TYPE   42    6
   clus
vv  TOR3A MUTATED TOR3A WILD-TYPE
  0            11              42
  1             0               6
[1] 2 2
[1] FALSE
D7V6, binary
                 cls
clus               0  1
  TOR3A MUTATED    7  5
  TOR3A WILD-TYPE 33 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      7    5
  TOR3A WILD-TYPE   33   17
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  FEMALE             7              33
  MALE               5              17
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus               0  1
  TOR3A MUTATED    1  4
  TOR3A WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      1    4
  TOR3A WILD-TYPE    6   23
                        clus
vv                       TOR3A MUTATED TOR3A WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(8) Variable = USP42 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  USP42 MUTATED   10  4
  USP42 WILD-TYPE 30 17
  USP42 MUTATED USP42 WILD-TYPE 
             14              47 
  USP42 MUTATED USP42 WILD-TYPE 
              4              17 
$`USP42 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       68.75        19.04        41.39        69.37        49.22        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KX TCGA-OR-A5L2 
       36.26       121.25        24.36        46.49        44.84        60.89 
TCGA-OR-A5LD TCGA-OR-A5LJ 
       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        88.87        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 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS 
       22.98         8.32        24.62        11.31        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63       127.50        50.14         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.58         5.23        73.05        53.03        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       106.52        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 
         43.115          39.580 
[1] "19.0 - 121.2 (43.1)" "4.1 - 153.6 (39.6)" 
[1] "hr=" "1.4"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  USP42 MUTATED         2        5         4        4
  USP42 WILD-TYPE       4       23        10        7
D8V3, multiclass
           clus
vv          USP42 MUTATED USP42 WILD-TYPE
  STAGE I               2               4
  STAGE II              5              23
  STAGE III             4              10
  STAGE IV              4               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
  USP42 MUTATED    2  7  2  4
  USP42 WILD-TYPE  4 25  5 10
D8V4, multiclass
    clus
vv   USP42 MUTATED USP42 WILD-TYPE
  T1             2               4
  T2             7              25
  T3             2               5
  T4             4              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
  USP42 MUTATED   13  2
  USP42 WILD-TYPE 40  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED     13    2
  USP42 WILD-TYPE   40    4
   clus
vv  USP42 MUTATED USP42 WILD-TYPE
  0            13              40
  1             2               4
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus               0  1
  USP42 MUTATED   11  4
  USP42 WILD-TYPE 29 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED     11    4
  USP42 WILD-TYPE   29   18
        clus
vv       USP42 MUTATED USP42 WILD-TYPE
  FEMALE            11              29
  MALE               4              18
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus               0  1
  USP42 MUTATED    2  7
  USP42 WILD-TYPE  5 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP42 MUTATED      2    7
  USP42 WILD-TYPE    5   20
                        clus
vv                       USP42 MUTATED USP42 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             7              20
[1] 2 2
[1] FALSE

Clustering(9) Variable = TP53 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    6  6
  TP53 WILD-TYPE 34 15
  TP53 MUTATED TP53 WILD-TYPE 
            12             49 
  TP53 MUTATED TP53 WILD-TYPE 
             6             15 
$`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-A5KB TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5LJ TCGA-PK-A5HB 
       22.98        24.36        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        68.75        15.45        88.87        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        69.37        46.82        49.22 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP 
       18.15        32.68         8.32        24.62        11.31        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       28.64        23.64        39.58         5.23        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 
      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 
         23.67          44.84 
[1] "4.1 - 55.1 (23.7)"  "5.2 - 153.6 (44.8)"
[1] "hr=" "3"  
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         1        3         2        5
  TP53 WILD-TYPE       5       25        12        6
D9V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              1              5
  STAGE II             3             25
  STAGE III            2             12
  STAGE IV             5              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
  TP53 MUTATED    1  4  1  5
  TP53 WILD-TYPE  5 28  6  9
D9V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            1              5
  T2            4             28
  T3            1              6
  T4            5              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"
D9V5, binary
                cls
clus              0  1
  TP53 MUTATED   10  1
  TP53 WILD-TYPE 43  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     10    1
  TP53 WILD-TYPE   43    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           10             43
  1            1              5
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus              0  1
  TP53 MUTATED    7  5
  TP53 WILD-TYPE 33 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7    5
  TP53 WILD-TYPE   33   17
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            7             33
  MALE              5             17
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus              0  1
  TP53 MUTATED    2  4
  TP53 WILD-TYPE  5 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    4
  TP53 WILD-TYPE    5   23
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            4             23
[1] 2 2
[1] FALSE

Clustering(10) Variable = APOE MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  APOE MUTATED    5  2
  APOE WILD-TYPE 35 19
  APOE MUTATED APOE WILD-TYPE 
             7             54 
  APOE MUTATED APOE WILD-TYPE 
             2             19 
$`APOE MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KS 
       18.12        72.39        22.98        24.62        11.31        83.80 
TCGA-PK-A5HB 
       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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        29.82        66.51        31.23        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        24.36        46.49        91.30        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 

  APOE MUTATED APOE WILD-TYPE 
         11.31           4.11 
  APOE MUTATED APOE WILD-TYPE 
         83.80         153.63 
  APOE MUTATED APOE WILD-TYPE 
        24.620         42.345 
[1] "11.3 - 83.8 (24.6)" "4.1 - 153.6 (42.3)"
[1] "hr=" "1.1"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  APOE MUTATED         0        4         1        1
  APOE WILD-TYPE       6       24        13       10
D10V3, multiclass
           clus
vv          APOE MUTATED APOE WILD-TYPE
  STAGE I              0              6
  STAGE II             4             24
  STAGE III            1             13
  STAGE IV             1             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
  APOE MUTATED    0  4  0  2
  APOE WILD-TYPE  6 28  7 12
D10V4, multiclass
    clus
vv   APOE MUTATED APOE WILD-TYPE
  T1            0              6
  T2            4             28
  T3            0              7
  T4            2             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"
D10V5, binary
                cls
clus              0  1
  APOE MUTATED    6  0
  APOE WILD-TYPE 47  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      6    0
  APOE WILD-TYPE   47    6
   clus
vv  APOE MUTATED APOE WILD-TYPE
  0            6             47
  1            0              6
[1] 2 2
[1] FALSE
D10V6, binary
                cls
clus              0  1
  APOE MUTATED    2  5
  APOE WILD-TYPE 38 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      2    5
  APOE WILD-TYPE   38   17
        clus
vv       APOE MUTATED APOE WILD-TYPE
  FEMALE            2             38
  MALE              5             17
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus              0  1
  APOE MUTATED    0  2
  APOE WILD-TYPE  7 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      0    2
  APOE WILD-TYPE    7   25
                        clus
vv                       APOE MUTATED APOE WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(11) Variable = ZAR1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  ZAR1 MUTATED    6  4
  ZAR1 WILD-TYPE 34 17
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            10             51 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
             4             17 
$`ZAR1 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K9 
       30.31        69.37        36.26        18.15        32.68        11.31 
TCGA-OR-A5KW TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LK 
       50.14        28.64        23.64        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        68.75        15.45        12.00        88.87 
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        49.22        22.03         4.90       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       66.51        72.39        31.23        22.98         8.32        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      127.50        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        43.30        28.31        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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 
        31.495         43.300 
[1] "11.3 - 73.0 (31.5)" "4.1 - 153.6 (43.3)"
[1] "hr=" "1.4"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ZAR1 MUTATED         0        6         2        3
  ZAR1 WILD-TYPE       6       22        12        8
D11V3, multiclass
           clus
vv          ZAR1 MUTATED ZAR1 WILD-TYPE
  STAGE I              0              6
  STAGE II             6             22
  STAGE III            2             12
  STAGE IV             3              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
  ZAR1 MUTATED    0  7  0  4
  ZAR1 WILD-TYPE  6 25  7 10
D11V4, multiclass
    clus
vv   ZAR1 MUTATED ZAR1 WILD-TYPE
  T1            0              6
  T2            7             25
  T3            0              7
  T4            4             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"
D11V5, binary
                cls
clus              0  1
  ZAR1 MUTATED    9  2
  ZAR1 WILD-TYPE 44  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      9    2
  ZAR1 WILD-TYPE   44    4
   clus
vv  ZAR1 MUTATED ZAR1 WILD-TYPE
  0            9             44
  1            2              4
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus              0  1
  ZAR1 MUTATED   10  1
  ZAR1 WILD-TYPE 30 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED     10    1
  ZAR1 WILD-TYPE   30   21
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  FEMALE           10             30
  MALE              1             21
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus              0  1
  ZAR1 MUTATED    0  4
  ZAR1 WILD-TYPE  7 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      0    4
  ZAR1 WILD-TYPE    7   23
                        clus
vv                       ZAR1 MUTATED ZAR1 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            4             23
[1] 2 2
[1] FALSE

Clustering(12) Variable = ASPDH MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  ASPDH MUTATED    4  4
  ASPDH WILD-TYPE 36 17
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              53 
  ASPDH MUTATED ASPDH WILD-TYPE 
              4              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        22.98         8.32        50.14 
TCGA-OR-A5KX TCGA-PK-A5HB 
       44.84        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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K8 
       29.82        66.51        72.39        31.23        18.15        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      153.63       127.50         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        28.31        28.64        23.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        15.45       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 
         37.595          41.390 
[1] "8.3 - 57.5 (37.6)"  "4.1 - 153.6 (41.4)"
[1] "hr=" "1.9"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASPDH MUTATED         0        0         5        1
  ASPDH WILD-TYPE       6       28         9       10
D12V3, multiclass
           clus
vv          ASPDH MUTATED ASPDH WILD-TYPE
  STAGE I               0               6
  STAGE II              0              28
  STAGE III             5               9
  STAGE IV              1              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
  ASPDH MUTATED    0  2  1  3
  ASPDH WILD-TYPE  6 30  6 11
D12V4, multiclass
    clus
vv   ASPDH MUTATED ASPDH WILD-TYPE
  T1             0               6
  T2             2              30
  T3             1               6
  T4             3              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"
D12V5, binary
                 cls
clus               0  1
  ASPDH MUTATED    4  2
  ASPDH WILD-TYPE 49  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      4    2
  ASPDH WILD-TYPE   49    4
   clus
vv  ASPDH MUTATED ASPDH WILD-TYPE
  0             4              49
  1             2               4
[1] 2 2
[1] FALSE
D12V6, binary
                 cls
clus               0  1
  ASPDH MUTATED    6  2
  ASPDH WILD-TYPE 34 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      6    2
  ASPDH WILD-TYPE   34   20
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  FEMALE             6              34
  MALE               2              20
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus               0  1
  ASPDH MUTATED    0  2
  ASPDH WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      0    2
  ASPDH WILD-TYPE    7   25
                        clus
vv                       ASPDH MUTATED ASPDH WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(13) Variable = KCNK17 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2               0  1
  KCNK17 MUTATED    7  2
  KCNK17 WILD-TYPE 33 19
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               52 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               2               19 
$`KCNK17 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JI TCGA-OR-A5JW TCGA-OR-A5KO 
       68.75        19.04        30.31        46.82        72.39        46.49 
TCGA-OR-A5KP TCGA-OR-A5LO TCGA-PK-A5HB 
       91.30        69.11        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        88.87        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        69.37        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15        32.68        22.98         8.32        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       11.31        24.36        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       50.14        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        28.31        28.64        23.64        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        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        15.45       106.52 

  KCNK17 MUTATED KCNK17 WILD-TYPE 
           19.04             4.11 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
           91.30           153.63 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
           46.82            37.84 
[1] "19.0 - 91.3 (46.8)" "4.1 - 153.6 (37.8)"
[1] "hr=" "2.1"
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KCNK17 MUTATED         1        3         2        2
  KCNK17 WILD-TYPE       5       25        12        9
D13V3, multiclass
           clus
vv          KCNK17 MUTATED KCNK17 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              2               12
  STAGE IV               2                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
  KCNK17 MUTATED    1  3  2  2
  KCNK17 WILD-TYPE  5 29  5 12
D13V4, multiclass
    clus
vv   KCNK17 MUTATED KCNK17 WILD-TYPE
  T1              1                5
  T2              3               29
  T3              2                5
  T4              2               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"
D13V5, binary
                  cls
clus                0  1
  KCNK17 MUTATED    8  0
  KCNK17 WILD-TYPE 45  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      8    0
  KCNK17 WILD-TYPE   45    6
   clus
vv  KCNK17 MUTATED KCNK17 WILD-TYPE
  0              8               45
  1              0                6
[1] 2 2
[1] FALSE
D13V6, binary
                  cls
clus                0  1
  KCNK17 MUTATED    5  4
  KCNK17 WILD-TYPE 35 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      5    4
  KCNK17 WILD-TYPE   35   18
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  FEMALE              5               35
  MALE                4               18
[1] 2 2
[1] FALSE
D13V7, binary
                  cls
clus                0  1
  KCNK17 MUTATED    2  2
  KCNK17 WILD-TYPE  5 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      2    2
  KCNK17 WILD-TYPE    5   25
                        clus
vv                       KCNK17 MUTATED KCNK17 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(14) Variable = LZTR1 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  LZTR1 MUTATED    3  3
  LZTR1 WILD-TYPE 37 18
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              55 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              3              18 
$`LZTR1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KV TCGA-OR-A5LB 
       19.04        11.31        24.36        91.30       127.50        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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS 
       32.68        22.98         8.32        24.62        46.49        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       23.64         5.23        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  LZTR1 MUTATED LZTR1 WILD-TYPE 
          11.31            4.11 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
         127.50          153.63 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
          31.97           42.51 
[1] "11.3 - 127.5 (32.0)" "4.1 - 153.6 (42.5)" 
[1] "hr=" "1.6"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LZTR1 MUTATED         0        3         2        1
  LZTR1 WILD-TYPE       6       25        12       10
D14V3, multiclass
           clus
vv          LZTR1 MUTATED LZTR1 WILD-TYPE
  STAGE I               0               6
  STAGE II              3              25
  STAGE III             2              12
  STAGE IV              1              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
  LZTR1 MUTATED    0  4  1  1
  LZTR1 WILD-TYPE  6 28  6 13
D14V4, multiclass
    clus
vv   LZTR1 MUTATED LZTR1 WILD-TYPE
  T1             0               6
  T2             4              28
  T3             1               6
  T4             1              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"
D14V5, binary
                 cls
clus               0  1
  LZTR1 MUTATED    5  1
  LZTR1 WILD-TYPE 48  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      5    1
  LZTR1 WILD-TYPE   48    5
   clus
vv  LZTR1 MUTATED LZTR1 WILD-TYPE
  0             5              48
  1             1               5
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus               0  1
  LZTR1 MUTATED    4  2
  LZTR1 WILD-TYPE 36 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      4    2
  LZTR1 WILD-TYPE   36   20
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  FEMALE             4              36
  MALE               2              20
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus               0  1
  LZTR1 MUTATED    1  4
  LZTR1 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      1    4
  LZTR1 WILD-TYPE    6   23
                        clus
vv                       LZTR1 MUTATED LZTR1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(15) Variable = ERCC2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  ERCC2 MUTATED    6  4
  ERCC2 WILD-TYPE 34 17
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              51 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
              4              17 
$`ERCC2 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 
       68.75         4.90       121.25        72.39        32.68         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KW TCGA-OR-A5LJ TCGA-OR-A5LO 
       11.31        50.14        36.33        69.11 

$`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        88.87        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 
       69.37        46.82        49.22        22.03        36.26        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB 
       66.51        31.23        18.15        22.98        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        83.80        95.18       153.63       127.50 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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          41.390 
[1] "4.9 - 121.2 (43.2)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.2"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         1        4         4        1
  ERCC2 WILD-TYPE       5       24        10       10
D15V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               1               5
  STAGE II              4              24
  STAGE III             4              10
  STAGE IV              1              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
  ERCC2 MUTATED    1  6  2  1
  ERCC2 WILD-TYPE  5 26  5 13
D15V4, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  T1             1               5
  T2             6              26
  T3             2               5
  T4             1              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"
D15V5, binary
                 cls
clus               0  1
  ERCC2 MUTATED    8  2
  ERCC2 WILD-TYPE 45  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      8    2
  ERCC2 WILD-TYPE   45    4
   clus
vv  ERCC2 MUTATED ERCC2 WILD-TYPE
  0             8              45
  1             2               4
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus               0  1
  ERCC2 MUTATED    7  3
  ERCC2 WILD-TYPE 33 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      7    3
  ERCC2 WILD-TYPE   33   19
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  FEMALE             7              33
  MALE               3              19
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  ERCC2 MUTATED    1  2
  ERCC2 WILD-TYPE  6 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      1    2
  ERCC2 WILD-TYPE    6   25
                        clus
vv                       ERCC2 MUTATED ERCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(16) Variable = RINL MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  RINL MUTATED    4  4
  RINL WILD-TYPE 36 17
  RINL MUTATED RINL WILD-TYPE 
             8             53 
  RINL MUTATED RINL WILD-TYPE 
             4             17 
$`RINL MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5KB 
       55.13        19.04        29.82        72.39        32.68        24.36 
TCGA-OR-A5KV TCGA-OR-A5LC 
      127.50         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        68.75        15.45        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       66.51        31.23        18.15        22.98         8.32        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       50.14        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        28.31        28.64        23.64        39.58 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       106.52        42.51 

  RINL MUTATED RINL WILD-TYPE 
          5.23           4.11 
  RINL MUTATED RINL WILD-TYPE 
        127.50         153.63 
  RINL MUTATED RINL WILD-TYPE 
         31.25          42.51 
[1] "5.2 - 127.5 (31.2)" "4.1 - 153.6 (42.5)"
[1] "hr=" "1.7"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RINL MUTATED         0        3         3        2
  RINL WILD-TYPE       6       25        11        9
D16V3, multiclass
           clus
vv          RINL MUTATED RINL WILD-TYPE
  STAGE I              0              6
  STAGE II             3             25
  STAGE III            3             11
  STAGE IV             2              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
  RINL MUTATED    0  4  2  2
  RINL WILD-TYPE  6 28  5 12
D16V4, multiclass
    clus
vv   RINL MUTATED RINL WILD-TYPE
  T1            0              6
  T2            4             28
  T3            2              5
  T4            2             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"
D16V5, binary
                cls
clus              0  1
  RINL MUTATED    7  1
  RINL WILD-TYPE 46  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      7    1
  RINL WILD-TYPE   46    5
   clus
vv  RINL MUTATED RINL WILD-TYPE
  0            7             46
  1            1              5
[1] 2 2
[1] FALSE
D16V6, binary
                cls
clus              0  1
  RINL MUTATED    6  2
  RINL WILD-TYPE 34 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      6    2
  RINL WILD-TYPE   34   20
        clus
vv       RINL MUTATED RINL WILD-TYPE
  FEMALE            6             34
  MALE              2             20
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus              0  1
  RINL MUTATED    2  3
  RINL WILD-TYPE  5 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      2    3
  RINL WILD-TYPE    5   24
                        clus
vv                       RINL MUTATED RINL WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(17) Variable = SYT8 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  SYT8 MUTATED    7  1
  SYT8 WILD-TYPE 33 20
  SYT8 MUTATED SYT8 WILD-TYPE 
             8             53 
  SYT8 MUTATED SYT8 WILD-TYPE 
             1             20 
$`SYT8 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5LB TCGA-OR-A5LO 
       41.39        46.49        91.30        83.80        39.58        69.11 
TCGA-OR-A5LR TCGA-PA-A5YG 
       28.04        15.45 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LP TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       53.03        61.05         6.81       106.52        42.51 

  SYT8 MUTATED SYT8 WILD-TYPE 
         15.45           4.11 
  SYT8 MUTATED SYT8 WILD-TYPE 
         91.30         153.63 
  SYT8 MUTATED SYT8 WILD-TYPE 
         43.94          39.35 
[1] "15.4 - 91.3 (43.9)" "4.1 - 153.6 (39.4)"
[1] "hr=" "3.5"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SYT8 MUTATED         0        6         0        2
  SYT8 WILD-TYPE       6       22        14        9
D17V3, multiclass
           clus
vv          SYT8 MUTATED SYT8 WILD-TYPE
  STAGE I              0              6
  STAGE II             6             22
  STAGE III            0             14
  STAGE IV             2              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
  SYT8 MUTATED    0  6  0  2
  SYT8 WILD-TYPE  6 26  7 12
D17V4, multiclass
    clus
vv   SYT8 MUTATED SYT8 WILD-TYPE
  T1            0              6
  T2            6             26
  T3            0              7
  T4            2             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"
D17V5, binary
                cls
clus              0  1
  SYT8 MUTATED    8  0
  SYT8 WILD-TYPE 45  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      8    0
  SYT8 WILD-TYPE   45    6
   clus
vv  SYT8 MUTATED SYT8 WILD-TYPE
  0            8             45
  1            0              6
[1] 2 2
[1] FALSE
D17V6, binary
                cls
clus              0  1
  SYT8 MUTATED    5  3
  SYT8 WILD-TYPE 35 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      5    3
  SYT8 WILD-TYPE   35   19
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  FEMALE            5             35
  MALE              3             19
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus              0  1
  SYT8 MUTATED    0  5
  SYT8 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      0    5
  SYT8 WILD-TYPE    7   22
                        clus
vv                       SYT8 MUTATED SYT8 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            5             22
[1] 2 2
[1] FALSE

Clustering(18) Variable = LRIG1 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  LRIG1 MUTATED   11  4
  LRIG1 WILD-TYPE 29 17
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             15              46 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
              4              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        69.37        46.82        22.03         8.32 
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L9 
       24.36        83.80        44.84        60.89        31.79        28.64 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-PK-A5HB 
       36.33        73.05        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        68.75        12.00        88.87        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        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
        4.90        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        18.15        32.68        22.98        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA 
        4.11        58.55       152.15        43.30        28.31        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.58         5.23        39.35        53.03        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        15.45       106.52 

  LRIG1 MUTATED LRIG1 WILD-TYPE 
           8.32            4.11 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          83.80          153.63 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          41.39           41.44 
[1] "8.3 - 83.8 (41.4)"  "4.1 - 153.6 (41.4)"
[1] "hr=" "1.4"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRIG1 MUTATED         2        7         3        3
  LRIG1 WILD-TYPE       4       21        11        8
D18V3, multiclass
           clus
vv          LRIG1 MUTATED LRIG1 WILD-TYPE
  STAGE I               2               4
  STAGE II              7              21
  STAGE III             3              11
  STAGE IV              3               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  9  2  2
  LRIG1 WILD-TYPE  4 23  5 12
D18V4, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  T1             2               4
  T2             9              23
  T3             2               5
  T4             2              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"
D18V5, binary
                 cls
clus               0  1
  LRIG1 MUTATED   12  3
  LRIG1 WILD-TYPE 41  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     12    3
  LRIG1 WILD-TYPE   41    3
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0            12              41
  1             3               3
[1] 2 2
[1] FALSE
D18V6, binary
                 cls
clus               0  1
  LRIG1 MUTATED   12  4
  LRIG1 WILD-TYPE 28 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     12    4
  LRIG1 WILD-TYPE   28   18
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  FEMALE            12              28
  MALE               4              18
[1] 2 2
[1] FALSE
D18V7, binary
                 cls
clus               0  1
  LRIG1 MUTATED    1  8
  LRIG1 WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      1    8
  LRIG1 WILD-TYPE    6   19
                        clus
vv                       LRIG1 MUTATED LRIG1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             8              19
[1] 2 2
[1] FALSE

Clustering(19) Variable = C1ORF106 MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  C1ORF106 MUTATED    8  1
  C1ORF106 WILD-TYPE 32 20
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 52 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 1                 20 
$`C1ORF106 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU 
       22.03         4.90        18.15        91.30        95.18       153.63 
TCGA-OR-A5KX TCGA-OR-A5LA TCGA-OR-A5LO 
       44.84        23.64        69.11 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        72.39        31.23        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
        8.32        24.62        11.31        24.36        46.49        83.80 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      127.50        50.14         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC 
       31.79        43.30        28.31        28.64        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        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
              4.90               4.11 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
            153.63             152.15 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
            44.840             40.485 
[1] "4.9 - 153.6 (44.8)" "4.1 - 152.2 (40.5)"
[1] "hr=" "3.8"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C1ORF106 MUTATED         2        5         1        1
  C1ORF106 WILD-TYPE       4       23        13       10
D19V3, multiclass
           clus
vv          C1ORF106 MUTATED C1ORF106 WILD-TYPE
  STAGE I                  2                  4
  STAGE II                 5                 23
  STAGE III                1                 13
  STAGE IV                 1                 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
  C1ORF106 MUTATED    2  6  0  1
  C1ORF106 WILD-TYPE  4 26  7 13
D19V4, multiclass
    clus
vv   C1ORF106 MUTATED C1ORF106 WILD-TYPE
  T1                2                  4
  T2                6                 26
  T3                0                  7
  T4                1                 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"
D19V5, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    7  2
  C1ORF106 WILD-TYPE 46  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      7    2
  C1ORF106 WILD-TYPE   46    4
   clus
vv  C1ORF106 MUTATED C1ORF106 WILD-TYPE
  0                7                 46
  1                2                  4
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    8  1
  C1ORF106 WILD-TYPE 32 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      8    1
  C1ORF106 WILD-TYPE   32   21
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  FEMALE                8                 32
  MALE                  1                 21
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    0  5
  C1ORF106 WILD-TYPE  7 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      0    5
  C1ORF106 WILD-TYPE    7   22
                        clus
vv                       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                5                 22
[1] 2 2
[1] FALSE

Clustering(20) Variable = GPRIN2 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2               0  1
  GPRIN2 MUTATED    5  2
  GPRIN2 WILD-TYPE 35 19
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               7               54 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               2               19 
$`GPRIN2 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KU 
       12.00        29.82        72.39        32.68        24.62       153.63 
TCGA-OR-A5LA 
       23.64 

$`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        68.75        15.45        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
      121.25        66.51        31.23        18.15        22.98         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        91.30        83.80        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB 
      152.15        31.79        43.30        28.31        28.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       61.05        28.04         6.81        15.45       106.52        42.51 

  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
           12.00             4.11 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          153.63           152.15 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          29.820           42.905 
[1] "12.0 - 153.6 (29.8)" "4.1 - 152.2 (42.9)" 
[1] "hr=" "1.1"
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GPRIN2 MUTATED         0        5         2        1
  GPRIN2 WILD-TYPE       6       23        12       10
D20V3, multiclass
           clus
vv          GPRIN2 MUTATED GPRIN2 WILD-TYPE
  STAGE I                0                6
  STAGE II               5               23
  STAGE III              2               12
  STAGE IV               1               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
  GPRIN2 MUTATED    0  5  0  3
  GPRIN2 WILD-TYPE  6 27  7 11
D20V4, multiclass
    clus
vv   GPRIN2 MUTATED GPRIN2 WILD-TYPE
  T1              0                6
  T2              5               27
  T3              0                7
  T4              3               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"
D20V5, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    8  0
  GPRIN2 WILD-TYPE 45  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      8    0
  GPRIN2 WILD-TYPE   45    6
   clus
vv  GPRIN2 MUTATED GPRIN2 WILD-TYPE
  0              8               45
  1              0                6
[1] 2 2
[1] FALSE
D20V6, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    5  3
  GPRIN2 WILD-TYPE 35 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      5    3
  GPRIN2 WILD-TYPE   35   19
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  FEMALE              5               35
  MALE                3               19
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    1  4
  GPRIN2 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      1    4
  GPRIN2 WILD-TYPE    6   23
                        clus
vv                       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(21) Variable = CTNNB1 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED    3  4
  CTNNB1 WILD-TYPE 37 17
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               7               54 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4               17 
$`CTNNB1 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5L1 TCGA-OR-A5L3 
       18.15         8.32        11.31       153.63        58.55       152.15 
TCGA-OR-A5LJ 
       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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       32.68        22.98        24.62        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       127.50        50.14        44.84         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
       60.89        31.79        43.30        28.31        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       39.58         5.23        39.35        73.05        53.03        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       61.05        28.04         6.81        15.45       106.52        42.51 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            8.32             4.11 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          153.63           127.50 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           36.33            41.95 
[1] "8.3 - 153.6 (36.3)" "4.1 - 127.5 (42.0)"
[1] "hr=" "1.9"
D21V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CTNNB1 MUTATED         1        3         1        2
  CTNNB1 WILD-TYPE       5       25        13        9
D21V3, multiclass
           clus
vv          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              1               13
  STAGE IV               2                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
  CTNNB1 MUTATED    1  4  1  1
  CTNNB1 WILD-TYPE  5 28  6 13
D21V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              1                5
  T2              4               28
  T3              1                6
  T4              1               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"
D21V5, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    5  2
  CTNNB1 WILD-TYPE 48  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      5    2
  CTNNB1 WILD-TYPE   48    4
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0              5               48
  1              2                4
[1] 2 2
[1] FALSE
D21V6, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    7  0
  CTNNB1 WILD-TYPE 33 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      7    0
  CTNNB1 WILD-TYPE   33   22
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              7               33
  MALE                0               22
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    0  4
  CTNNB1 WILD-TYPE  7 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0    4
  CTNNB1 WILD-TYPE    7   23
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(22) Variable = C16ORF3 MUTATION ANALYSIS
D22V1, survival
                   sevent
clus2                0  1
  C16ORF3 MUTATED    4  1
  C16ORF3 WILD-TYPE 36 20
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                5                56 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
                1                20 
$`C16ORF3 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5LR 
       55.13        46.49        50.14       152.15        28.04 

$`C16ORF3 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX 
       91.30        83.80        95.18       153.63       127.50        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF TCGA-PA-A5YG 
       73.05        53.03        69.11        61.05         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
            28.04              4.11 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
           152.15            153.63 
  C16ORF3 MUTATED C16ORF3 WILD-TYPE 
           50.140            39.465 
[1] "28.0 - 152.2 (50.1)" "4.1 - 153.6 (39.5)" 
[1] "hr=" "2.1"
D22V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C16ORF3 MUTATED         1        1         1        2
  C16ORF3 WILD-TYPE       5       27        13        9
D22V3, multiclass
           clus
vv          C16ORF3 MUTATED C16ORF3 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                27
  STAGE III               1                13
  STAGE IV                2                 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
  C16ORF3 MUTATED    1  2  1  1
  C16ORF3 WILD-TYPE  5 30  6 13
D22V4, multiclass
    clus
vv   C16ORF3 MUTATED C16ORF3 WILD-TYPE
  T1               1                 5
  T2               2                30
  T3               1                 6
  T4               1                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"
D22V5, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    4  1
  C16ORF3 WILD-TYPE 49  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      4    1
  C16ORF3 WILD-TYPE   49    5
   clus
vv  C16ORF3 MUTATED C16ORF3 WILD-TYPE
  0               4                49
  1               1                 5
[1] 2 2
[1] FALSE
D22V6, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    5  0
  C16ORF3 WILD-TYPE 35 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      5    0
  C16ORF3 WILD-TYPE   35   22
        clus
vv       C16ORF3 MUTATED C16ORF3 WILD-TYPE
  FEMALE               5                35
  MALE                 0                22
[1] 2 2
[1] FALSE
D22V7, binary
                   cls
clus                 0  1
  C16ORF3 MUTATED    1  3
  C16ORF3 WILD-TYPE  6 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF3 MUTATED      1    3
  C16ORF3 WILD-TYPE    6   24
                        clus
vv                       C16ORF3 MUTATED C16ORF3 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(23) Variable = CCDC105 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                0  1
  CCDC105 MUTATED    3  3
  CCDC105 WILD-TYPE 37 18
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                55 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                3                18 
$`CCDC105 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5L5 TCGA-OR-A5LJ TCGA-OR-A5LL 
       68.75        22.03        11.31        43.30        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        88.87        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 
       69.37        46.82        49.22         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98         8.32        24.62        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       28.64        23.64        39.58         5.23        39.35        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  CCDC105 MUTATED CCDC105 WILD-TYPE 
            11.31              4.11 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
            68.75            153.63 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
           39.815            41.390 
[1] "11.3 - 68.8 (39.8)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.7"
D23V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC105 MUTATED         2        2         1        1
  CCDC105 WILD-TYPE       4       26        13       10
D23V3, multiclass
           clus
vv          CCDC105 MUTATED CCDC105 WILD-TYPE
  STAGE I                 2                 4
  STAGE II                2                26
  STAGE III               1                13
  STAGE IV                1                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
  CCDC105 MUTATED    2  3  1  0
  CCDC105 WILD-TYPE  4 29  6 14
D23V4, multiclass
    clus
vv   CCDC105 MUTATED CCDC105 WILD-TYPE
  T1               2                 4
  T2               3                29
  T3               1                 6
  T4               0                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"
D23V5, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    5  1
  CCDC105 WILD-TYPE 48  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      5    1
  CCDC105 WILD-TYPE   48    5
   clus
vv  CCDC105 MUTATED CCDC105 WILD-TYPE
  0               5                48
  1               1                 5
[1] 2 2
[1] FALSE
D23V6, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    6  0
  CCDC105 WILD-TYPE 34 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      6    0
  CCDC105 WILD-TYPE   34   22
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  FEMALE               6                34
  MALE                 0                22
[1] 2 2
[1] FALSE
D23V7, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    1  2
  CCDC105 WILD-TYPE  6 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      1    2
  CCDC105 WILD-TYPE    6   25
                        clus
vv                       CCDC105 MUTATED CCDC105 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(24) Variable = RGS9BP MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2               0  1
  RGS9BP MUTATED    5  3
  RGS9BP WILD-TYPE 35 18
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8               53 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               3               18 
$`RGS9BP MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JR TCGA-OR-A5JX TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       15.45       121.25        31.23         8.32        24.62        11.31 
TCGA-OR-A5LA TCGA-PK-A5HB 
       23.64        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        68.75        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        72.39        18.15        32.68        22.98 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB 
      152.15        31.79        43.30        28.31        28.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        15.45       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 
           24.13            44.55 
[1] "8.3 - 121.2 (24.1)" "4.1 - 153.6 (44.5)"
[1] "hr=" "1.8"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RGS9BP MUTATED         1        3         2        1
  RGS9BP WILD-TYPE       5       25        12       10
D24V3, multiclass
           clus
vv          RGS9BP MUTATED RGS9BP WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              2               12
  STAGE IV               1               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
  RGS9BP MUTATED    1  3  3  0
  RGS9BP WILD-TYPE  5 29  4 14
D24V4, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  T1              1                5
  T2              3               29
  T3              3                4
  T4              0               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
  RGS9BP MUTATED    6  1
  RGS9BP WILD-TYPE 47  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      6    1
  RGS9BP WILD-TYPE   47    5
   clus
vv  RGS9BP MUTATED RGS9BP WILD-TYPE
  0              6               47
  1              1                5
[1] 2 2
[1] FALSE
D24V6, binary
                  cls
clus                0  1
  RGS9BP MUTATED    4  4
  RGS9BP WILD-TYPE 36 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      4    4
  RGS9BP WILD-TYPE   36   18
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  FEMALE              4               36
  MALE                4               18
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                0  1
  RGS9BP MUTATED    1  2
  RGS9BP WILD-TYPE  6 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      1    2
  RGS9BP WILD-TYPE    6   25
                        clus
vv                       RGS9BP MUTATED RGS9BP WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(25) Variable = HHIPL1 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2               0  1
  HHIPL1 MUTATED    4  2
  HHIPL1 WILD-TYPE 36 19
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               55 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               2               19 
$`HHIPL1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KZ 
       19.04        49.22        22.03        24.36       127.50         4.11 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
        8.32        24.62        11.31        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 
       95.18       153.63        50.14        44.84        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
            4.11             4.90 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          127.50           153.63 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          23.195           42.510 
[1] "4.1 - 127.5 (23.2)" "4.9 - 153.6 (42.5)"
[1] "hr=" "1.3"
D25V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HHIPL1 MUTATED         1        2         2        1
  HHIPL1 WILD-TYPE       5       26        12       10
D25V3, multiclass
           clus
vv          HHIPL1 MUTATED HHIPL1 WILD-TYPE
  STAGE I                1                5
  STAGE II               2               26
  STAGE III              2               12
  STAGE IV               1               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  3  1  1
  HHIPL1 WILD-TYPE  5 29  6 13
D25V4, multiclass
    clus
vv   HHIPL1 MUTATED HHIPL1 WILD-TYPE
  T1              1                5
  T2              3               29
  T3              1                6
  T4              1               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"
D25V5, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    5  1
  HHIPL1 WILD-TYPE 48  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      5    1
  HHIPL1 WILD-TYPE   48    5
   clus
vv  HHIPL1 MUTATED HHIPL1 WILD-TYPE
  0              5               48
  1              1                5
[1] 2 2
[1] FALSE
D25V6, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    3  3
  HHIPL1 WILD-TYPE 37 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      3    3
  HHIPL1 WILD-TYPE   37   19
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  FEMALE              3               37
  MALE                3               19
[1] 2 2
[1] FALSE
D25V7, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    1  3
  HHIPL1 WILD-TYPE  6 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      1    3
  HHIPL1 WILD-TYPE    6   24
                        clus
vv                       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               24
[1] 2 2
[1] FALSE

Clustering(26) Variable = C10ORF95 MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  C10ORF95 MUTATED    4  2
  C10ORF95 WILD-TYPE 36 19
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 55 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 2                 19 
$`C10ORF95 MUTATED`
TCGA-OR-A5JQ TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5LB TCGA-OR-A5LO TCGA-PK-A5H8 
       36.26        11.31        24.36        39.58        69.11       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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP 
       32.68        22.98         8.32        24.62        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.31        28.64        23.64         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       73.05        53.03        61.05        28.04         6.81        15.45 
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 
             37.92              42.51 
[1] "11.3 - 106.5 (37.9)" "4.1 - 153.6 (42.5)" 
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C10ORF95 MUTATED         0        4         0        1
  C10ORF95 WILD-TYPE       6       24        14       10
D26V3, multiclass
           clus
vv          C10ORF95 MUTATED C10ORF95 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 4                 24
  STAGE III                0                 14
  STAGE IV                 1                 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  4  0  1
  C10ORF95 WILD-TYPE  6 28  7 13
D26V4, multiclass
    clus
vv   C10ORF95 MUTATED C10ORF95 WILD-TYPE
  T1                0                  6
  T2                4                 28
  T3                0                  7
  T4                1                 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"
D26V5, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    5  0
  C10ORF95 WILD-TYPE 48  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      5    0
  C10ORF95 WILD-TYPE   48    6
   clus
vv  C10ORF95 MUTATED C10ORF95 WILD-TYPE
  0                5                 48
  1                0                  6
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    4  2
  C10ORF95 WILD-TYPE 36 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      4    2
  C10ORF95 WILD-TYPE   36   20
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  FEMALE                4                 36
  MALE                  2                 20
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    0  3
  C10ORF95 WILD-TYPE  7 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      0    3
  C10ORF95 WILD-TYPE    7   24
                        clus
vv                       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                 24
[1] 2 2
[1] FALSE

Clustering(27) Variable = TSC22D2 MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                0  1
  TSC22D2 MUTATED    3  4
  TSC22D2 WILD-TYPE 37 17
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                7                54 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                4                17 
$`TSC22D2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JQ TCGA-OR-A5K2 TCGA-OR-A5LC TCGA-OR-A5LP 
       19.04        30.31        36.26        32.68         5.23        61.05 
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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22        22.03         4.90       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        72.39        31.23        18.15        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64        39.58        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       53.03        69.11        28.04         6.81        15.45       106.52 

  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
             5.23              4.11 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
            61.05            153.63 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
           32.680            43.925 
[1] "5.2 - 61.0 (32.7)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "2.4"
D27V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TSC22D2 MUTATED         0        2         2        3
  TSC22D2 WILD-TYPE       6       26        12        8
D27V3, multiclass
           clus
vv          TSC22D2 MUTATED TSC22D2 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                26
  STAGE III               2                12
  STAGE IV                3                 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
  TSC22D2 MUTATED    0  2  1  4
  TSC22D2 WILD-TYPE  6 30  6 10
D27V4, multiclass
    clus
vv   TSC22D2 MUTATED TSC22D2 WILD-TYPE
  T1               0                 6
  T2               2                30
  T3               1                 6
  T4               4                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"
D27V5, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    7  0
  TSC22D2 WILD-TYPE 46  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      7    0
  TSC22D2 WILD-TYPE   46    6
   clus
vv  TSC22D2 MUTATED TSC22D2 WILD-TYPE
  0               7                46
  1               0                 6
[1] 2 2
[1] FALSE
D27V6, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    6  2
  TSC22D2 WILD-TYPE 34 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      6    2
  TSC22D2 WILD-TYPE   34   20
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  FEMALE               6                34
  MALE                 2                20
[1] 2 2
[1] FALSE
D27V7, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    1  2
  TSC22D2 WILD-TYPE  6 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      1    2
  TSC22D2 WILD-TYPE    6   25
                        clus
vv                       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(28) Variable = NOXA1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2              0  1
  NOXA1 MUTATED    3  1
  NOXA1 WILD-TYPE 37 20
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              4              57 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              1              20 
$`NOXA1 MUTATED`
TCGA-OR-A5K2 TCGA-OR-A5KB TCGA-OR-A5KX TCGA-OR-A5LO 
       32.68        24.36        44.84        69.11 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        22.98         8.32        24.62        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  NOXA1 MUTATED NOXA1 WILD-TYPE 
          24.36            4.11 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          69.11          153.63 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          38.76           41.39 
[1] "24.4 - 69.1 (38.8)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.5"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NOXA1 MUTATED         0        2         2        1
  NOXA1 WILD-TYPE       6       26        12       10
D28V3, multiclass
           clus
vv          NOXA1 MUTATED NOXA1 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             2              12
  STAGE IV              1              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
  NOXA1 MUTATED    0  3  0  2
  NOXA1 WILD-TYPE  6 29  7 12
D28V4, multiclass
    clus
vv   NOXA1 MUTATED NOXA1 WILD-TYPE
  T1             0               6
  T2             3              29
  T3             0               7
  T4             2              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"
D28V5, binary
                 cls
clus               0  1
  NOXA1 MUTATED    4  1
  NOXA1 WILD-TYPE 49  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      4    1
  NOXA1 WILD-TYPE   49    5
   clus
vv  NOXA1 MUTATED NOXA1 WILD-TYPE
  0             4              49
  1             1               5
[1] 2 2
[1] FALSE
D28V6, binary
                 cls
clus               0  1
  NOXA1 MUTATED    5  0
  NOXA1 WILD-TYPE 35 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      5    0
  NOXA1 WILD-TYPE   35   22
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  FEMALE             5              35
  MALE               0              22
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus               0  1
  NOXA1 MUTATED    0  3
  NOXA1 WILD-TYPE  7 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      0    3
  NOXA1 WILD-TYPE    7   24
                        clus
vv                       NOXA1 MUTATED NOXA1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              24
[1] 2 2
[1] FALSE

Clustering(29) Variable = THEM4 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  THEM4 MUTATED    3  2
  THEM4 WILD-TYPE 37 19
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              56 
  THEM4 MUTATED THEM4 WILD-TYPE 
              2              19 
$`THEM4 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5LJ TCGA-PK-A5HB 
       22.03        11.31        24.36        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP 
       32.68        22.98         8.32        24.62        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       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 
         24.360          43.925 
[1] "11.3 - 42.5 (24.4)" "4.1 - 153.6 (43.9)"
[1] "hr=" "1.9"
D29V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  THEM4 MUTATED         1        2         0        1
  THEM4 WILD-TYPE       5       26        14       10
D29V3, multiclass
           clus
vv          THEM4 MUTATED THEM4 WILD-TYPE
  STAGE I               1               5
  STAGE II              2              26
  STAGE III             0              14
  STAGE IV              1              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
  THEM4 MUTATED    1  3  0  0
  THEM4 WILD-TYPE  5 29  7 14
D29V4, multiclass
    clus
vv   THEM4 MUTATED THEM4 WILD-TYPE
  T1             1               5
  T2             3              29
  T3             0               7
  T4             0              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"
D29V5, binary
                 cls
clus               0  1
  THEM4 MUTATED    3  1
  THEM4 WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      3    1
  THEM4 WILD-TYPE   50    5
   clus
vv  THEM4 MUTATED THEM4 WILD-TYPE
  0             3              50
  1             1               5
[1] 2 2
[1] FALSE
D29V6, binary
                 cls
clus               0  1
  THEM4 MUTATED    4  1
  THEM4 WILD-TYPE 36 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      4    1
  THEM4 WILD-TYPE   36   21
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  FEMALE             4              36
  MALE               1              21
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus               0  1
  THEM4 MUTATED    0  2
  THEM4 WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      0    2
  THEM4 WILD-TYPE    7   25
                        clus
vv                       THEM4 MUTATED THEM4 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(30) Variable = ATXN1 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  ATXN1 MUTATED    7  3
  ATXN1 WILD-TYPE 33 18
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              51 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              3              18 
$`ATXN1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.00        41.39        24.36        46.49       152.15        31.79 
TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        36.33        69.11        61.05 

$`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        68.75        15.45        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS 
       22.98         8.32        24.62        11.31        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
       58.55        60.89        43.30        28.31        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF 
       39.58        39.35        73.05        53.03        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  ATXN1 MUTATED ATXN1 WILD-TYPE 
           5.23            4.11 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         152.15          153.63 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
          38.86           42.51 
[1] "5.2 - 152.2 (38.9)" "4.1 - 153.6 (42.5)"
[1] "hr=" "1.1"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ATXN1 MUTATED         1        4         2        3
  ATXN1 WILD-TYPE       5       24        12        8
D30V3, multiclass
           clus
vv          ATXN1 MUTATED ATXN1 WILD-TYPE
  STAGE I               1               5
  STAGE II              4              24
  STAGE III             2              12
  STAGE IV              3               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
  ATXN1 MUTATED    1  5  0  4
  ATXN1 WILD-TYPE  5 27  7 10
D30V4, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  T1             1               5
  T2             5              27
  T3             0               7
  T4             4              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"
D30V5, binary
                 cls
clus               0  1
  ATXN1 MUTATED    9  1
  ATXN1 WILD-TYPE 44  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      9    1
  ATXN1 WILD-TYPE   44    5
   clus
vv  ATXN1 MUTATED ATXN1 WILD-TYPE
  0             9              44
  1             1               5
[1] 2 2
[1] FALSE
D30V6, binary
                 cls
clus               0  1
  ATXN1 MUTATED    9  1
  ATXN1 WILD-TYPE 31 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      9    1
  ATXN1 WILD-TYPE   31   21
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  FEMALE             9              31
  MALE               1              21
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus               0  1
  ATXN1 MUTATED    1  6
  ATXN1 WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      1    6
  ATXN1 WILD-TYPE    6   21
                        clus
vv                       ATXN1 MUTATED ATXN1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             6              21
[1] 2 2
[1] FALSE

Clustering(31) Variable = PLIN5 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2              0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 36 20
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              56 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              1              20 
$`PLIN5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JF TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5L9 
       68.75        41.39        72.39        18.15        28.64 

$`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        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       29.82        66.51        31.23        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  PLIN5 MUTATED PLIN5 WILD-TYPE 
          18.15            4.11 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
          72.39          153.63 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
         41.390          41.045 
[1] "18.1 - 72.4 (41.4)" "4.1 - 153.6 (41.0)"
[1] "hr=" "2"  
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PLIN5 MUTATED         0        3         1        1
  PLIN5 WILD-TYPE       6       25        13       10
D31V3, multiclass
           clus
vv          PLIN5 MUTATED PLIN5 WILD-TYPE
  STAGE I               0               6
  STAGE II              3              25
  STAGE III             1              13
  STAGE IV              1              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
  PLIN5 MUTATED    0  3  1  1
  PLIN5 WILD-TYPE  6 29  6 13
D31V4, multiclass
    clus
vv   PLIN5 MUTATED PLIN5 WILD-TYPE
  T1             0               6
  T2             3              29
  T3             1               6
  T4             1              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"
D31V5, binary
                 cls
clus               0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 49  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      4    1
  PLIN5 WILD-TYPE   49    5
   clus
vv  PLIN5 MUTATED PLIN5 WILD-TYPE
  0             4              49
  1             1               5
[1] 2 2
[1] FALSE
D31V6, binary
                 cls
clus               0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 36 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      4    1
  PLIN5 WILD-TYPE   36   21
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  FEMALE             4              36
  MALE               1              21
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus               0  1
  PLIN5 MUTATED    1  1
  PLIN5 WILD-TYPE  6 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      1    1
  PLIN5 WILD-TYPE    6   26
                        clus
vv                       PLIN5 MUTATED PLIN5 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(32) Variable = OPRD1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  OPRD1 MUTATED    8  3
  OPRD1 WILD-TYPE 32 18
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             11              50 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
              3              18 
$`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-A5K8 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5LP TCGA-OR-A5LR 
       24.62       153.63       127.50        61.05        28.04 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       49.22        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       31.23        18.15        22.98         8.32        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        91.30        83.80        95.18        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-P6-A5OF TCGA-PA-A5YG 
       36.33        73.05        53.03        69.11         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  OPRD1 MUTATED OPRD1 WILD-TYPE 
           4.90            4.11 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         153.63          152.15 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         30.310          43.925 
[1] "4.9 - 153.6 (30.3)" "4.1 - 152.2 (43.9)"
[1] "hr=" "1.2"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OPRD1 MUTATED         1        6         3        2
  OPRD1 WILD-TYPE       5       22        11        9
D32V3, multiclass
           clus
vv          OPRD1 MUTATED OPRD1 WILD-TYPE
  STAGE I               1               5
  STAGE II              6              22
  STAGE III             3              11
  STAGE IV              2               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
  OPRD1 MUTATED    1  7  1  3
  OPRD1 WILD-TYPE  5 25  6 11
D32V4, multiclass
    clus
vv   OPRD1 MUTATED OPRD1 WILD-TYPE
  T1             1               5
  T2             7              25
  T3             1               6
  T4             3              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"
D32V5, binary
                 cls
clus               0  1
  OPRD1 MUTATED   11  1
  OPRD1 WILD-TYPE 42  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED     11    1
  OPRD1 WILD-TYPE   42    5
   clus
vv  OPRD1 MUTATED OPRD1 WILD-TYPE
  0            11              42
  1             1               5
[1] 2 2
[1] FALSE
D32V6, binary
                 cls
clus               0  1
  OPRD1 MUTATED    9  3
  OPRD1 WILD-TYPE 31 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      9    3
  OPRD1 WILD-TYPE   31   19
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  FEMALE             9              31
  MALE               3              19
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus               0  1
  OPRD1 MUTATED    1  4
  OPRD1 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      1    4
  OPRD1 WILD-TYPE    6   23
                        clus
vv                       OPRD1 MUTATED OPRD1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(33) Variable = KRTAP4-5 MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  KRTAP4-5 MUTATED    5  0
  KRTAP4-5 WILD-TYPE 35 21
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                 56 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 0                 21 
$`KRTAP4-5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L9 
       68.75         4.90        58.55       152.15        28.64 

$`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        88.87        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 
       69.37        46.82        49.22        22.03        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       44.84         4.11        60.89        31.79        43.30        28.31 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
              4.90               4.11 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
            152.15             153.63 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
            58.550             40.485 
[1] "4.9 - 152.2 (58.5)" "4.1 - 153.6 (40.5)"
[1] "hr="     "7.7e+07"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP4-5 MUTATED         1        3         1        0
  KRTAP4-5 WILD-TYPE       5       25        13       11
D33V3, multiclass
           clus
vv          KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  STAGE I                  1                  5
  STAGE II                 3                 25
  STAGE III                1                 13
  STAGE IV                 0                 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
  KRTAP4-5 MUTATED    1  3  1  0
  KRTAP4-5 WILD-TYPE  5 29  6 14
D33V4, multiclass
    clus
vv   KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  T1                1                  5
  T2                3                 29
  T3                1                  6
  T4                0                 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"
D33V5, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    5  0
  KRTAP4-5 WILD-TYPE 48  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      5    0
  KRTAP4-5 WILD-TYPE   48    6
   clus
vv  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  0                5                 48
  1                0                  6
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    4  1
  KRTAP4-5 WILD-TYPE 36 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      4    1
  KRTAP4-5 WILD-TYPE   36   21
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  FEMALE                4                 36
  MALE                  1                 21
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    1  3
  KRTAP4-5 WILD-TYPE  6 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      1    3
  KRTAP4-5 WILD-TYPE    6   24
                        clus
vv                       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                3                 24
[1] 2 2
[1] FALSE

Clustering(34) Variable = C19ORF10 MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  C19ORF10 MUTATED    4  3
  C19ORF10 WILD-TYPE 36 18
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 54 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 3                 18 
$`C19ORF10 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JW TCGA-OR-A5K5 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5L2 
       68.75        72.39         8.32       153.63       127.50        60.89 
TCGA-P6-A5OF 
        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        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        29.82        66.51        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80        95.18        50.14        44.84         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       69.11        61.05        28.04        15.45       106.52        42.51 

  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
              6.81               4.11 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
            153.63             152.15 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
            68.750             39.465 
[1] "6.8 - 153.6 (68.8)" "4.1 - 152.2 (39.5)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C19ORF10 MUTATED         0        3         4        0
  C19ORF10 WILD-TYPE       6       25        10       11
D34V3, multiclass
           clus
vv          C19ORF10 MUTATED C19ORF10 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 3                 25
  STAGE III                4                 10
  STAGE IV                 0                 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
  C19ORF10 MUTATED    0  4  2  1
  C19ORF10 WILD-TYPE  6 28  5 13
D34V4, multiclass
    clus
vv   C19ORF10 MUTATED C19ORF10 WILD-TYPE
  T1                0                  6
  T2                4                 28
  T3                2                  5
  T4                1                 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"
D34V5, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    6  1
  C19ORF10 WILD-TYPE 47  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      6    1
  C19ORF10 WILD-TYPE   47    5
   clus
vv  C19ORF10 MUTATED C19ORF10 WILD-TYPE
  0                6                 47
  1                1                  5
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    6  1
  C19ORF10 WILD-TYPE 34 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      6    1
  C19ORF10 WILD-TYPE   34   21
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  FEMALE                6                 34
  MALE                  1                 21
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    1  4
  C19ORF10 WILD-TYPE  6 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      1    4
  C19ORF10 WILD-TYPE    6   23
                        clus
vv                       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                4                 23
[1] 2 2
[1] FALSE

Clustering(35) Variable = AATK MUTATION ANALYSIS
D35V1, survival
                sevent
clus2             0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 35 20
  AATK MUTATED AATK WILD-TYPE 
             6             55 
  AATK MUTATED AATK WILD-TYPE 
             1             20 
$`AATK MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JH TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5LR 
       12.00        69.37       153.63        50.14        58.55        28.04 

$`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        68.75        15.45        88.87        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        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ 
       91.30        83.80        95.18       127.50        44.84         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       53.03        69.11        61.05         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  AATK MUTATED AATK WILD-TYPE 
         12.00           4.11 
  AATK MUTATED AATK WILD-TYPE 
        153.63         152.15 
  AATK MUTATED AATK WILD-TYPE 
        54.345         39.580 
[1] "12.0 - 153.6 (54.3)" "4.1 - 152.2 (39.6)" 
[1] "hr=" "2.6"
D35V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  AATK MUTATED         0        4         2        0
  AATK WILD-TYPE       6       24        12       11
D35V3, multiclass
           clus
vv          AATK MUTATED AATK WILD-TYPE
  STAGE I              0              6
  STAGE II             4             24
  STAGE III            2             12
  STAGE IV             0             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
  AATK MUTATED    0  5  0  1
  AATK WILD-TYPE  6 27  7 13
D35V4, multiclass
    clus
vv   AATK MUTATED AATK WILD-TYPE
  T1            0              6
  T2            5             27
  T3            0              7
  T4            1             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"
D35V5, binary
                cls
clus              0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 48  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      5    1
  AATK WILD-TYPE   48    5
   clus
vv  AATK MUTATED AATK WILD-TYPE
  0            5             48
  1            1              5
[1] 2 2
[1] FALSE
D35V6, binary
                cls
clus              0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 35 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      5    1
  AATK WILD-TYPE   35   21
        clus
vv       AATK MUTATED AATK WILD-TYPE
  FEMALE            5             35
  MALE              1             21
[1] 2 2
[1] FALSE
D35V7, binary
                cls
clus              0  1
  AATK MUTATED    1  3
  AATK WILD-TYPE  6 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    3
  AATK WILD-TYPE    6   24
                        clus
vv                       AATK MUTATED AATK WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(36) Variable = SARM1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2              0  1
  SARM1 MUTATED    2  4
  SARM1 WILD-TYPE 38 17
  SARM1 MUTATED SARM1 WILD-TYPE 
              6              55 
  SARM1 MUTATED SARM1 WILD-TYPE 
              4              17 
$`SARM1 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JW TCGA-OR-A5KB 
       55.13        19.04        30.31        57.53        72.39        24.36 

$`SARM1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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        69.37        46.82        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15        32.68        22.98         8.32        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  SARM1 MUTATED SARM1 WILD-TYPE 
          19.04            4.11 
  SARM1 MUTATED SARM1 WILD-TYPE 
          72.39          153.63 
  SARM1 MUTATED SARM1 WILD-TYPE 
          42.72           41.39 
[1] "19.0 - 72.4 (42.7)" "4.1 - 153.6 (41.4)"
[1] "hr=" "2"  
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SARM1 MUTATED         0        2         1        2
  SARM1 WILD-TYPE       6       26        13        9
D36V3, multiclass
           clus
vv          SARM1 MUTATED SARM1 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              2               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  2  2  1
  SARM1 WILD-TYPE  6 30  5 13
D36V4, multiclass
    clus
vv   SARM1 MUTATED SARM1 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             2               5
  T4             1              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"
D36V5, binary
                 cls
clus               0  1
  SARM1 MUTATED    5  0
  SARM1 WILD-TYPE 48  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      5    0
  SARM1 WILD-TYPE   48    6
   clus
vv  SARM1 MUTATED SARM1 WILD-TYPE
  0             5              48
  1             0               6
[1] 2 2
[1] FALSE
D36V6, binary
                 cls
clus               0  1
  SARM1 MUTATED    3  3
  SARM1 WILD-TYPE 37 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      3    3
  SARM1 WILD-TYPE   37   19
        clus
vv       SARM1 MUTATED SARM1 WILD-TYPE
  FEMALE             3              37
  MALE               3              19
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus               0  1
  SARM1 MUTATED    2  1
  SARM1 WILD-TYPE  5 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARM1 MUTATED      2    1
  SARM1 WILD-TYPE    5   26
                        clus
vv                       SARM1 MUTATED SARM1 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(37) Variable = TRIOBP MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2               0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 33 18
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               51 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               3               18 
$`TRIOBP MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5KP TCGA-OR-A5KV 
       15.45        66.51        32.68        22.98        91.30       127.50 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LJ 
       43.30        28.64        23.64        36.33 

$`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        68.75        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K5 
      121.25        29.82        72.39        31.23        18.15         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        11.31        24.36        46.49        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      153.63        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
      152.15        31.79        28.31        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
           15.45             4.11 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          127.50           153.63 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          34.505           42.510 
[1] "15.4 - 127.5 (34.5)" "4.1 - 153.6 (42.5)" 
[1] "hr=" "1.1"
D37V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TRIOBP MUTATED         1        4         3        2
  TRIOBP WILD-TYPE       5       24        11        9
D37V3, multiclass
           clus
vv          TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                1                5
  STAGE II               4               24
  STAGE III              3               11
  STAGE IV               2                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  6  1  2
  TRIOBP WILD-TYPE  5 26  6 12
D37V4, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  T1              1                5
  T2              6               26
  T3              1                6
  T4              2               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"
D37V5, binary
                  cls
clus                0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 46  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      7    3
  TRIOBP WILD-TYPE   46    3
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0              7               46
  1              3                3
[1] 2 2
[1] FALSE
D37V6, binary
                  cls
clus                0  1
  TRIOBP MUTATED    9  1
  TRIOBP WILD-TYPE 31 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      9    1
  TRIOBP WILD-TYPE   31   21
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  FEMALE              9               31
  MALE                1               21
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                0  1
  TRIOBP MUTATED    1  6
  TRIOBP WILD-TYPE  6 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      1    6
  TRIOBP WILD-TYPE    6   21
                        clus
vv                       TRIOBP MUTATED TRIOBP WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              6               21
[1] 2 2
[1] FALSE

Clustering(38) Variable = ZNF598 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2               0  1
  ZNF598 MUTATED    7  4
  ZNF598 WILD-TYPE 33 17
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              11               50 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               4               17 
$`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        29.82        66.51        11.31 
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5LD TCGA-OR-A5LK TCGA-PK-A5HB 
       24.36        83.80        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        68.75        15.45        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JW 
       46.82        49.22        22.03        36.26       121.25        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15        32.68        22.98         8.32        24.62 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        39.58         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       106.52 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
            4.90             4.11 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           83.80           153.63 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          29.820           43.925 
[1] "4.9 - 83.8 (29.8)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "1.3"
D38V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         0        7         3        1
  ZNF598 WILD-TYPE       6       21        11       10
D38V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                0                6
  STAGE II               7               21
  STAGE III              3               11
  STAGE IV               1               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
  ZNF598 MUTATED    0  7  1  3
  ZNF598 WILD-TYPE  6 25  6 11
D38V4, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  T1              0                6
  T2              7               25
  T3              1                6
  T4              3               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"
D38V5, binary
                  cls
clus                0  1
  ZNF598 MUTATED   11  0
  ZNF598 WILD-TYPE 42  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED     11    0
  ZNF598 WILD-TYPE   42    6
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0             11               42
  1              0                6
[1] 2 2
[1] FALSE
D38V6, binary
                  cls
clus                0  1
  ZNF598 MUTATED    4  8
  ZNF598 WILD-TYPE 36 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      4    8
  ZNF598 WILD-TYPE   36   14
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              4               36
  MALE                8               14
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                0  1
  ZNF598 MUTATED    2  4
  ZNF598 WILD-TYPE  5 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    4
  ZNF598 WILD-TYPE    5   23
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(39) Variable = WDR34 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2              0  1
  WDR34 MUTATED    4  1
  WDR34 WILD-TYPE 36 20
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              56 
  WDR34 MUTATED WDR34 WILD-TYPE 
              1              20 
$`WDR34 MUTATED`
TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5LD TCGA-PK-A5HB 
       91.46        49.22         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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        22.03        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       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 
         42.510          40.485 
[1] "4.9 - 91.5 (42.5)"  "4.1 - 153.6 (40.5)"
[1] "hr=" "1.7"
D39V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  WDR34 MUTATED         0        2         1        1
  WDR34 WILD-TYPE       6       26        13       10
D39V3, multiclass
           clus
vv          WDR34 MUTATED WDR34 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              1              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
  WDR34 MUTATED    0  2  0  2
  WDR34 WILD-TYPE  6 30  7 12
D39V4, multiclass
    clus
vv   WDR34 MUTATED WDR34 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             0               7
  T4             2              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"
D39V5, binary
                 cls
clus               0  1
  WDR34 MUTATED    4  0
  WDR34 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      4    0
  WDR34 WILD-TYPE   49    6
   clus
vv  WDR34 MUTATED WDR34 WILD-TYPE
  0             4              49
  1             0               6
[1] 2 2
[1] FALSE
D39V6, binary
                 cls
clus               0  1
  WDR34 MUTATED    1  4
  WDR34 WILD-TYPE 39 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      1    4
  WDR34 WILD-TYPE   39   18
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  FEMALE             1              39
  MALE               4              18
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus               0  1
  WDR34 MUTATED    0  1
  WDR34 WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      0    1
  WDR34 WILD-TYPE    7   26
                        clus
vv                       WDR34 MUTATED WDR34 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(40) Variable = ZNF628 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2               0  1
  ZNF628 MUTATED    2  4
  ZNF628 WILD-TYPE 38 17
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               6               55 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               4               17 
$`ZNF628 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5L1 
       55.13        18.12        72.39         8.32        11.31        58.55 

$`ZNF628 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        31.23        18.15        32.68        22.98 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        24.36        46.49        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 
      153.63       127.50        50.14        44.84         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  ZNF628 MUTATED ZNF628 WILD-TYPE 
            8.32             4.11 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
           72.39           153.63 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
          36.625           41.390 
[1] "8.3 - 72.4 (36.6)"  "4.1 - 153.6 (41.4)"
[1] "hr=" "2.4"
D40V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF628 MUTATED         0        3         1        3
  ZNF628 WILD-TYPE       6       25        13        8
D40V3, multiclass
           clus
vv          ZNF628 MUTATED ZNF628 WILD-TYPE
  STAGE I                0                6
  STAGE II               3               25
  STAGE III              1               13
  STAGE IV               3                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
  ZNF628 MUTATED    0  3  2  2
  ZNF628 WILD-TYPE  6 29  5 12
D40V4, multiclass
    clus
vv   ZNF628 MUTATED ZNF628 WILD-TYPE
  T1              0                6
  T2              3               29
  T3              2                5
  T4              2               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"
D40V5, binary
                  cls
clus                0  1
  ZNF628 MUTATED    7  0
  ZNF628 WILD-TYPE 46  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      7    0
  ZNF628 WILD-TYPE   46    6
   clus
vv  ZNF628 MUTATED ZNF628 WILD-TYPE
  0              7               46
  1              0                6
[1] 2 2
[1] FALSE
D40V6, binary
                  cls
clus                0  1
  ZNF628 MUTATED    5  2
  ZNF628 WILD-TYPE 35 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      5    2
  ZNF628 WILD-TYPE   35   20
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  FEMALE              5               35
  MALE                2               20
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                0  1
  ZNF628 MUTATED    1  2
  ZNF628 WILD-TYPE  6 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      1    2
  ZNF628 WILD-TYPE    6   25
                        clus
vv                       ZNF628 MUTATED ZNF628 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(41) Variable = BTBD11 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2               0  1
  BTBD11 MUTATED    4  2
  BTBD11 WILD-TYPE 36 19
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               55 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               2               19 
$`BTBD11 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5KB TCGA-OR-A5KW TCGA-OR-A5L5 
       12.00        22.03        32.68        24.36        50.14        43.30 

$`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        68.75        15.45        88.87        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 
       69.37        46.82        49.22         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       29.82        66.51        72.39        31.23        18.15        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
        8.32        24.62        11.31        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63       127.50        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
       60.89       152.15        31.79        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       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 
           28.52            42.51 
[1] "12.0 - 50.1 (28.5)" "4.1 - 153.6 (42.5)"
[1] "hr=" "1.4"
D41V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BTBD11 MUTATED         2        1         3        0
  BTBD11 WILD-TYPE       4       27        11       11
D41V3, multiclass
           clus
vv          BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                2                4
  STAGE II               1               27
  STAGE III              3               11
  STAGE IV               0               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
  BTBD11 MUTATED    2  2  0  2
  BTBD11 WILD-TYPE  4 30  7 12
D41V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              2                4
  T2              2               30
  T3              0                7
  T4              2               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
  BTBD11 MUTATED    5  1
  BTBD11 WILD-TYPE 48  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      5    1
  BTBD11 WILD-TYPE   48    5
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0              5               48
  1              1                5
[1] 2 2
[1] FALSE
D41V6, binary
                  cls
clus                0  1
  BTBD11 MUTATED    5  1
  BTBD11 WILD-TYPE 35 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      5    1
  BTBD11 WILD-TYPE   35   21
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE              5               35
  MALE                1               21
[1] 2 2
[1] FALSE
D41V7, binary
                  cls
clus                0  1
  BTBD11 MUTATED    1  3
  BTBD11 WILD-TYPE  6 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      1    3
  BTBD11 WILD-TYPE    6   24
                        clus
vv                       BTBD11 MUTATED BTBD11 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               24
[1] 2 2
[1] FALSE

Clustering(42) Variable = IRX3 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2             0  1
  IRX3 MUTATED    3  2
  IRX3 WILD-TYPE 37 19
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             56 
  IRX3 MUTATED IRX3 WILD-TYPE 
             2             19 
$`IRX3 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5KP TCGA-OR-A5L3 TCGA-OR-A5LO 
       30.31        18.12        91.30       152.15        69.11 

$`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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       73.05        53.03        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  IRX3 MUTATED IRX3 WILD-TYPE 
         18.12           4.11 
  IRX3 MUTATED IRX3 WILD-TYPE 
        152.15         153.63 
  IRX3 MUTATED IRX3 WILD-TYPE 
        69.110         40.485 
[1] "18.1 - 152.2 (69.1)" "4.1 - 153.6 (40.5)" 
[1] "hr=" "1.1"
D42V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IRX3 MUTATED         1        2         0        2
  IRX3 WILD-TYPE       5       26        14        9
D42V3, multiclass
           clus
vv          IRX3 MUTATED IRX3 WILD-TYPE
  STAGE I              1              5
  STAGE II             2             26
  STAGE III            0             14
  STAGE IV             2              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
  IRX3 MUTATED    1  2  0  2
  IRX3 WILD-TYPE  5 30  7 12
D42V4, multiclass
    clus
vv   IRX3 MUTATED IRX3 WILD-TYPE
  T1            1              5
  T2            2             30
  T3            0              7
  T4            2             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"
D42V5, binary
                cls
clus              0  1
  IRX3 MUTATED    5  0
  IRX3 WILD-TYPE 48  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      5    0
  IRX3 WILD-TYPE   48    6
   clus
vv  IRX3 MUTATED IRX3 WILD-TYPE
  0            5             48
  1            0              6
[1] 2 2
[1] FALSE
D42V6, binary
                cls
clus              0  1
  IRX3 MUTATED    4  1
  IRX3 WILD-TYPE 36 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      4    1
  IRX3 WILD-TYPE   36   21
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  FEMALE            4             36
  MALE              1             21
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus              0  1
  IRX3 MUTATED    0  2
  IRX3 WILD-TYPE  7 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      0    2
  IRX3 WILD-TYPE    7   25
                        clus
vv                       IRX3 MUTATED IRX3 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(43) Variable = FPGS MUTATION ANALYSIS
D43V1, survival
                sevent
clus2             0  1
  FPGS MUTATED    2  2
  FPGS WILD-TYPE 38 19
  FPGS MUTATED FPGS WILD-TYPE 
             4             57 
  FPGS MUTATED FPGS WILD-TYPE 
             2             19 
$`FPGS MUTATED`
TCGA-OR-A5JR TCGA-OR-A5K5 TCGA-OR-A5L6 TCGA-OR-A5LJ 
      121.25         8.32        28.31        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68        22.98        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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 
         32.32          42.51 
[1] "8.3 - 121.2 (32.3)" "4.1 - 153.6 (42.5)"
[1] "hr=" "1.8"
D43V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FPGS MUTATED         1        1         1        2
  FPGS WILD-TYPE       5       27        13        9
D43V3, multiclass
           clus
vv          FPGS MUTATED FPGS WILD-TYPE
  STAGE I              1              5
  STAGE II             1             27
  STAGE III            1             13
  STAGE IV             2              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
  FPGS MUTATED    1  2  1  1
  FPGS WILD-TYPE  5 30  6 13
D43V4, multiclass
    clus
vv   FPGS MUTATED FPGS WILD-TYPE
  T1            1              5
  T2            2             30
  T3            1              6
  T4            1             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"
D43V5, binary
                cls
clus              0  1
  FPGS MUTATED    4  1
  FPGS WILD-TYPE 49  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      4    1
  FPGS WILD-TYPE   49    5
   clus
vv  FPGS MUTATED FPGS WILD-TYPE
  0            4             49
  1            1              5
[1] 2 2
[1] FALSE
D43V6, binary
                cls
clus              0  1
  FPGS MUTATED    3  2
  FPGS WILD-TYPE 37 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      3    2
  FPGS WILD-TYPE   37   20
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  FEMALE            3             37
  MALE              2             20
[1] 2 2
[1] FALSE
D43V7, binary
                cls
clus              0  1
  FPGS MUTATED    0  3
  FPGS WILD-TYPE  7 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      0    3
  FPGS WILD-TYPE    7   24
                        clus
vv                       FPGS MUTATED FPGS WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(44) Variable = MEN1 MUTATION ANALYSIS
D44V1, survival
                sevent
clus2             0  1
  MEN1 MUTATED    2  3
  MEN1 WILD-TYPE 38 18
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             56 
  MEN1 MUTATED MEN1 WILD-TYPE 
             3             18 
$`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        68.75        15.45        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX 
       91.30        83.80        95.18       153.63       127.50        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       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 
        30.310         42.345 
[1] "6.8 - 50.1 (30.3)"  "4.1 - 153.6 (42.3)"
[1] "hr=" "3.1"
D44V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MEN1 MUTATED         0        0         3        1
  MEN1 WILD-TYPE       6       28        11       10
D44V3, multiclass
           clus
vv          MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             28
  STAGE III            3             11
  STAGE IV             1             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
  MEN1 MUTATED    0  1  0  3
  MEN1 WILD-TYPE  6 31  7 11
D44V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            0              6
  T2            1             31
  T3            0              7
  T4            3             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"
D44V5, binary
                cls
clus              0  1
  MEN1 MUTATED    3  1
  MEN1 WILD-TYPE 50  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    1
  MEN1 WILD-TYPE   50    5
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0            3             50
  1            1              5
[1] 2 2
[1] FALSE
D44V6, binary
                cls
clus              0  1
  MEN1 MUTATED    3  2
  MEN1 WILD-TYPE 37 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    2
  MEN1 WILD-TYPE   37   20
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE            3             37
  MALE              2             20
[1] 2 2
[1] FALSE
D44V7, binary
                cls
clus              0  1
  MEN1 MUTATED    1  2
  MEN1 WILD-TYPE  6 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      1    2
  MEN1 WILD-TYPE    6   25
                        clus
vv                       MEN1 MUTATED MEN1 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(45) Variable = BHLHE22 MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  BHLHE22 MUTATED    2  3
  BHLHE22 WILD-TYPE 38 18
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                56 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                3                18 
$`BHLHE22 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5JT TCGA-OR-A5KW TCGA-OR-A5LJ 
       55.13        12.00        29.82        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        68.75        15.45        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63       127.50        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK 
       28.64        23.64        39.58         5.23        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
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             41.95 
[1] "12.0 - 55.1 (36.3)" "4.1 - 153.6 (42.0)"
[1] "hr=" "2.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  BHLHE22 MUTATED         0        1         2        2
  BHLHE22 WILD-TYPE       6       27        12        9
D45V3, multiclass
           clus
vv          BHLHE22 MUTATED BHLHE22 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                1                27
  STAGE III               2                12
  STAGE IV                2                 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
  BHLHE22 MUTATED    0  3  1  1
  BHLHE22 WILD-TYPE  6 29  6 13
D45V4, multiclass
    clus
vv   BHLHE22 MUTATED BHLHE22 WILD-TYPE
  T1               0                 6
  T2               3                29
  T3               1                 6
  T4               1                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"
D45V5, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    3  2
  BHLHE22 WILD-TYPE 50  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      3    2
  BHLHE22 WILD-TYPE   50    4
   clus
vv  BHLHE22 MUTATED BHLHE22 WILD-TYPE
  0               3                50
  1               2                 4
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    4  1
  BHLHE22 WILD-TYPE 36 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      4    1
  BHLHE22 WILD-TYPE   36   21
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  FEMALE               4                36
  MALE                 1                21
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    2  2
  BHLHE22 WILD-TYPE  5 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      2    2
  BHLHE22 WILD-TYPE    5   25
                        clus
vv                       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(46) Variable = DMKN MUTATION ANALYSIS
D46V1, survival
                sevent
clus2             0  1
  DMKN MUTATED    3  0
  DMKN WILD-TYPE 37 21
  DMKN MUTATED DMKN WILD-TYPE 
             3             58 
  DMKN MUTATED DMKN WILD-TYPE 
             0             21 
$`DMKN MUTATED`
TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-PK-A5HB 
      153.63       152.15        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       24.36        46.49        91.30        83.80        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
       50.14        44.84         4.11        58.55        60.89        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        15.45       106.52 

  DMKN MUTATED DMKN WILD-TYPE 
         42.51           4.11 
  DMKN MUTATED DMKN WILD-TYPE 
        153.63         127.50 
  DMKN MUTATED DMKN WILD-TYPE 
       152.150         39.465 
[1] "42.5 - 153.6 (152.2)" "4.1 - 127.5 (39.5)"  
[1] "hr="     "7.5e+07"
D46V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DMKN MUTATED         1        1         0        0
  DMKN WILD-TYPE       5       27        14       11
D46V3, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             57 
    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-A5K8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K9     TCGA-OR-A5KB     TCGA-OR-A5KO     TCGA-OR-A5KP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KS     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-A5L1     TCGA-OR-A5L2 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L4     TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LA     TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LP     TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-P6-A5OH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-PA-A5YG 
"DMKN WILD-TYPE" 
                vv
clus             T1 T2 T3 T4
  DMKN MUTATED    1  1  0  0
  DMKN WILD-TYPE  5 31  7 14
D46V4, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             57 
    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-A5K8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K9     TCGA-OR-A5KB     TCGA-OR-A5KO     TCGA-OR-A5KP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KS     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-A5L1     TCGA-OR-A5L2 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L4     TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LA     TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LP     TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-P6-A5OH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-PA-A5YG 
"DMKN WILD-TYPE" 
D46V5, binary
                cls
clus              0  1
  DMKN MUTATED    2  0
  DMKN WILD-TYPE 51  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    0
  DMKN WILD-TYPE   51    6
   clus
vv  DMKN MUTATED DMKN WILD-TYPE
  0            2             51
  1            0              6
[1] 2 2
[1] FALSE
D46V6, binary
                cls
clus              0  1
  DMKN MUTATED    2  1
  DMKN WILD-TYPE 38 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    1
  DMKN WILD-TYPE   38   21
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  FEMALE            2             38
  MALE              1             21
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus              0  1
  DMKN MUTATED    0  2
  DMKN WILD-TYPE  7 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      0    2
  DMKN WILD-TYPE    7   25
                        clus
vv                       DMKN MUTATED DMKN WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(47) Variable = OBSCN MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2              0  1
  OBSCN MUTATED   11  7
  OBSCN WILD-TYPE 29 14
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              43 
  OBSCN MUTATED OBSCN WILD-TYPE 
              7              14 
$`OBSCN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JV 
       68.75        19.04        18.12        41.39        46.82        66.51 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KV 
       18.15        22.98        11.31        24.36        46.49       127.50 
TCGA-OR-A5L2 TCGA-OR-A5L5 TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-PK-A5HB 
       60.89        43.30         5.23        36.33        61.05        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        88.87        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        69.37        49.22        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX 
        4.90        36.26       121.25        29.82        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       32.68         8.32        24.62        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
      153.63        50.14        44.84         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64        39.58        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       73.05        53.03        69.11        28.04         6.81        15.45 
TCGA-PK-A5H8 
      106.52 

  OBSCN MUTATED OBSCN WILD-TYPE 
           5.23            4.11 
  OBSCN MUTATED OBSCN WILD-TYPE 
         127.50          153.63 
  OBSCN MUTATED OBSCN WILD-TYPE 
          41.95           39.58 
[1] "5.2 - 127.5 (42.0)" "4.1 - 153.6 (39.6)"
[1] "hr=" "1.2"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OBSCN MUTATED         2        6         4        5
  OBSCN WILD-TYPE       4       22        10        6
D47V3, multiclass
           clus
vv          OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I               2               4
  STAGE II              6              22
  STAGE III             4              10
  STAGE IV              5               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  8  2  5
  OBSCN WILD-TYPE  4 24  5  9
D47V4, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  T1             2               4
  T2             8              24
  T3             2               5
  T4             5               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"
D47V5, binary
                 cls
clus               0  1
  OBSCN MUTATED   14  3
  OBSCN WILD-TYPE 39  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     14    3
  OBSCN WILD-TYPE   39    3
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0            14              39
  1             3               3
[1] 2 2
[1] FALSE
D47V6, binary
                 cls
clus               0  1
  OBSCN MUTATED   13  5
  OBSCN WILD-TYPE 27 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     13    5
  OBSCN WILD-TYPE   27   17
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  FEMALE            13              27
  MALE               5              17
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus               0  1
  OBSCN MUTATED    2  7
  OBSCN WILD-TYPE  5 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      2    7
  OBSCN WILD-TYPE    5   20
                        clus
vv                       OBSCN MUTATED OBSCN WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             7              20
[1] 2 2
[1] FALSE

Clustering(48) Variable = PANK2 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2              0  1
  PANK2 MUTATED    1  3
  PANK2 WILD-TYPE 39 18
  PANK2 MUTATED PANK2 WILD-TYPE 
              4              57 
  PANK2 MUTATED PANK2 WILD-TYPE 
              3              18 
$`PANK2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KS TCGA-OR-A5KZ TCGA-OR-A5LD 
       19.04        83.80         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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       44.84        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  PANK2 MUTATED PANK2 WILD-TYPE 
           4.11            4.90 
  PANK2 MUTATED PANK2 WILD-TYPE 
          83.80          153.63 
  PANK2 MUTATED PANK2 WILD-TYPE 
         29.195          42.510 
[1] "4.1 - 83.8 (29.2)"  "4.9 - 153.6 (42.5)"
[1] "hr=" "3"  
D48V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PANK2 MUTATED         0        2         2        1
  PANK2 WILD-TYPE       6       26        12       10
D48V3, multiclass
           clus
vv          PANK2 MUTATED PANK2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             2              12
  STAGE IV              1              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
  PANK2 MUTATED    0  2  1  2
  PANK2 WILD-TYPE  6 30  6 12
D48V4, multiclass
    clus
vv   PANK2 MUTATED PANK2 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             1               6
  T4             2              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"
D48V5, binary
                 cls
clus               0  1
  PANK2 MUTATED    5  0
  PANK2 WILD-TYPE 48  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      5    0
  PANK2 WILD-TYPE   48    6
   clus
vv  PANK2 MUTATED PANK2 WILD-TYPE
  0             5              48
  1             0               6
[1] 2 2
[1] FALSE
D48V6, binary
                 cls
clus               0  1
  PANK2 MUTATED    1  4
  PANK2 WILD-TYPE 39 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      1    4
  PANK2 WILD-TYPE   39   18
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  FEMALE             1              39
  MALE               4              18
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus               0  1
  PANK2 MUTATED    1  4
  PANK2 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      1    4
  PANK2 WILD-TYPE    6   23
                        clus
vv                       PANK2 MUTATED PANK2 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(49) Variable = RREB1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 37 19
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              56 
  RREB1 MUTATED RREB1 WILD-TYPE 
              2              19 
$`RREB1 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5KP 
       15.45        66.51        31.23        18.15        91.30 

$`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        68.75        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
      121.25        29.82        72.39        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        11.31        24.36        46.49        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  RREB1 MUTATED RREB1 WILD-TYPE 
          15.45            4.11 
  RREB1 MUTATED RREB1 WILD-TYPE 
          91.30          153.63 
  RREB1 MUTATED RREB1 WILD-TYPE 
          31.23           41.95 
[1] "15.4 - 91.3 (31.2)" "4.1 - 153.6 (42.0)"
[1] "hr=" "1.2"
D49V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RREB1 MUTATED         0        2         1        2
  RREB1 WILD-TYPE       6       26        13        9
D49V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              2               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
  RREB1 MUTATED    0  2  2  1
  RREB1 WILD-TYPE  6 30  5 13
D49V4, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             2               5
  T4             1              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
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 50  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    2
  RREB1 WILD-TYPE   50    4
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             3              50
  1             2               4
[1] 2 2
[1] FALSE
D49V6, binary
                 cls
clus               0  1
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 37 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    2
  RREB1 WILD-TYPE   37   20
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             3              37
  MALE               2              20
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    1  1
  RREB1 WILD-TYPE  6 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      1    1
  RREB1 WILD-TYPE    6   26
                        clus
vv                       RREB1 MUTATED RREB1 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(50) Variable = RNF149 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2               0  1
  RNF149 MUTATED    4  0
  RNF149 WILD-TYPE 36 21
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               57 
  RNF149 MUTATED RNF149 WILD-TYPE 
               0               21 
$`RNF149 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5LP 
       22.03        24.62       153.63        61.05 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68        22.98         8.32        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        83.80        95.18       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  RNF149 MUTATED RNF149 WILD-TYPE 
           22.03             4.11 
  RNF149 MUTATED RNF149 WILD-TYPE 
          153.63           152.15 
  RNF149 MUTATED RNF149 WILD-TYPE 
          42.835           41.390 
[1] "22.0 - 153.6 (42.8)" "4.1 - 152.2 (41.4)" 
[1] "hr="     "7.5e+07"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF149 MUTATED         1        3         0        0
  RNF149 WILD-TYPE       5       25        14       11
D50V3, multiclass
           clus
vv          RNF149 MUTATED RNF149 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              0               14
  STAGE IV               0               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
  RNF149 MUTATED    1  3  0  0
  RNF149 WILD-TYPE  5 29  7 14
D50V4, multiclass
    clus
vv   RNF149 MUTATED RNF149 WILD-TYPE
  T1              1                5
  T2              3               29
  T3              0                7
  T4              0               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
  RNF149 MUTATED    4  0
  RNF149 WILD-TYPE 49  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      4    0
  RNF149 WILD-TYPE   49    6
   clus
vv  RNF149 MUTATED RNF149 WILD-TYPE
  0              4               49
  1              0                6
[1] 2 2
[1] FALSE
D50V6, binary
                  cls
clus                0  1
  RNF149 MUTATED    3  1
  RNF149 WILD-TYPE 37 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      3    1
  RNF149 WILD-TYPE   37   21
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  FEMALE              3               37
  MALE                1               21
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                0  1
  RNF149 MUTATED    0  2
  RNF149 WILD-TYPE  7 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      0    2
  RNF149 WILD-TYPE    7   25
                        clus
vv                       RNF149 MUTATED RNF149 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(51) Variable = GLTPD2 MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2               0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 37 18
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               55 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               3               18 
$`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        49.22        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        68.75        15.45        12.00        88.87 
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        69.37        46.82 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       72.39        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        24.36        46.49        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
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 
           36.41            41.39 
[1] "11.3 - 91.5 (36.4)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.8"
D51V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GLTPD2 MUTATED         0        2         1        2
  GLTPD2 WILD-TYPE       6       26        13        9
D51V3, multiclass
           clus
vv          GLTPD2 MUTATED GLTPD2 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               26
  STAGE III              1               13
  STAGE IV               2                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
  GLTPD2 MUTATED    0  2  1  2
  GLTPD2 WILD-TYPE  6 30  6 12
D51V4, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  T1              0                6
  T2              2               30
  T3              1                6
  T4              2               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"
D51V5, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    5  0
  GLTPD2 WILD-TYPE 48  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      5    0
  GLTPD2 WILD-TYPE   48    6
   clus
vv  GLTPD2 MUTATED GLTPD2 WILD-TYPE
  0              5               48
  1              0                6
[1] 2 2
[1] FALSE
D51V6, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 37 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      3    3
  GLTPD2 WILD-TYPE   37   19
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  FEMALE              3               37
  MALE                3               19
[1] 2 2
[1] FALSE
D51V7, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    1  0
  GLTPD2 WILD-TYPE  6 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      1    0
  GLTPD2 WILD-TYPE    6   27
                        clus
vv                       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              0               27
[1] 2 2
[1] FALSE

Clustering(52) Variable = SNED1 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  SNED1 MUTATED    4  1
  SNED1 WILD-TYPE 36 20
  SNED1 MUTATED SNED1 WILD-TYPE 
              5              56 
  SNED1 MUTATED SNED1 WILD-TYPE 
              1              20 
$`SNED1 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JY TCGA-OR-A5KV TCGA-OR-A5L3 
       41.39        46.82        18.15       127.50       152.15 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        72.39        31.23        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  SNED1 MUTATED SNED1 WILD-TYPE 
          18.15            4.11 
  SNED1 MUTATED SNED1 WILD-TYPE 
         152.15          153.63 
  SNED1 MUTATED SNED1 WILD-TYPE 
         46.820          39.465 
[1] "18.1 - 152.2 (46.8)" "4.1 - 153.6 (39.5)" 
[1] "hr=" "2.2"
D52V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SNED1 MUTATED         2        1         1        1
  SNED1 WILD-TYPE       4       27        13       10
D52V3, multiclass
           clus
vv          SNED1 MUTATED SNED1 WILD-TYPE
  STAGE I               2               4
  STAGE II              1              27
  STAGE III             1              13
  STAGE IV              1              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  1
  SNED1 WILD-TYPE  4 30  7 13
D52V4, multiclass
    clus
vv   SNED1 MUTATED SNED1 WILD-TYPE
  T1             2               4
  T2             2              30
  T3             0               7
  T4             1              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"
D52V5, binary
                 cls
clus               0  1
  SNED1 MUTATED    3  2
  SNED1 WILD-TYPE 50  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      3    2
  SNED1 WILD-TYPE   50    4
   clus
vv  SNED1 MUTATED SNED1 WILD-TYPE
  0             3              50
  1             2               4
[1] 2 2
[1] FALSE
D52V6, binary
                 cls
clus               0  1
  SNED1 MUTATED    4  1
  SNED1 WILD-TYPE 36 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      4    1
  SNED1 WILD-TYPE   36   21
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  FEMALE             4              36
  MALE               1              21
[1] 2 2
[1] FALSE
D52V7, binary
                 cls
clus               0  1
  SNED1 MUTATED    0  2
  SNED1 WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      0    2
  SNED1 WILD-TYPE    7   25
                        clus
vv                       SNED1 MUTATED SNED1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(53) Variable = TPO MUTATION ANALYSIS
D53V1, survival
               sevent
clus2            0  1
  TPO MUTATED    7  5
  TPO WILD-TYPE 33 16
  TPO MUTATED TPO WILD-TYPE 
           12            49 
  TPO MUTATED TPO WILD-TYPE 
            5            16 
$`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        69.37        46.82        11.31 
TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5LD TCGA-OR-A5LJ 
       24.36        91.30       127.50        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        68.75        15.45        12.00        88.87 
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        49.22        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
        4.90        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15        32.68        22.98         8.32        24.62 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KZ 
       46.49        83.80        95.18       153.63        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64        39.58         5.23        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  TPO MUTATED TPO WILD-TYPE 
        11.31          4.11 
  TPO MUTATED TPO WILD-TYPE 
       127.50        153.63 
  TPO MUTATED TPO WILD-TYPE 
        40.37         42.51 
[1] "11.3 - 127.5 (40.4)" "4.1 - 153.6 (42.5)" 
[1] "hr=" "1.3"
D53V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TPO MUTATED         1        5         4        2
  TPO WILD-TYPE       5       23        10        9
D53V3, multiclass
           clus
vv          TPO MUTATED TPO WILD-TYPE
  STAGE I             1             5
  STAGE II            5            23
  STAGE III           4            10
  STAGE IV            2             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
  TPO MUTATED    1  8  1  2
  TPO WILD-TYPE  5 24  6 12
D53V4, multiclass
    clus
vv   TPO MUTATED TPO WILD-TYPE
  T1           1             5
  T2           8            24
  T3           1             6
  T4           2            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"
D53V5, binary
               cls
clus             0  1
  TPO MUTATED    9  3
  TPO WILD-TYPE 44  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      9    3
  TPO WILD-TYPE   44    3
   clus
vv  TPO MUTATED TPO WILD-TYPE
  0           9            44
  1           3             3
[1] 2 2
[1] FALSE
D53V6, binary
               cls
clus             0  1
  TPO MUTATED    8  4
  TPO WILD-TYPE 32 18
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      8    4
  TPO WILD-TYPE   32   18
        clus
vv       TPO MUTATED TPO WILD-TYPE
  FEMALE           8            32
  MALE             4            18
[1] 2 2
[1] FALSE
D53V7, binary
               cls
clus             0  1
  TPO MUTATED    1  6
  TPO WILD-TYPE  6 21
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      1    6
  TPO WILD-TYPE    6   21
                        clus
vv                       TPO MUTATED TPO WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           6            21
[1] 2 2
[1] FALSE

Clustering(54) Variable = PTPLA MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2              0  1
  PTPLA MUTATED    3  1
  PTPLA WILD-TYPE 37 20
  PTPLA MUTATED PTPLA WILD-TYPE 
              4              57 
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              20 
$`PTPLA MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JW TCGA-OR-A5KB TCGA-OR-A5L3 
       12.00        72.39        24.36       152.15 

$`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        68.75        15.45        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        29.82        66.51        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98         8.32        24.62        11.31        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  PTPLA MUTATED PTPLA WILD-TYPE 
          12.00            4.11 
  PTPLA MUTATED PTPLA WILD-TYPE 
         152.15          153.63 
  PTPLA MUTATED PTPLA WILD-TYPE 
         48.375          41.390 
[1] "12.0 - 152.2 (48.4)" "4.1 - 153.6 (41.4)" 
[1] "hr=" "1.5"
D54V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTPLA MUTATED         1        2         1        0
  PTPLA WILD-TYPE       5       26        13       11
D54V3, multiclass
           clus
vv          PTPLA MUTATED PTPLA WILD-TYPE
  STAGE I               1               5
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              0              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
  PTPLA MUTATED    1  2  0  1
  PTPLA WILD-TYPE  5 30  7 13
D54V4, multiclass
    clus
vv   PTPLA MUTATED PTPLA WILD-TYPE
  T1             1               5
  T2             2              30
  T3             0               7
  T4             1              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
  PTPLA MUTATED    4  0
  PTPLA WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      4    0
  PTPLA WILD-TYPE   49    6
   clus
vv  PTPLA MUTATED PTPLA WILD-TYPE
  0             4              49
  1             0               6
[1] 2 2
[1] FALSE
D54V6, binary
                 cls
clus               0  1
  PTPLA MUTATED    2  2
  PTPLA WILD-TYPE 38 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      2    2
  PTPLA WILD-TYPE   38   20
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  FEMALE             2              38
  MALE               2              20
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus               0  1
  PTPLA MUTATED    1  2
  PTPLA WILD-TYPE  6 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      1    2
  PTPLA WILD-TYPE    6   25
                        clus
vv                       PTPLA MUTATED PTPLA WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(55) Variable = PRSS27 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2               0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 39 19
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               58 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               2               19 
$`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        68.75        15.45        88.87        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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        22.03         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       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 
          19.040           42.905 
[1] "12.0 - 41.4 (19.0)" "4.1 - 153.6 (42.9)"
[1] "hr=" "3.4"
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PRSS27 MUTATED         0        1         2        0
  PRSS27 WILD-TYPE       6       27        12       11
D55V3, multiclass
           clus
vv          PRSS27 MUTATED PRSS27 WILD-TYPE
  STAGE I                0                6
  STAGE II               1               27
  STAGE III              2               12
  STAGE IV               0               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
  PRSS27 MUTATED    0  1  1  1
  PRSS27 WILD-TYPE  6 31  6 13
D55V4, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  T1              0                6
  T2              1               31
  T3              1                6
  T4              1               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"
D55V5, binary
                  cls
clus                0  1
  PRSS27 MUTATED    3  0
  PRSS27 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      3    0
  PRSS27 WILD-TYPE   50    6
   clus
vv  PRSS27 MUTATED PRSS27 WILD-TYPE
  0              3               50
  1              0                6
[1] 2 2
[1] FALSE
D55V6, binary
                  cls
clus                0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 39 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      1    2
  PRSS27 WILD-TYPE   39   20
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  FEMALE              1               39
  MALE                2               20
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                0  1
  PRSS27 MUTATED    2  0
  PRSS27 WILD-TYPE  5 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      2    0
  PRSS27 WILD-TYPE    5   27
                        clus
vv                       PRSS27 MUTATED PRSS27 WILD-TYPE
  HISPANIC OR LATINO                  2                5
  NOT HISPANIC OR LATINO              0               27
[1] 2 2
[1] FALSE

Clustering(56) Variable = CD320 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  CD320 MUTATED    2  2
  CD320 WILD-TYPE 38 19
  CD320 MUTATED CD320 WILD-TYPE 
              4              57 
  CD320 MUTATED CD320 WILD-TYPE 
              2              19 
$`CD320 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5K5 TCGA-OR-A5L4 
       12.00        88.87         8.32        31.79 

$`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        68.75        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  CD320 MUTATED CD320 WILD-TYPE 
           8.32            4.11 
  CD320 MUTATED CD320 WILD-TYPE 
          88.87          153.63 
  CD320 MUTATED CD320 WILD-TYPE 
         21.895          42.510 
[1] "8.3 - 88.9 (21.9)"  "4.1 - 153.6 (42.5)"
[1] "hr=" "2.2"
D56V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CD320 MUTATED         0        1         3        0
  CD320 WILD-TYPE       6       27        11       11
D56V3, multiclass
           clus
vv          CD320 MUTATED CD320 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              27
  STAGE III             3              11
  STAGE IV              0              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
  CD320 MUTATED    0  1  1  2
  CD320 WILD-TYPE  6 31  6 12
D56V4, multiclass
    clus
vv   CD320 MUTATED CD320 WILD-TYPE
  T1             0               6
  T2             1              31
  T3             1               6
  T4             2              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"
D56V5, binary
                 cls
clus               0  1
  CD320 MUTATED    4  0
  CD320 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      4    0
  CD320 WILD-TYPE   49    6
   clus
vv  CD320 MUTATED CD320 WILD-TYPE
  0             4              49
  1             0               6
[1] 2 2
[1] FALSE
D56V6, binary
                 cls
clus               0  1
  CD320 MUTATED    3  1
  CD320 WILD-TYPE 37 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      3    1
  CD320 WILD-TYPE   37   21
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  FEMALE             3              37
  MALE               1              21
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus               0  1
  CD320 MUTATED    2  1
  CD320 WILD-TYPE  5 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      2    1
  CD320 WILD-TYPE    5   26
                        clus
vv                       CD320 MUTATED CD320 WILD-TYPE
  HISPANIC OR LATINO                 2               5
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(57) Variable = SEMA5B MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2               0  1
  SEMA5B MUTATED    5  3
  SEMA5B WILD-TYPE 35 18
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               53 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               3               18 
$`SEMA5B MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JR TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5L1 
       55.13        18.12       121.25        24.36       127.50        58.55 
TCGA-OR-A5LD TCGA-OR-A5LK 
       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        68.75        15.45        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT 
       46.82        49.22        22.03         4.90        36.26        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
        8.32        24.62        11.31        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 
       95.18       153.63        50.14        44.84         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       106.52        42.51 

  SEMA5B MUTATED SEMA5B WILD-TYPE 
           18.12             4.11 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
          127.50           153.63 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
           56.84            39.58 
[1] "18.1 - 127.5 (56.8)" "4.1 - 153.6 (39.6)" 
[1] "hr=" "1.2"
D57V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEMA5B MUTATED         1        3         2        2
  SEMA5B WILD-TYPE       5       25        12        9
D57V3, multiclass
           clus
vv          SEMA5B MUTATED SEMA5B WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              2               12
  STAGE IV               2                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
  SEMA5B MUTATED    1  4  1  2
  SEMA5B WILD-TYPE  5 28  6 12
D57V4, multiclass
    clus
vv   SEMA5B MUTATED SEMA5B WILD-TYPE
  T1              1                5
  T2              4               28
  T3              1                6
  T4              2               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"
D57V5, binary
                  cls
clus                0  1
  SEMA5B MUTATED    7  1
  SEMA5B WILD-TYPE 46  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      7    1
  SEMA5B WILD-TYPE   46    5
   clus
vv  SEMA5B MUTATED SEMA5B WILD-TYPE
  0              7               46
  1              1                5
[1] 2 2
[1] FALSE
D57V6, binary
                  cls
clus                0  1
  SEMA5B MUTATED    4  4
  SEMA5B WILD-TYPE 36 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      4    4
  SEMA5B WILD-TYPE   36   18
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  FEMALE              4               36
  MALE                4               18
[1] 2 2
[1] FALSE
D57V7, binary
                  cls
clus                0  1
  SEMA5B MUTATED    1  4
  SEMA5B WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      1    4
  SEMA5B WILD-TYPE    6   23
                        clus
vv                       SEMA5B MUTATED SEMA5B WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(58) Variable = CCDC150 MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  CCDC150 MUTATED    1  3
  CCDC150 WILD-TYPE 39 18
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                57 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                3                18 
$`CCDC150 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5KV 
       16.11        19.04        30.31       127.50 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        22.03         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
            16.11              4.11 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           127.50            153.63 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           24.675            42.510 
[1] "16.1 - 127.5 (24.7)" "4.1 - 153.6 (42.5)" 
[1] "hr=" "2.9"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC150 MUTATED         0        0         3        1
  CCDC150 WILD-TYPE       6       28        11       10
D58V3, multiclass
           clus
vv          CCDC150 MUTATED CCDC150 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                0                28
  STAGE III               3                11
  STAGE IV                1                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
  CCDC150 MUTATED    0  1  2  1
  CCDC150 WILD-TYPE  6 31  5 13
D58V4, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  T1               0                 6
  T2               1                31
  T3               2                 5
  T4               1                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"
D58V5, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    3  1
  CCDC150 WILD-TYPE 50  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      3    1
  CCDC150 WILD-TYPE   50    5
   clus
vv  CCDC150 MUTATED CCDC150 WILD-TYPE
  0               3                50
  1               1                 5
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    3  1
  CCDC150 WILD-TYPE 37 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      3    1
  CCDC150 WILD-TYPE   37   21
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  FEMALE               3                37
  MALE                 1                21
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    2  1
  CCDC150 WILD-TYPE  5 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      2    1
  CCDC150 WILD-TYPE    5   26
                        clus
vv                       CCDC150 MUTATED CCDC150 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(59) Variable = TAF5 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2             0  1
  TAF5 MUTATED    2  2
  TAF5 WILD-TYPE 38 19
  TAF5 MUTATED TAF5 WILD-TYPE 
             4             57 
  TAF5 MUTATED TAF5 WILD-TYPE 
             2             19 
$`TAF5 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JY TCGA-OR-A5K8 TCGA-OR-A5LR 
       55.13        18.15        24.62        28.04 

$`TAF5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 
      121.25        29.82        66.51        72.39        31.23        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98         8.32        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF 
       36.33        73.05        53.03        69.11        61.05         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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 
         26.33          42.51 
[1] "18.1 - 55.1 (26.3)" "4.1 - 153.6 (42.5)"
[1] "hr=" "2"  
D59V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TAF5 MUTATED         0        2         0        2
  TAF5 WILD-TYPE       6       26        14        9
D59V3, multiclass
           clus
vv          TAF5 MUTATED TAF5 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             26
  STAGE III            0             14
  STAGE IV             2              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
  TAF5 MUTATED    0  2  1  1
  TAF5 WILD-TYPE  6 30  6 13
D59V4, multiclass
    clus
vv   TAF5 MUTATED TAF5 WILD-TYPE
  T1            0              6
  T2            2             30
  T3            1              6
  T4            1             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
  TAF5 MUTATED    3  1
  TAF5 WILD-TYPE 50  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      3    1
  TAF5 WILD-TYPE   50    5
   clus
vv  TAF5 MUTATED TAF5 WILD-TYPE
  0            3             50
  1            1              5
[1] 2 2
[1] FALSE
D59V6, binary
                cls
clus              0  1
  TAF5 MUTATED    3  1
  TAF5 WILD-TYPE 37 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      3    1
  TAF5 WILD-TYPE   37   21
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  FEMALE            3             37
  MALE              1             21
[1] 2 2
[1] FALSE
D59V7, binary
                cls
clus              0  1
  TAF5 MUTATED    1  1
  TAF5 WILD-TYPE  6 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      1    1
  TAF5 WILD-TYPE    6   26
                        clus
vv                       TAF5 MUTATED TAF5 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(60) Variable = GARS MUTATION ANALYSIS
D60V1, survival
                sevent
clus2             0  1
  GARS MUTATED   16  2
  GARS WILD-TYPE 24 19
  GARS MUTATED GARS WILD-TYPE 
            18             43 
  GARS MUTATED GARS WILD-TYPE 
             2             19 
$`GARS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JC TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ 
       88.87        57.53        69.37        46.82        22.03        36.26 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       29.82        66.51        24.62        91.30        83.80        95.18 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L5 TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
       44.84         4.11        43.30        73.05        69.11        61.05 

$`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        68.75        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        49.22 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
        4.90       121.25        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KU 
       22.98         8.32        11.31        24.36        46.49       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
      127.50        50.14        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       36.33        53.03        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  GARS MUTATED GARS WILD-TYPE 
          4.11           4.90 
  GARS MUTATED GARS WILD-TYPE 
         95.18         153.63 
  GARS MUTATED GARS WILD-TYPE 
         59.29          32.68 
[1] "4.1 - 95.2 (59.3)"  "4.9 - 153.6 (32.7)"
[1] "hr=" "5.7"
D60V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GARS MUTATED         4       12         1        1
  GARS WILD-TYPE       2       16        13       10
D60V3, multiclass
           clus
vv          GARS MUTATED GARS WILD-TYPE
  STAGE I              4              2
  STAGE II            12             16
  STAGE III            1             13
  STAGE IV             1             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 13  0  1
  GARS WILD-TYPE  2 19  7 13
D60V4, multiclass
    clus
vv   GARS MUTATED GARS WILD-TYPE
  T1            4              2
  T2           13             19
  T3            0              7
  T4            1             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"
D60V5, binary
                cls
clus              0  1
  GARS MUTATED   17  1
  GARS WILD-TYPE 36  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     17    1
  GARS WILD-TYPE   36    5
   clus
vv  GARS MUTATED GARS WILD-TYPE
  0           17             36
  1            1              5
[1] 2 2
[1] FALSE
D60V6, binary
                cls
clus              0  1
  GARS MUTATED   12  7
  GARS WILD-TYPE 28 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     12    7
  GARS WILD-TYPE   28   15
        clus
vv       GARS MUTATED GARS WILD-TYPE
  FEMALE           12             28
  MALE              7             15
[1] 2 2
[1] FALSE
D60V7, binary
                cls
clus              0  1
  GARS MUTATED    1  8
  GARS WILD-TYPE  6 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED      1    8
  GARS WILD-TYPE    6   19
                        clus
vv                       GARS MUTATED GARS WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            8             19
[1] 2 2
[1] FALSE

Clustering(61) Variable = MUC5B MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2              0  1
  MUC5B MUTATED   14  8
  MUC5B WILD-TYPE 26 13
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              39 
  MUC5B MUTATED MUC5B WILD-TYPE 
              8              13 
$`MUC5B MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JQ TCGA-OR-A5JV 
       68.75        12.00        19.04        18.12        36.26        66.51 
TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KU 
       72.39        32.68        11.31        24.36        46.49       153.63 
TCGA-OR-A5L2 TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LO 
       60.89        43.30        23.64         5.23        36.33        69.11 
TCGA-OR-A5LP TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       61.05        15.45       106.52        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        88.87        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        69.37        46.82        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JY 
       22.03         4.90       121.25        29.82        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       22.98         8.32        24.62        91.30        83.80        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
      127.50        50.14        44.84         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LK 
       31.79        28.31        28.64        39.58        39.35        73.05 
TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF 
       53.03        28.04         6.81 

  MUC5B MUTATED MUC5B WILD-TYPE 
           5.23            4.11 
  MUC5B MUTATED MUC5B WILD-TYPE 
         153.63          152.15 
  MUC5B MUTATED MUC5B WILD-TYPE 
          39.42           41.39 
[1] "5.2 - 153.6 (39.4)" "4.1 - 152.2 (41.4)"
[1] "hr=" "1.1"
D61V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED         1       11         4        4
  MUC5B WILD-TYPE       5       17        10        7
D61V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I               1               5
  STAGE II             11              17
  STAGE III             4              10
  STAGE IV              4               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
  MUC5B MUTATED    1 12  2  5
  MUC5B WILD-TYPE  5 20  5  9
D61V4, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  T1             1               5
  T2            12              20
  T3             2               5
  T4             5               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"
D61V5, binary
                 cls
clus               0  1
  MUC5B MUTATED   19  1
  MUC5B WILD-TYPE 34  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     19    1
  MUC5B WILD-TYPE   34    5
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0            19              34
  1             1               5
[1] 2 2
[1] FALSE
D61V6, binary
                 cls
clus               0  1
  MUC5B MUTATED   14  8
  MUC5B WILD-TYPE 26 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     14    8
  MUC5B WILD-TYPE   26   14
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE            14              26
  MALE               8              14
[1] 2 2
[1] FALSE
D61V7, binary
                 cls
clus               0  1
  MUC5B MUTATED    3 10
  MUC5B WILD-TYPE  4 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      3   10
  MUC5B WILD-TYPE    4   17
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 3               4
  NOT HISPANIC OR LATINO            10              17
[1] 2 2
[1] FALSE

Clustering(62) Variable = KIAA1984 MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  KIAA1984 MUTATED    3  1
  KIAA1984 WILD-TYPE 37 20
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 57 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 1                 20 
$`KIAA1984 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-PK-A5HB 
       19.04        24.62        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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP 
       32.68        22.98         8.32        11.31        24.36        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        15.45       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 
            33.565             41.390 
[1] "19.0 - 46.5 (33.6)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1984 MUTATED         0        1         1        1
  KIAA1984 WILD-TYPE       6       27        13       10
D62V3, multiclass
           clus
vv          KIAA1984 MUTATED KIAA1984 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 1                 27
  STAGE III                1                 13
  STAGE IV                 1                 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
  KIAA1984 MUTATED    0  1  1  1
  KIAA1984 WILD-TYPE  6 31  6 13
D62V4, multiclass
    clus
vv   KIAA1984 MUTATED KIAA1984 WILD-TYPE
  T1                0                  6
  T2                1                 31
  T3                1                  6
  T4                1                 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"
D62V5, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    3  0
  KIAA1984 WILD-TYPE 50  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      3    0
  KIAA1984 WILD-TYPE   50    6
   clus
vv  KIAA1984 MUTATED KIAA1984 WILD-TYPE
  0                3                 50
  1                0                  6
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    1  3
  KIAA1984 WILD-TYPE 39 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      1    3
  KIAA1984 WILD-TYPE   39   19
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  FEMALE                1                 39
  MALE                  3                 19
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    1  2
  KIAA1984 WILD-TYPE  6 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      1    2
  KIAA1984 WILD-TYPE    6   25
                        clus
vv                       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(63) Variable = SRPX MUTATION ANALYSIS
D63V1, survival
                sevent
clus2             0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 38 20
  SRPX MUTATED SRPX WILD-TYPE 
             3             58 
  SRPX MUTATED SRPX WILD-TYPE 
             1             20 
$`SRPX MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5KW TCGA-OR-A5L9 
       55.13        50.14        28.64 

$`SRPX WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        83.80        95.18       153.63       127.50 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  SRPX MUTATED SRPX WILD-TYPE 
         28.64           4.11 
  SRPX MUTATED SRPX WILD-TYPE 
         55.13         153.63 
  SRPX MUTATED SRPX WILD-TYPE 
        50.140         40.485 
[1] "28.6 - 55.1 (50.1)" "4.1 - 153.6 (40.5)"
[1] "hr=" "1.1"
D63V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SRPX MUTATED         0        1         1        1
  SRPX WILD-TYPE       6       27        13       10
D63V3, multiclass
           clus
vv          SRPX MUTATED SRPX WILD-TYPE
  STAGE I              0              6
  STAGE II             1             27
  STAGE III            1             13
  STAGE IV             1             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
  SRPX MUTATED    0  2  1  0
  SRPX WILD-TYPE  6 30  6 14
D63V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            0              6
  T2            2             30
  T3            1              6
  T4            0             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"
D63V5, binary
                cls
clus              0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 51  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      2    1
  SRPX WILD-TYPE   51    5
   clus
vv  SRPX MUTATED SRPX WILD-TYPE
  0            2             51
  1            1              5
[1] 2 2
[1] FALSE
D63V6, binary
                cls
clus              0  1
  SRPX MUTATED    3  0
  SRPX WILD-TYPE 37 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      3    0
  SRPX WILD-TYPE   37   22
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE            3             37
  MALE              0             22
[1] 2 2
[1] FALSE
D63V7, binary
                cls
clus              0  1
  SRPX MUTATED    1  2
  SRPX WILD-TYPE  6 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    2
  SRPX WILD-TYPE    6   25
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(64) Variable = TNIP2 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  TNIP2 MUTATED    4  0
  TNIP2 WILD-TYPE 36 21
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              4              57 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              0              21 
$`TNIP2 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5KV TCGA-OR-A5KW TCGA-PK-A5HB 
       46.82       127.50        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        68.75        15.45        12.00        88.87 
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        69.37        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX 
       46.49        91.30        83.80        95.18       153.63        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        15.45       106.52 

  TNIP2 MUTATED TNIP2 WILD-TYPE 
          42.51            4.11 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
         127.50          153.63 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
          48.48           39.35 
[1] "42.5 - 127.5 (48.5)" "4.1 - 153.6 (39.4)" 
[1] "hr="     "7.6e+07"
D64V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TNIP2 MUTATED         1        0         2        1
  TNIP2 WILD-TYPE       5       28        12       10
D64V3, multiclass
           clus
vv          TNIP2 MUTATED TNIP2 WILD-TYPE
  STAGE I               1               5
  STAGE II              0              28
  STAGE III             2              12
  STAGE IV              1              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
  TNIP2 MUTATED    1  2  0  1
  TNIP2 WILD-TYPE  5 30  7 13
D64V4, multiclass
    clus
vv   TNIP2 MUTATED TNIP2 WILD-TYPE
  T1             1               5
  T2             2              30
  T3             0               7
  T4             1              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"
D64V5, binary
                 cls
clus               0  1
  TNIP2 MUTATED    2  2
  TNIP2 WILD-TYPE 51  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      2    2
  TNIP2 WILD-TYPE   51    4
   clus
vv  TNIP2 MUTATED TNIP2 WILD-TYPE
  0             2              51
  1             2               4
[1] 2 2
[1] FALSE
D64V6, binary
                 cls
clus               0  1
  TNIP2 MUTATED    3  2
  TNIP2 WILD-TYPE 37 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      3    2
  TNIP2 WILD-TYPE   37   20
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  FEMALE             3              37
  MALE               2              20
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus               0  1
  TNIP2 MUTATED    0  3
  TNIP2 WILD-TYPE  7 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      0    3
  TNIP2 WILD-TYPE    7   24
                        clus
vv                       TNIP2 MUTATED TNIP2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              24
[1] 2 2
[1] FALSE

Clustering(65) Variable = IDUA MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  IDUA MUTATED    7  1
  IDUA WILD-TYPE 33 20
  IDUA MUTATED IDUA WILD-TYPE 
             8             53 
  IDUA MUTATED IDUA WILD-TYPE 
             1             20 
$`IDUA MUTATED`
TCGA-OR-A5JP TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-OR-A5LK 
        4.90        11.31        91.30       153.63       152.15        73.05 
TCGA-OR-A5LO TCGA-PK-A5HB 
       69.11        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68        22.98         8.32        24.62        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL 
       23.64        39.58         5.23        39.35        36.33        53.03 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        15.45       106.52 

  IDUA MUTATED IDUA WILD-TYPE 
          4.90           4.11 
  IDUA MUTATED IDUA WILD-TYPE 
        153.63         127.50 
  IDUA MUTATED IDUA WILD-TYPE 
         71.08          39.35 
[1] "4.9 - 153.6 (71.1)" "4.1 - 127.5 (39.4)"
[1] "hr=" "3.9"
D65V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         1        6         0        0
  IDUA WILD-TYPE       5       22        14       11
D65V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              1              5
  STAGE II             6             22
  STAGE III            0             14
  STAGE IV             0             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  6  0  0
  IDUA WILD-TYPE  5 26  7 14
D65V4, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  T1            1              5
  T2            6             26
  T3            0              7
  T4            0             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"
D65V5, binary
                cls
clus              0  1
  IDUA MUTATED    7  0
  IDUA WILD-TYPE 46  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      7    0
  IDUA WILD-TYPE   46    6
   clus
vv  IDUA MUTATED IDUA WILD-TYPE
  0            7             46
  1            0              6
[1] 2 2
[1] FALSE
D65V6, binary
                cls
clus              0  1
  IDUA MUTATED    5  3
  IDUA WILD-TYPE 35 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      5    3
  IDUA WILD-TYPE   35   19
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  FEMALE            5             35
  MALE              3             19
[1] 2 2
[1] FALSE
D65V7, binary
                cls
clus              0  1
  IDUA MUTATED    0  3
  IDUA WILD-TYPE  7 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      0    3
  IDUA WILD-TYPE    7   24
                        clus
vv                       IDUA MUTATED IDUA WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(66) Variable = RNF39 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2              0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 37 19
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              56 
  RNF39 MUTATED RNF39 WILD-TYPE 
              2              19 
$`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        68.75        15.45        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22        22.03        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63       127.50        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       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 
         42.510          40.485 
[1] "4.9 - 55.1 (42.5)"  "4.1 - 153.6 (40.5)"
[1] "hr=" "1.4"
D66V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RNF39 MUTATED         0        1         1        2
  RNF39 WILD-TYPE       6       27        13        9
D66V3, multiclass
           clus
vv          RNF39 MUTATED RNF39 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              27
  STAGE III             1              13
  STAGE IV              2               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
  RNF39 MUTATED    0  2  1  1
  RNF39 WILD-TYPE  6 30  6 13
D66V4, multiclass
    clus
vv   RNF39 MUTATED RNF39 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             1               6
  T4             1              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"
D66V5, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  1
  RNF39 WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    1
  RNF39 WILD-TYPE   50    5
   clus
vv  RNF39 MUTATED RNF39 WILD-TYPE
  0             3              50
  1             1               5
[1] 2 2
[1] FALSE
D66V6, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 37 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    2
  RNF39 WILD-TYPE   37   20
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  FEMALE             3              37
  MALE               2              20
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  1
  RNF39 WILD-TYPE  6 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    1
  RNF39 WILD-TYPE    6   26
                        clus
vv                       RNF39 MUTATED RNF39 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(67) Variable = PABPC1 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    3  1
  PABPC1 WILD-TYPE 37 20
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               57 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               20 
$`PABPC1 MUTATED`
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5LB 
       24.36        83.80        44.84        39.58 

$`PABPC1 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.31        28.64        23.64         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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
           24.36             4.11 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           83.80           153.63 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           42.21            41.39 
[1] "24.4 - 83.8 (42.2)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.6"
D67V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PABPC1 MUTATED         0        2         1        1
  PABPC1 WILD-TYPE       6       26        13       10
D67V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               26
  STAGE III              1               13
  STAGE IV               1               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
  PABPC1 MUTATED    0  3  0  1
  PABPC1 WILD-TYPE  6 29  7 13
D67V4, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  T1              0                6
  T2              3               29
  T3              0                7
  T4              1               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"
D67V5, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  1
  PABPC1 WILD-TYPE 50  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    1
  PABPC1 WILD-TYPE   50    5
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              3               50
  1              1                5
[1] 2 2
[1] FALSE
D67V6, binary
                  cls
clus                0  1
  PABPC1 MUTATED    2  2
  PABPC1 WILD-TYPE 38 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      2    2
  PABPC1 WILD-TYPE   38   20
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              2               38
  MALE                2               20
[1] 2 2
[1] FALSE
D67V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    0  4
  PABPC1 WILD-TYPE  7 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    4
  PABPC1 WILD-TYPE    7   23
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(68) Variable = SCRT1 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  SCRT1 MUTATED    1  2
  SCRT1 WILD-TYPE 39 19
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              58 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              2              19 
$`SCRT1 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K9 TCGA-OR-A5L4 
       18.15        11.31        31.79 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68        22.98         8.32        24.62        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 
       44.84         4.11        58.55        60.89       152.15        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  SCRT1 MUTATED SCRT1 WILD-TYPE 
          11.31            4.11 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
          31.79          153.63 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
         18.150          42.905 
[1] "11.3 - 31.8 (18.1)" "4.1 - 153.6 (42.9)"
[1] "hr=" "4.7"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SCRT1 MUTATED         0        1         1        1
  SCRT1 WILD-TYPE       6       27        13       10
D68V3, multiclass
           clus
vv          SCRT1 MUTATED SCRT1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              27
  STAGE III             1              13
  STAGE IV              1              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
  SCRT1 MUTATED    0  1  0  2
  SCRT1 WILD-TYPE  6 31  7 12
D68V4, multiclass
    clus
vv   SCRT1 MUTATED SCRT1 WILD-TYPE
  T1             0               6
  T2             1              31
  T3             0               7
  T4             2              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"
D68V5, binary
                 cls
clus               0  1
  SCRT1 MUTATED    2  1
  SCRT1 WILD-TYPE 51  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      2    1
  SCRT1 WILD-TYPE   51    5
   clus
vv  SCRT1 MUTATED SCRT1 WILD-TYPE
  0             2              51
  1             1               5
[1] 2 2
[1] FALSE
D68V6, binary
                 cls
clus               0  1
  SCRT1 MUTATED    3  0
  SCRT1 WILD-TYPE 37 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      3    0
  SCRT1 WILD-TYPE   37   22
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  FEMALE             3              37
  MALE               0              22
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus               0  1
  SCRT1 MUTATED    0  1
  SCRT1 WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      0    1
  SCRT1 WILD-TYPE    7   26
                        clus
vv                       SCRT1 MUTATED SCRT1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(69) Variable = MAP1S MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2              0  1
  MAP1S MUTATED    3  2
  MAP1S WILD-TYPE 37 19
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              56 
  MAP1S MUTATED MAP1S WILD-TYPE 
              2              19 
$`MAP1S MUTATED`
TCGA-OR-A5JK TCGA-OR-A5JT TCGA-OR-A5KZ TCGA-OR-A5LJ TCGA-OR-A5LK 
       49.22        29.82         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        68.75        15.45        12.00        88.87 
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        69.37        46.82        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       44.84        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
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           41.95 
[1] "4.1 - 73.0 (36.3)"  "4.9 - 153.6 (42.0)"
[1] "hr=" "1.4"
D69V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MAP1S MUTATED         0        3         0        2
  MAP1S WILD-TYPE       6       25        14        9
D69V3, multiclass
           clus
vv          MAP1S MUTATED MAP1S WILD-TYPE
  STAGE I               0               6
  STAGE II              3              25
  STAGE III             0              14
  STAGE IV              2               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
  MAP1S MUTATED    0  4  0  1
  MAP1S WILD-TYPE  6 28  7 13
D69V4, multiclass
    clus
vv   MAP1S MUTATED MAP1S WILD-TYPE
  T1             0               6
  T2             4              28
  T3             0               7
  T4             1              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
  MAP1S MUTATED    4  1
  MAP1S WILD-TYPE 49  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      4    1
  MAP1S WILD-TYPE   49    5
   clus
vv  MAP1S MUTATED MAP1S WILD-TYPE
  0             4              49
  1             1               5
[1] 2 2
[1] FALSE
D69V6, binary
                 cls
clus               0  1
  MAP1S MUTATED    2  3
  MAP1S WILD-TYPE 38 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      2    3
  MAP1S WILD-TYPE   38   19
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  FEMALE             2              38
  MALE               3              19
[1] 2 2
[1] FALSE
D69V7, binary
                 cls
clus               0  1
  MAP1S MUTATED    0  2
  MAP1S WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      0    2
  MAP1S WILD-TYPE    7   25
                        clus
vv                       MAP1S MUTATED MAP1S WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(70) Variable = NF1 MUTATION ANALYSIS
D70V1, survival
               sevent
clus2            0  1
  NF1 MUTATED    4  3
  NF1 WILD-TYPE 36 18
  NF1 MUTATED NF1 WILD-TYPE 
            7            54 
  NF1 MUTATED NF1 WILD-TYPE 
            3            18 
$`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        72.39         4.11        23.64 
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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22        22.03        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L1 
       95.18       153.63       127.50        50.14        44.84        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 

  NF1 MUTATED NF1 WILD-TYPE 
         4.11          5.23 
  NF1 MUTATED NF1 WILD-TYPE 
        72.39        153.63 
  NF1 MUTATED NF1 WILD-TYPE 
       19.040        43.925 
[1] "4.1 - 72.4 (19.0)"  "5.2 - 153.6 (43.9)"
[1] "hr=" "2.1"
D70V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF1 MUTATED         0        4         1        1
  NF1 WILD-TYPE       6       24        13       10
D70V3, multiclass
           clus
vv          NF1 MUTATED NF1 WILD-TYPE
  STAGE I             0             6
  STAGE II            4            24
  STAGE III           1            13
  STAGE IV            1            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
  NF1 MUTATED    0  4  1  1
  NF1 WILD-TYPE  6 28  6 13
D70V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           0             6
  T2           4            28
  T3           1             6
  T4           1            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"
D70V5, binary
               cls
clus             0  1
  NF1 MUTATED    6  0
  NF1 WILD-TYPE 47  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6    0
  NF1 WILD-TYPE   47    6
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0           6            47
  1           0             6
[1] 2 2
[1] FALSE
D70V6, binary
               cls
clus             0  1
  NF1 MUTATED    1  6
  NF1 WILD-TYPE 39 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    6
  NF1 WILD-TYPE   39   16
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           1            39
  MALE             6            16
[1] 2 2
[1] FALSE
D70V7, binary
               cls
clus             0  1
  NF1 MUTATED    1  2
  NF1 WILD-TYPE  6 25
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    2
  NF1 WILD-TYPE    6   25
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           2            25
[1] 2 2
[1] FALSE

Clustering(71) Variable = AKAP2 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2              0  1
  AKAP2 MUTATED    2  2
  AKAP2 WILD-TYPE 38 19
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              4              57 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              2              19 
$`AKAP2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5LK 
       30.31        18.12        72.39        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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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 
          51.35           41.39 
[1] "18.1 - 73.0 (51.4)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.3"
D71V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  AKAP2 MUTATED         0        2         0        2
  AKAP2 WILD-TYPE       6       26        14        9
D71V3, multiclass
           clus
vv          AKAP2 MUTATED AKAP2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             0              14
  STAGE IV              2               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
  AKAP2 MUTATED    0  2  0  2
  AKAP2 WILD-TYPE  6 30  7 12
D71V4, multiclass
    clus
vv   AKAP2 MUTATED AKAP2 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             0               7
  T4             2              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
  AKAP2 MUTATED    4  0
  AKAP2 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      4    0
  AKAP2 WILD-TYPE   49    6
   clus
vv  AKAP2 MUTATED AKAP2 WILD-TYPE
  0             4              49
  1             0               6
[1] 2 2
[1] FALSE
D71V6, binary
                 cls
clus               0  1
  AKAP2 MUTATED    1  3
  AKAP2 WILD-TYPE 39 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      1    3
  AKAP2 WILD-TYPE   39   19
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  FEMALE             1              39
  MALE               3              19
[1] 2 2
[1] FALSE
D71V7, binary
                 cls
clus               0  1
  AKAP2 MUTATED    0  0
  AKAP2 WILD-TYPE  7 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      0    0
  AKAP2 WILD-TYPE    7   27

Clustering(72) Variable = NOTCH2 MUTATION ANALYSIS
D72V1, survival
                  sevent
clus2               0  1
  NOTCH2 MUTATED    4  1
  NOTCH2 WILD-TYPE 36 20
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               56 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               1               20 
$`NOTCH2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KB TCGA-OR-A5KU TCGA-OR-A5KV TCGA-PK-A5HB 
       19.04        24.36       153.63       127.50        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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        22.98         8.32        24.62        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       91.30        83.80        95.18        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       15.45       106.52 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           19.04             4.11 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          153.63           152.15 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          42.510           40.485 
[1] "19.0 - 153.6 (42.5)" "4.1 - 152.2 (40.5)" 
[1] "hr=" "2"  
D72V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NOTCH2 MUTATED         0        2         2        0
  NOTCH2 WILD-TYPE       6       26        12       11
D72V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               26
  STAGE III              2               12
  STAGE IV               0               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  3  1  0
  NOTCH2 WILD-TYPE  6 29  6 14
D72V4, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T1              0                6
  T2              3               29
  T3              1                6
  T4              0               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
  NOTCH2 MUTATED    3  1
  NOTCH2 WILD-TYPE 50  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    1
  NOTCH2 WILD-TYPE   50    5
   clus
vv  NOTCH2 MUTATED NOTCH2 WILD-TYPE
  0              3               50
  1              1                5
[1] 2 2
[1] FALSE
D72V6, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    3  2
  NOTCH2 WILD-TYPE 37 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    2
  NOTCH2 WILD-TYPE   37   20
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE              3               37
  MALE                2               20
[1] 2 2
[1] FALSE
D72V7, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    1  3
  NOTCH2 WILD-TYPE  6 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      1    3
  NOTCH2 WILD-TYPE    6   24
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               24
[1] 2 2
[1] FALSE

Clustering(73) Variable = FANK1 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2              0  1
  FANK1 MUTATED    3  1
  FANK1 WILD-TYPE 37 20
  FANK1 MUTATED FANK1 WILD-TYPE 
              4              57 
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              20 
$`FANK1 MUTATED`
TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5L5 TCGA-OR-A5LJ 
       24.36        95.18        43.30        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        83.80       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  FANK1 MUTATED FANK1 WILD-TYPE 
          24.36            4.11 
  FANK1 MUTATED FANK1 WILD-TYPE 
          95.18          153.63 
  FANK1 MUTATED FANK1 WILD-TYPE 
         39.815          41.390 
[1] "24.4 - 95.2 (39.8)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.4"
D73V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FANK1 MUTATED         2        1         0        1
  FANK1 WILD-TYPE       4       27        14       10
D73V3, multiclass
           clus
vv          FANK1 MUTATED FANK1 WILD-TYPE
  STAGE I               2               4
  STAGE II              1              27
  STAGE III             0              14
  STAGE IV              1              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
  FANK1 MUTATED    2  2  0  0
  FANK1 WILD-TYPE  4 30  7 14
D73V4, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  T1             2               4
  T2             2              30
  T3             0               7
  T4             0              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
  FANK1 MUTATED    3  1
  FANK1 WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      3    1
  FANK1 WILD-TYPE   50    5
   clus
vv  FANK1 MUTATED FANK1 WILD-TYPE
  0             3              50
  1             1               5
[1] 2 2
[1] FALSE
D73V6, binary
                 cls
clus               0  1
  FANK1 MUTATED    4  0
  FANK1 WILD-TYPE 36 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      4    0
  FANK1 WILD-TYPE   36   22
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  FEMALE             4              36
  MALE               0              22
[1] 2 2
[1] FALSE
D73V7, binary
                 cls
clus               0  1
  FANK1 MUTATED    0  4
  FANK1 WILD-TYPE  7 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      0    4
  FANK1 WILD-TYPE    7   23
                        clus
vv                       FANK1 MUTATED FANK1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(74) Variable = NEFH MUTATION ANALYSIS
D74V1, survival
                sevent
clus2             0  1
  NEFH MUTATED    3  3
  NEFH WILD-TYPE 37 18
  NEFH MUTATED NEFH WILD-TYPE 
             6             55 
  NEFH MUTATED NEFH WILD-TYPE 
             3             18 
$`NEFH MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5JP TCGA-OR-A5K2 TCGA-OR-A5KB TCGA-OR-A5KP 
       15.45        19.04         4.90        32.68        24.36        91.30 

$`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        68.75        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22        22.03        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        72.39        31.23        18.15        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.62        11.31        46.49        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  NEFH MUTATED NEFH WILD-TYPE 
          4.90           4.11 
  NEFH MUTATED NEFH WILD-TYPE 
         91.30         153.63 
  NEFH MUTATED NEFH WILD-TYPE 
          21.7           43.3 
[1] "4.9 - 91.3 (21.7)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "2.4"
D74V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         0        3         2        1
  NEFH WILD-TYPE       6       25        12       10
D74V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              0              6
  STAGE II             3             25
  STAGE III            2             12
  STAGE IV             1             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  3  2  1
  NEFH WILD-TYPE  6 29  5 13
D74V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0              6
  T2            3             29
  T3            2              5
  T4            1             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"
D74V5, binary
                cls
clus              0  1
  NEFH MUTATED    5  1
  NEFH WILD-TYPE 48  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      5    1
  NEFH WILD-TYPE   48    5
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            5             48
  1            1              5
[1] 2 2
[1] FALSE
D74V6, binary
                cls
clus              0  1
  NEFH MUTATED    4  2
  NEFH WILD-TYPE 36 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    2
  NEFH WILD-TYPE   36   20
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            4             36
  MALE              2             20
[1] 2 2
[1] FALSE
D74V7, binary
                cls
clus              0  1
  NEFH MUTATED    2  2
  NEFH WILD-TYPE  5 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    2
  NEFH WILD-TYPE    5   25
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                2              5
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE

Clustering(75) Variable = NPTX1 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2              0  1
  NPTX1 MUTATED    2  1
  NPTX1 WILD-TYPE 38 20
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              58 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              1              20 
$`NPTX1 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JV TCGA-OR-A5LC 
       46.82        66.51         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        68.75        15.45        12.00        88.87 
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        69.37        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
      121.25        29.82        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       43.30        28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           5.23            4.11 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          66.51          153.63 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
         46.820          40.485 
[1] "5.2 - 66.5 (46.8)"  "4.1 - 153.6 (40.5)"
[1] "hr=" "1"  
D75V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NPTX1 MUTATED         1        1         0        1
  NPTX1 WILD-TYPE       5       27        14       10
D75V3, multiclass
           clus
vv          NPTX1 MUTATED NPTX1 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              27
  STAGE III             0              14
  STAGE IV              1              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
  NPTX1 MUTATED    1  1  0  1
  NPTX1 WILD-TYPE  5 31  7 13
D75V4, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  T1             1               5
  T2             1              31
  T3             0               7
  T4             1              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"
D75V5, binary
                 cls
clus               0  1
  NPTX1 MUTATED    3  0
  NPTX1 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      3    0
  NPTX1 WILD-TYPE   50    6
   clus
vv  NPTX1 MUTATED NPTX1 WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D75V6, binary
                 cls
clus               0  1
  NPTX1 MUTATED    1  2
  NPTX1 WILD-TYPE 39 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      1    2
  NPTX1 WILD-TYPE   39   20
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  FEMALE             1              39
  MALE               2              20
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus               0  1
  NPTX1 MUTATED    0  1
  NPTX1 WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    1
  NPTX1 WILD-TYPE    7   26
                        clus
vv                       NPTX1 MUTATED NPTX1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(76) Variable = KBTBD13 MUTATION ANALYSIS
D76V1, survival
                   sevent
clus2                0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 33 19
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                52 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                2                19 
$`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        95.18       127.50 
TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LP 
       43.30        28.64        61.05 

$`KBTBD13 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        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 
       69.37        46.82        49.22        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        72.39        31.23        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      153.63        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
      152.15        31.79        28.31        23.64        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        69.11        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
             4.90              4.11 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
           127.50            153.63 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
           43.300            40.485 
[1] "4.9 - 127.5 (43.3)" "4.1 - 153.6 (40.5)"
[1] "hr=" "1.7"
D76V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  KBTBD13 MUTATED         3        3         1        2
  KBTBD13 WILD-TYPE       3       25        13        9
D76V3, multiclass
           clus
vv          KBTBD13 MUTATED KBTBD13 WILD-TYPE
  STAGE I                 3                 3
  STAGE II                3                25
  STAGE III               1                13
  STAGE IV                2                 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
  KBTBD13 MUTATED    3  4  1  1
  KBTBD13 WILD-TYPE  3 28  6 13
D76V4, multiclass
    clus
vv   KBTBD13 MUTATED KBTBD13 WILD-TYPE
  T1               3                 3
  T2               4                28
  T3               1                 6
  T4               1                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"
D76V5, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 46  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      7    2
  KBTBD13 WILD-TYPE   46    4
   clus
vv  KBTBD13 MUTATED KBTBD13 WILD-TYPE
  0               7                46
  1               2                 4
[1] 2 2
[1] FALSE
D76V6, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    8  1
  KBTBD13 WILD-TYPE 32 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      8    1
  KBTBD13 WILD-TYPE   32   21
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  FEMALE               8                32
  MALE                 1                21
[1] 2 2
[1] FALSE
D76V7, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    1  4
  KBTBD13 WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      1    4
  KBTBD13 WILD-TYPE    6   23
                        clus
vv                       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(77) Variable = RASIP1 MUTATION ANALYSIS
D77V1, survival
                  sevent
clus2               0  1
  RASIP1 MUTATED    2  4
  RASIP1 WILD-TYPE 38 17
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               6               55 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               4               17 
$`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 

$`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        68.75        15.45        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 
       29.82        66.51        72.39        31.23        18.15        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64        39.58        39.35        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  RASIP1 MUTATED RASIP1 WILD-TYPE 
            5.23             4.11 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          153.63           152.15 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          34.505           43.300 
[1] "5.2 - 153.6 (34.5)" "4.1 - 152.2 (43.3)"
[1] "hr=" "2.9"
D77V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RASIP1 MUTATED         0        2         2        2
  RASIP1 WILD-TYPE       6       26        12        9
D77V3, multiclass
           clus
vv          RASIP1 MUTATED RASIP1 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               26
  STAGE III              2               12
  STAGE IV               2                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  3
  RASIP1 WILD-TYPE  6 29  7 11
D77V4, multiclass
    clus
vv   RASIP1 MUTATED RASIP1 WILD-TYPE
  T1              0                6
  T2              3               29
  T3              0                7
  T4              3               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"
D77V5, binary
                  cls
clus                0  1
  RASIP1 MUTATED    5  1
  RASIP1 WILD-TYPE 48  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      5    1
  RASIP1 WILD-TYPE   48    5
   clus
vv  RASIP1 MUTATED RASIP1 WILD-TYPE
  0              5               48
  1              1                5
[1] 2 2
[1] FALSE
D77V6, binary
                  cls
clus                0  1
  RASIP1 MUTATED    5  1
  RASIP1 WILD-TYPE 35 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      5    1
  RASIP1 WILD-TYPE   35   21
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  FEMALE              5               35
  MALE                1               21
[1] 2 2
[1] FALSE
D77V7, binary
                  cls
clus                0  1
  RASIP1 MUTATED    1  3
  RASIP1 WILD-TYPE  6 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      1    3
  RASIP1 WILD-TYPE    6   24
                        clus
vv                       RASIP1 MUTATED RASIP1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               24
[1] 2 2
[1] FALSE

Clustering(78) Variable = AR MUTATION ANALYSIS
D78V1, survival
              sevent
clus2           0  1
  AR MUTATED    1  3
  AR WILD-TYPE 39 18
  AR MUTATED AR WILD-TYPE 
           4           57 
  AR MUTATED AR WILD-TYPE 
           3           18 
$`AR MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JH TCGA-OR-A5JY TCGA-OR-A5LD 
       30.31        69.37        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        68.75        15.45        12.00        88.87 
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        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        72.39        31.23        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  AR MUTATED AR WILD-TYPE 
       18.15         4.11 
  AR MUTATED AR WILD-TYPE 
       69.37       153.63 
  AR MUTATED AR WILD-TYPE 
       34.83        42.51 
[1] "18.1 - 69.4 (34.8)" "4.1 - 153.6 (42.5)"
[1] "hr=" "2.5"
D78V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV
  AR MUTATED         0        1         1        2
  AR WILD-TYPE       6       27        13        9
D78V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            0            6
  STAGE II           1           27
  STAGE III          1           13
  STAGE IV           2            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
  AR MUTATED    0  1  0  3
  AR WILD-TYPE  6 31  7 11
D78V4, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  T1          0            6
  T2          1           31
  T3          0            7
  T4          3           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"
D78V5, binary
              cls
clus            0  1
  AR MUTATED    3  1
  AR WILD-TYPE 50  5
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   50    5
   clus
vv  AR MUTATED AR WILD-TYPE
  0          3           50
  1          1            5
[1] 2 2
[1] FALSE
D78V6, binary
              cls
clus            0  1
  AR MUTATED    3  1
  AR WILD-TYPE 37 21
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   37   21
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          3           37
  MALE            1           21
[1] 2 2
[1] FALSE
D78V7, binary
              cls
clus            0  1
  AR MUTATED    0  1
  AR WILD-TYPE  7 26
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      0    1
  AR WILD-TYPE    7   26
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              0            7
  NOT HISPANIC OR LATINO          1           26
[1] 2 2
[1] FALSE

Clustering(79) Variable = KNDC1 MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2              0  1
  KNDC1 MUTATED    8  1
  KNDC1 WILD-TYPE 32 20
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              52 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              1              20 
$`KNDC1 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JT TCGA-OR-A5KP TCGA-OR-A5LA 
       41.39        46.82        22.03        29.82        91.30        23.64 
TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LR 
       36.33        69.11        28.04 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        49.22         4.90        36.26       121.25        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       72.39        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        11.31        24.36        46.49        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
       39.58         5.23        39.35        73.05        53.03        61.05 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  KNDC1 MUTATED KNDC1 WILD-TYPE 
          22.03            4.11 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
          91.30          153.63 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
         36.330          42.905 
[1] "22.0 - 91.3 (36.3)" "4.1 - 153.6 (42.9)"
[1] "hr=" "3.3"
D79V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KNDC1 MUTATED         2        6         0        1
  KNDC1 WILD-TYPE       4       22        14       10
D79V3, multiclass
           clus
vv          KNDC1 MUTATED KNDC1 WILD-TYPE
  STAGE I               2               4
  STAGE II              6              22
  STAGE III             0              14
  STAGE IV              1              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  7  0  0
  KNDC1 WILD-TYPE  4 25  7 14
D79V4, multiclass
    clus
vv   KNDC1 MUTATED KNDC1 WILD-TYPE
  T1             2               4
  T2             7              25
  T3             0               7
  T4             0              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 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      8    1
  KNDC1 WILD-TYPE   45    5
   clus
vv  KNDC1 MUTATED KNDC1 WILD-TYPE
  0             8              45
  1             1               5
[1] 2 2
[1] FALSE
D79V6, binary
                 cls
clus               0  1
  KNDC1 MUTATED    8  1
  KNDC1 WILD-TYPE 32 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      8    1
  KNDC1 WILD-TYPE   32   21
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  FEMALE             8              32
  MALE               1              21
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus               0  1
  KNDC1 MUTATED    0  3
  KNDC1 WILD-TYPE  7 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      0    3
  KNDC1 WILD-TYPE    7   24
                        clus
vv                       KNDC1 MUTATED KNDC1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              24
[1] 2 2
[1] FALSE

Clustering(80) Variable = SEZ6L2 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2               0  1
  SEZ6L2 MUTATED    6  2
  SEZ6L2 WILD-TYPE 34 19
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               53 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               2               19 
$`SEZ6L2 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KW 
       46.82        32.68        46.49        91.30        83.80        50.14 
TCGA-OR-A5LC TCGA-PA-A5YG 
        5.23        15.45 

$`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        68.75        15.45        12.00        88.87 
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        69.37        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KT 
       22.98         8.32        24.62        11.31        24.36        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      153.63       127.50        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5HB 
       61.05        28.04         6.81       106.52        42.51 

  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
            5.23             4.11 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
           91.30           153.63 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
          46.655           39.580 
[1] "5.2 - 91.3 (46.7)"  "4.1 - 153.6 (39.6)"
[1] "hr=" "1.4"
D80V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEZ6L2 MUTATED         1        3         2        2
  SEZ6L2 WILD-TYPE       5       25        12        9
D80V3, multiclass
           clus
vv          SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               25
  STAGE III              2               12
  STAGE IV               2                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
  SEZ6L2 MUTATED    1  4  0  3
  SEZ6L2 WILD-TYPE  5 28  7 11
D80V4, multiclass
    clus
vv   SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  T1              1                5
  T2              4               28
  T3              0                7
  T4              3               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"
D80V5, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    7  1
  SEZ6L2 WILD-TYPE 46  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      7    1
  SEZ6L2 WILD-TYPE   46    5
   clus
vv  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  0              7               46
  1              1                5
[1] 2 2
[1] FALSE
D80V6, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    5  3
  SEZ6L2 WILD-TYPE 35 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      5    3
  SEZ6L2 WILD-TYPE   35   19
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  FEMALE              5               35
  MALE                3               19
[1] 2 2
[1] FALSE
D80V7, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    0  6
  SEZ6L2 WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      0    6
  SEZ6L2 WILD-TYPE    7   21
                        clus
vv                       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              6               21
[1] 2 2
[1] FALSE

Clustering(81) Variable = VARS MUTATION ANALYSIS
D81V1, survival
                sevent
clus2             0  1
  VARS MUTATED    4  2
  VARS WILD-TYPE 36 19
  VARS MUTATED VARS WILD-TYPE 
             6             55 
  VARS MUTATED VARS WILD-TYPE 
             2             19 
$`VARS MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JW TCGA-OR-A5L9 TCGA-PK-A5HB 
       68.75        12.00        19.04        72.39        28.64        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        88.87        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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        22.03         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 
      106.52 

  VARS MUTATED VARS WILD-TYPE 
         12.00           4.11 
  VARS MUTATED VARS WILD-TYPE 
         72.39         153.63 
  VARS MUTATED VARS WILD-TYPE 
        35.575         41.390 
[1] "12.0 - 72.4 (35.6)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1"  
D81V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  VARS MUTATED         0        2         3        0
  VARS WILD-TYPE       6       26        11       11
D81V3, multiclass
           clus
vv          VARS MUTATED VARS WILD-TYPE
  STAGE I              0              6
  STAGE II             2             26
  STAGE III            3             11
  STAGE IV             0             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
  VARS MUTATED    0  2  2  1
  VARS WILD-TYPE  6 30  5 13
D81V4, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  T1            0              6
  T2            2             30
  T3            2              5
  T4            1             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"
D81V5, binary
                cls
clus              0  1
  VARS MUTATED    5  0
  VARS WILD-TYPE 48  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      5    0
  VARS WILD-TYPE   48    6
   clus
vv  VARS MUTATED VARS WILD-TYPE
  0            5             48
  1            0              6
[1] 2 2
[1] FALSE
D81V6, binary
                cls
clus              0  1
  VARS MUTATED    2  4
  VARS WILD-TYPE 38 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      2    4
  VARS WILD-TYPE   38   18
        clus
vv       VARS MUTATED VARS WILD-TYPE
  FEMALE            2             38
  MALE              4             18
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus              0  1
  VARS MUTATED    3  1
  VARS WILD-TYPE  4 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      3    1
  VARS WILD-TYPE    4   26
                        clus
vv                       VARS MUTATED VARS WILD-TYPE
  HISPANIC OR LATINO                3              4
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(82) Variable = IER5 MUTATION ANALYSIS
D82V1, survival
                sevent
clus2             0  1
  IER5 MUTATED    0  2
  IER5 WILD-TYPE 40 19
  IER5 MUTATED IER5 WILD-TYPE 
             2             59 
  IER5 MUTATED IER5 WILD-TYPE 
             2             19 
$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       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         42.510 
[1] "18.1 - 32.7 (25.4)" "4.1 - 153.6 (42.5)"
[1] "Remove cluster labels:" "IER5 MUTATED"          
D82V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IER5 MUTATED         0        0         1        2
  IER5 WILD-TYPE       6       28        13        9
D82V3, multiclass
           clus
vv          IER5 MUTATED IER5 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             28
  STAGE III            1             13
  STAGE IV             2              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
  IER5 MUTATED    0  0  0  3
  IER5 WILD-TYPE  6 32  7 11
D82V4, multiclass
    clus
vv   IER5 MUTATED IER5 WILD-TYPE
  T1            0              6
  T2            0             32
  T3            0              7
  T4            3             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"
D82V5, binary
                cls
clus              0  1
  IER5 MUTATED    2  1
  IER5 WILD-TYPE 51  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      2    1
  IER5 WILD-TYPE   51    5
   clus
vv  IER5 MUTATED IER5 WILD-TYPE
  0            2             51
  1            1              5
[1] 2 2
[1] FALSE
D82V6, binary
                cls
clus              0  1
  IER5 MUTATED    3  0
  IER5 WILD-TYPE 37 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      3    0
  IER5 WILD-TYPE   37   22
        clus
vv       IER5 MUTATED IER5 WILD-TYPE
  FEMALE            3             37
  MALE              0             22
[1] 2 2
[1] FALSE
D82V7, binary
                cls
clus              0  1
  IER5 MUTATED    0  1
  IER5 WILD-TYPE  7 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      0    1
  IER5 WILD-TYPE    7   26
                        clus
vv                       IER5 MUTATED IER5 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(83) Variable = NMU MUTATION ANALYSIS
D83V1, survival
               sevent
clus2            0  1
  NMU MUTATED    3  2
  NMU WILD-TYPE 37 19
  NMU MUTATED NMU WILD-TYPE 
            5            56 
  NMU MUTATED NMU WILD-TYPE 
            2            19 
$`NMU MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JF TCGA-OR-A5JT TCGA-OR-A5KB TCGA-P6-A5OF 
       15.45        41.39        29.82        24.36         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        68.75        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
        8.32        24.62        11.31        46.49        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.14        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       73.05        53.03        69.11        61.05        28.04        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      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 
       24.360        43.925 
[1] "6.8 - 41.4 (24.4)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "2.4"
D83V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NMU MUTATED         0        3         1        1
  NMU WILD-TYPE       6       25        13       10
D83V3, multiclass
           clus
vv          NMU MUTATED NMU WILD-TYPE
  STAGE I             0             6
  STAGE II            3            25
  STAGE III           1            13
  STAGE IV            1            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
  NMU MUTATED    0  3  1  1
  NMU WILD-TYPE  6 29  6 13
D83V4, multiclass
    clus
vv   NMU MUTATED NMU WILD-TYPE
  T1           0             6
  T2           3            29
  T3           1             6
  T4           1            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
  NMU MUTATED    4  1
  NMU WILD-TYPE 49  5
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      4    1
  NMU WILD-TYPE   49    5
   clus
vv  NMU MUTATED NMU WILD-TYPE
  0           4            49
  1           1             5
[1] 2 2
[1] FALSE
D83V6, binary
               cls
clus             0  1
  NMU MUTATED    5  0
  NMU WILD-TYPE 35 22
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      5    0
  NMU WILD-TYPE   35   22
        clus
vv       NMU MUTATED NMU WILD-TYPE
  FEMALE           5            35
  MALE             0            22
[1] 2 2
[1] FALSE
D83V7, binary
               cls
clus             0  1
  NMU MUTATED    1  2
  NMU WILD-TYPE  6 25
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      1    2
  NMU WILD-TYPE    6   25
                        clus
vv                       NMU MUTATED NMU WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           2            25
[1] 2 2
[1] FALSE

Clustering(84) Variable = TMEM189 MUTATION ANALYSIS
D84V1, survival
                   sevent
clus2                0  1
  TMEM189 MUTATED    1  1
  TMEM189 WILD-TYPE 39 20
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                59 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                1                20 
$`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        68.75        15.45        12.00        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       50.14        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        28.31        28.64        23.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        15.45       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             39.58 
[1] "42.5 - 55.1 (48.8)" "4.1 - 153.6 (39.6)"
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
D84V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TMEM189 MUTATED         0        0         0        2
  TMEM189 WILD-TYPE       6       28        14        9
D84V3, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                57 
       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-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KB        TCGA-OR-A5KO        TCGA-OR-A5KP        TCGA-OR-A5KS 
"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-A5L1        TCGA-OR-A5L2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L3        TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L9        TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LD        TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  TMEM189 MUTATED    0  0  1  1
  TMEM189 WILD-TYPE  6 32  6 13
D84V4, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                57 
       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-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KB        TCGA-OR-A5KO        TCGA-OR-A5KP        TCGA-OR-A5KS 
"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-A5L1        TCGA-OR-A5L2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L3        TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L9        TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LD        TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" 
D84V5, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  0
  TMEM189 WILD-TYPE 51  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    0
  TMEM189 WILD-TYPE   51    6
   clus
vv  TMEM189 MUTATED TMEM189 WILD-TYPE
  0               2                51
  1               0                 6
[1] 2 2
[1] FALSE
D84V6, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  1
  TMEM189 WILD-TYPE 38 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    1
  TMEM189 WILD-TYPE   38   21
        clus
vv       TMEM189 MUTATED TMEM189 WILD-TYPE
  FEMALE               2                38
  MALE                 1                21
[1] 2 2
[1] FALSE
D84V7, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    1  1
  TMEM189 WILD-TYPE  6 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      1    1
  TMEM189 WILD-TYPE    6   26
                        clus
vv                       TMEM189 MUTATED TMEM189 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(85) Variable = ADAD2 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2              0  1
  ADAD2 MUTATED    3  1
  ADAD2 WILD-TYPE 37 20
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              57 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              1              20 
$`ADAD2 MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JQ TCGA-OR-A5K8 TCGA-PK-A5HB 
       18.12        36.26        24.62        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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       22.98         8.32        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        15.45       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 
          30.44           43.30 
[1] "18.1 - 42.5 (30.4)" "4.1 - 153.6 (43.3)"
[1] "hr=" "1"  
D85V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ADAD2 MUTATED         0        2         0        1
  ADAD2 WILD-TYPE       6       26        14       10
D85V3, multiclass
           clus
vv          ADAD2 MUTATED ADAD2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             0              14
  STAGE IV              1              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
  ADAD2 MUTATED    0  2  0  1
  ADAD2 WILD-TYPE  6 30  7 13
D85V4, multiclass
    clus
vv   ADAD2 MUTATED ADAD2 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             0               7
  T4             1              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"
D85V5, binary
                 cls
clus               0  1
  ADAD2 MUTATED    3  0
  ADAD2 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      3    0
  ADAD2 WILD-TYPE   50    6
   clus
vv  ADAD2 MUTATED ADAD2 WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D85V6, binary
                 cls
clus               0  1
  ADAD2 MUTATED    1  3
  ADAD2 WILD-TYPE 39 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      1    3
  ADAD2 WILD-TYPE   39   19
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  FEMALE             1              39
  MALE               3              19
[1] 2 2
[1] FALSE
D85V7, binary
                 cls
clus               0  1
  ADAD2 MUTATED    0  1
  ADAD2 WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      0    1
  ADAD2 WILD-TYPE    7   26
                        clus
vv                       ADAD2 MUTATED ADAD2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(86) Variable = PLEC MUTATION ANALYSIS
D86V1, survival
                sevent
clus2             0  1
  PLEC MUTATED   10  2
  PLEC WILD-TYPE 30 19
  PLEC MUTATED PLEC WILD-TYPE 
            12             49 
  PLEC MUTATED PLEC WILD-TYPE 
             2             19 
$`PLEC MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       68.75        49.22        22.03        22.98         8.32        24.62 
TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KW TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       24.36        91.30        50.14        28.64        23.64         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        88.87        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 
       69.37        46.82         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K9 
       66.51        72.39        31.23        18.15        32.68        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX 
       46.49        83.80        95.18       153.63       127.50        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       28.31        39.58        39.35        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       69.11        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  PLEC MUTATED PLEC WILD-TYPE 
          5.23           4.11 
  PLEC MUTATED PLEC WILD-TYPE 
         91.30         153.63 
  PLEC MUTATED PLEC WILD-TYPE 
         24.49          43.30 
[1] "5.2 - 91.3 (24.5)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "1.7"
D86V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PLEC MUTATED         1        5         4        3
  PLEC WILD-TYPE       5       23        10        8
D86V3, multiclass
           clus
vv          PLEC MUTATED PLEC WILD-TYPE
  STAGE I              1              5
  STAGE II             5             23
  STAGE III            4             10
  STAGE IV             3              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
  PLEC MUTATED    1  6  2  4
  PLEC WILD-TYPE  5 26  5 10
D86V4, multiclass
    clus
vv   PLEC MUTATED PLEC WILD-TYPE
  T1            1              5
  T2            6             26
  T3            2              5
  T4            4             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"
D86V5, binary
                cls
clus              0  1
  PLEC MUTATED   12  1
  PLEC WILD-TYPE 41  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED     12    1
  PLEC WILD-TYPE   41    5
   clus
vv  PLEC MUTATED PLEC WILD-TYPE
  0           12             41
  1            1              5
[1] 2 2
[1] FALSE
D86V6, binary
                cls
clus              0  1
  PLEC MUTATED   11  2
  PLEC WILD-TYPE 29 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED     11    2
  PLEC WILD-TYPE   29   20
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  FEMALE           11             29
  MALE              2             20
[1] 2 2
[1] FALSE
D86V7, binary
                cls
clus              0  1
  PLEC MUTATED    1  8
  PLEC WILD-TYPE  6 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      1    8
  PLEC WILD-TYPE    6   19
                        clus
vv                       PLEC MUTATED PLEC WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            8             19
[1] 2 2
[1] FALSE

Clustering(87) Variable = RGMB MUTATION ANALYSIS
D87V1, survival
                sevent
clus2             0  1
  RGMB MUTATED    4  1
  RGMB WILD-TYPE 36 20
  RGMB MUTATED RGMB WILD-TYPE 
             5             56 
  RGMB MUTATED RGMB WILD-TYPE 
             1             20 
$`RGMB MUTATED`
TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 
       24.62        83.80        44.84        58.55        60.89 

$`RGMB WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       18.15        32.68        22.98         8.32        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
        4.11       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  RGMB MUTATED RGMB WILD-TYPE 
         24.62           4.11 
  RGMB MUTATED RGMB WILD-TYPE 
         83.80         153.63 
  RGMB MUTATED RGMB WILD-TYPE 
        58.550         39.465 
[1] "24.6 - 83.8 (58.5)" "4.1 - 153.6 (39.5)"
[1] "hr=" "2.4"
D87V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RGMB MUTATED         0        4         1        1
  RGMB WILD-TYPE       6       24        13       10
D87V3, multiclass
           clus
vv          RGMB MUTATED RGMB WILD-TYPE
  STAGE I              0              6
  STAGE II             4             24
  STAGE III            1             13
  STAGE IV             1             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
  RGMB MUTATED    0  5  0  1
  RGMB WILD-TYPE  6 27  7 13
D87V4, multiclass
    clus
vv   RGMB MUTATED RGMB WILD-TYPE
  T1            0              6
  T2            5             27
  T3            0              7
  T4            1             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"
D87V5, binary
                cls
clus              0  1
  RGMB MUTATED    5  1
  RGMB WILD-TYPE 48  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      5    1
  RGMB WILD-TYPE   48    5
   clus
vv  RGMB MUTATED RGMB WILD-TYPE
  0            5             48
  1            1              5
[1] 2 2
[1] FALSE
D87V6, binary
                cls
clus              0  1
  RGMB MUTATED    4  2
  RGMB WILD-TYPE 36 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      4    2
  RGMB WILD-TYPE   36   20
        clus
vv       RGMB MUTATED RGMB WILD-TYPE
  FEMALE            4             36
  MALE              2             20
[1] 2 2
[1] FALSE
D87V7, binary
                cls
clus              0  1
  RGMB MUTATED    0  6
  RGMB WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      0    6
  RGMB WILD-TYPE    7   21
                        clus
vv                       RGMB MUTATED RGMB WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            6             21
[1] 2 2
[1] FALSE

Clustering(88) Variable = CLIC6 MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2              0  1
  CLIC6 MUTATED    4  1
  CLIC6 WILD-TYPE 36 20
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              56 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              1              20 
$`CLIC6 MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5L3 TCGA-OR-A5LC 
       88.87        83.80       153.63       152.15         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        68.75        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        91.30        95.18       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64        39.58        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  CLIC6 MUTATED CLIC6 WILD-TYPE 
           5.23            4.11 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
         153.63          127.50 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
         88.870          39.465 
[1] "5.2 - 153.6 (88.9)" "4.1 - 127.5 (39.5)"
[1] "hr=" "2.6"
D88V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CLIC6 MUTATED         1        3         0        1
  CLIC6 WILD-TYPE       5       25        14       10
D88V3, multiclass
           clus
vv          CLIC6 MUTATED CLIC6 WILD-TYPE
  STAGE I               1               5
  STAGE II              3              25
  STAGE III             0              14
  STAGE IV              1              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
  CLIC6 MUTATED    1  3  0  1
  CLIC6 WILD-TYPE  5 29  7 13
D88V4, multiclass
    clus
vv   CLIC6 MUTATED CLIC6 WILD-TYPE
  T1             1               5
  T2             3              29
  T3             0               7
  T4             1              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"
D88V5, binary
                 cls
clus               0  1
  CLIC6 MUTATED    5  0
  CLIC6 WILD-TYPE 48  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      5    0
  CLIC6 WILD-TYPE   48    6
   clus
vv  CLIC6 MUTATED CLIC6 WILD-TYPE
  0             5              48
  1             0               6
[1] 2 2
[1] FALSE
D88V6, binary
                 cls
clus               0  1
  CLIC6 MUTATED    4  1
  CLIC6 WILD-TYPE 36 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      4    1
  CLIC6 WILD-TYPE   36   21
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  FEMALE             4              36
  MALE               1              21
[1] 2 2
[1] FALSE
D88V7, binary
                 cls
clus               0  1
  CLIC6 MUTATED    1  4
  CLIC6 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      1    4
  CLIC6 WILD-TYPE    6   23
                        clus
vv                       CLIC6 MUTATED CLIC6 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(89) Variable = ZNF814 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2               0  1
  ZNF814 MUTATED    1  1
  ZNF814 WILD-TYPE 39 20
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               59 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               20 
$`ZNF814 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JR 
       30.31       121.25 

$`ZNF814 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       106.52        42.51 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
           30.31             4.11 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          121.25           153.63 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           75.78            41.39 
[1] "30.3 - 121.2 (75.8)" "4.1 - 153.6 (41.4)" 
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
D89V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         1        0         0        2
  ZNF814 WILD-TYPE       5       28        14        9
D89V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                1                5
  STAGE II               0               28
  STAGE III              0               14
  STAGE IV               2                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
  ZNF814 MUTATED    1  0  0  2
  ZNF814 WILD-TYPE  5 32  7 12
D89V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              1                5
  T2              0               32
  T3              0                7
  T4              2               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"
D89V5, binary
                  cls
clus                0  1
  ZNF814 MUTATED    3  0
  ZNF814 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3    0
  ZNF814 WILD-TYPE   50    6
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              3               50
  1              0                6
[1] 2 2
[1] FALSE
D89V6, binary
                  cls
clus                0  1
  ZNF814 MUTATED    2  1
  ZNF814 WILD-TYPE 38 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      2    1
  ZNF814 WILD-TYPE   38   21
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              2               38
  MALE                1               21
[1] 2 2
[1] FALSE
D89V7, binary
                  cls
clus                0  1
  ZNF814 MUTATED    0  1
  ZNF814 WILD-TYPE  7 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    1
  ZNF814 WILD-TYPE    7   26
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              1               26
[1] 2 2
[1] FALSE

Clustering(90) Variable = DSPP MUTATION ANALYSIS
D90V1, survival
                sevent
clus2             0  1
  DSPP MUTATED    6  3
  DSPP WILD-TYPE 34 18
  DSPP MUTATED DSPP WILD-TYPE 
             9             52 
  DSPP MUTATED DSPP WILD-TYPE 
             3             18 
$`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        44.84       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LL 
       28.31        28.64        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        68.75        15.45        12.00        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KZ 
       91.30        83.80        95.18       153.63       127.50         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       58.55        60.89        43.30        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  DSPP MUTATED DSPP WILD-TYPE 
         18.12           4.11 
  DSPP MUTATED DSPP WILD-TYPE 
        152.15         153.63 
  DSPP MUTATED DSPP WILD-TYPE 
        44.840         40.485 
[1] "18.1 - 152.2 (44.8)" "4.1 - 153.6 (40.5)" 
[1] "hr=" "1"  
D90V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DSPP MUTATED         1        3         3        2
  DSPP WILD-TYPE       5       25        11        9
D90V3, multiclass
           clus
vv          DSPP MUTATED DSPP WILD-TYPE
  STAGE I              1              5
  STAGE II             3             25
  STAGE III            3             11
  STAGE IV             2              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
  DSPP MUTATED    1  5  1  2
  DSPP WILD-TYPE  5 27  6 12
D90V4, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  T1            1              5
  T2            5             27
  T3            1              6
  T4            2             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"
D90V5, binary
                cls
clus              0  1
  DSPP MUTATED    7  2
  DSPP WILD-TYPE 46  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    2
  DSPP WILD-TYPE   46    4
   clus
vv  DSPP MUTATED DSPP WILD-TYPE
  0            7             46
  1            2              4
[1] 2 2
[1] FALSE
D90V6, binary
                cls
clus              0  1
  DSPP MUTATED    7  2
  DSPP WILD-TYPE 33 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    2
  DSPP WILD-TYPE   33   20
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  FEMALE            7             33
  MALE              2             20
[1] 2 2
[1] FALSE
D90V7, binary
                cls
clus              0  1
  DSPP MUTATED    1  6
  DSPP WILD-TYPE  6 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      1    6
  DSPP WILD-TYPE    6   21
                        clus
vv                       DSPP MUTATED DSPP WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            6             21
[1] 2 2
[1] FALSE

Clustering(91) Variable = AMDHD1 MUTATION ANALYSIS
D91V1, survival
                  sevent
clus2               0  1
  AMDHD1 MUTATED    6  3
  AMDHD1 WILD-TYPE 34 18
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               9               52 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               3               18 
$`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        72.39        11.31 
TCGA-OR-A5L6 TCGA-OR-A5LO TCGA-PK-A5HB 
       28.31        69.11        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        68.75        15.45        12.00        88.87 
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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15        32.68        22.98         8.32        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
      152.15        31.79        43.30        28.64        23.64        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        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        15.45       106.52 

  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           11.31             4.11 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           72.39           153.63 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
          28.310           43.925 
[1] "11.3 - 72.4 (28.3)" "4.1 - 153.6 (43.9)"
[1] "hr=" "1.1"
D91V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AMDHD1 MUTATED         1        5         1        2
  AMDHD1 WILD-TYPE       5       23        13        9
D91V3, multiclass
           clus
vv          AMDHD1 MUTATED AMDHD1 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               23
  STAGE III              1               13
  STAGE IV               2                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
  AMDHD1 MUTATED    1  5  1  2
  AMDHD1 WILD-TYPE  5 27  6 12
D91V4, multiclass
    clus
vv   AMDHD1 MUTATED AMDHD1 WILD-TYPE
  T1              1                5
  T2              5               27
  T3              1                6
  T4              2               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"
D91V5, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    9  0
  AMDHD1 WILD-TYPE 44  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      9    0
  AMDHD1 WILD-TYPE   44    6
   clus
vv  AMDHD1 MUTATED AMDHD1 WILD-TYPE
  0              9               44
  1              0                6
[1] 2 2
[1] FALSE
D91V6, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    5  5
  AMDHD1 WILD-TYPE 35 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      5    5
  AMDHD1 WILD-TYPE   35   17
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  FEMALE              5               35
  MALE                5               17
[1] 2 2
[1] FALSE
D91V7, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    1  2
  AMDHD1 WILD-TYPE  6 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      1    2
  AMDHD1 WILD-TYPE    6   25
                        clus
vv                       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(92) Variable = CRIPAK MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED    8  2
  CRIPAK WILD-TYPE 32 19
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               51 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               2               19 
$`CRIPAK MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KZ 
       88.87        22.03        24.62        11.31        46.49         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LR 
       58.55        28.31        28.64        28.04 

$`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        68.75        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 
       69.37        46.82        49.22         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       22.98         8.32        24.36        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 
      153.63       127.50        50.14        44.84        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        43.30        23.64        39.58         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-P6-A5OF 
       36.33        73.05        53.03        69.11        61.05         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            4.11             4.90 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           88.87           153.63 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          28.175           43.300 
[1] "4.1 - 88.9 (28.2)"  "4.9 - 153.6 (43.3)"
[1] "hr=" "1.3"
D92V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CRIPAK MUTATED         1        8         0        1
  CRIPAK WILD-TYPE       5       20        14       10
D92V3, multiclass
           clus
vv          CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                1                5
  STAGE II               8               20
  STAGE III              0               14
  STAGE IV               1               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
  CRIPAK MUTATED    1  8  0  1
  CRIPAK WILD-TYPE  5 24  7 13
D92V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              1                5
  T2              8               24
  T3              0                7
  T4              1               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"
D92V5, binary
                  cls
clus                0  1
  CRIPAK MUTATED   10  0
  CRIPAK WILD-TYPE 43  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     10    0
  CRIPAK WILD-TYPE   43    6
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0             10               43
  1              0                6
[1] 2 2
[1] FALSE
D92V6, binary
                  cls
clus                0  1
  CRIPAK MUTATED    7  3
  CRIPAK WILD-TYPE 33 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      7    3
  CRIPAK WILD-TYPE   33   19
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE              7               33
  MALE                3               19
[1] 2 2
[1] FALSE
D92V7, binary
                  cls
clus                0  1
  CRIPAK MUTATED    1  6
  CRIPAK WILD-TYPE  6 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      1    6
  CRIPAK WILD-TYPE    6   21
                        clus
vv                       CRIPAK MUTATED CRIPAK WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              6               21
[1] 2 2
[1] FALSE

Clustering(93) Variable = NOM1 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  NOM1 MUTATED    4  2
  NOM1 WILD-TYPE 36 19
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             55 
  NOM1 MUTATED NOM1 WILD-TYPE 
             2             19 
$`NOM1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5KB TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5LP 
       12.00        24.36         4.11       152.15        43.30        61.05 

$`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        68.75        15.45        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        22.98         8.32        24.62        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       44.84        58.55        60.89        31.79        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       53.03        69.11        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  NOM1 MUTATED NOM1 WILD-TYPE 
          4.11           4.90 
  NOM1 MUTATED NOM1 WILD-TYPE 
        152.15         153.63 
  NOM1 MUTATED NOM1 WILD-TYPE 
         33.83          41.39 
[1] "4.1 - 152.2 (33.8)" "4.9 - 153.6 (41.4)"
[1] "hr=" "1.1"
D93V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NOM1 MUTATED         2        3         1        0
  NOM1 WILD-TYPE       4       25        13       11
D93V3, multiclass
           clus
vv          NOM1 MUTATED NOM1 WILD-TYPE
  STAGE I              2              4
  STAGE II             3             25
  STAGE III            1             13
  STAGE IV             0             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
  NOM1 MUTATED    2  3  0  1
  NOM1 WILD-TYPE  4 29  7 13
D93V4, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  T1            2              4
  T2            3             29
  T3            0              7
  T4            1             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"
D93V5, binary
                cls
clus              0  1
  NOM1 MUTATED    6  0
  NOM1 WILD-TYPE 47  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      6    0
  NOM1 WILD-TYPE   47    6
   clus
vv  NOM1 MUTATED NOM1 WILD-TYPE
  0            6             47
  1            0              6
[1] 2 2
[1] FALSE
D93V6, binary
                cls
clus              0  1
  NOM1 MUTATED    4  2
  NOM1 WILD-TYPE 36 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      4    2
  NOM1 WILD-TYPE   36   20
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  FEMALE            4             36
  MALE              2             20
[1] 2 2
[1] FALSE
D93V7, binary
                cls
clus              0  1
  NOM1 MUTATED    1  4
  NOM1 WILD-TYPE  6 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      1    4
  NOM1 WILD-TYPE    6   23
                        clus
vv                       NOM1 MUTATED NOM1 WILD-TYPE
  HISPANIC OR LATINO                1              6
  NOT HISPANIC OR LATINO            4             23
[1] 2 2
[1] FALSE

Clustering(94) Variable = MAP7 MUTATION ANALYSIS
D94V1, survival
                sevent
clus2             0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 38 20
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             58 
  MAP7 MUTATED MAP7 WILD-TYPE 
             1             20 
$`MAP7 MUTATED`
TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5LA 
       66.51        32.68        23.64 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26       121.25        29.82        72.39        31.23        18.15 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        28.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  MAP7 MUTATED MAP7 WILD-TYPE 
         23.64           4.11 
  MAP7 MUTATED MAP7 WILD-TYPE 
         66.51         153.63 
  MAP7 MUTATED MAP7 WILD-TYPE 
         32.68          41.95 
[1] "23.6 - 66.5 (32.7)" "4.1 - 153.6 (42.0)"
[1] "hr=" "1"  
D94V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAP7 MUTATED         0        2         1        0
  MAP7 WILD-TYPE       6       26        13       11
D94V3, multiclass
           clus
vv          MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             26
  STAGE III            1             13
  STAGE IV             0             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
  MAP7 MUTATED    0  2  0  1
  MAP7 WILD-TYPE  6 30  7 13
D94V4, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            0              6
  T2            2             30
  T3            0              7
  T4            1             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
  MAP7 MUTATED    3  0
  MAP7 WILD-TYPE 50  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      3    0
  MAP7 WILD-TYPE   50    6
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0            3             50
  1            0              6
[1] 2 2
[1] FALSE
D94V6, binary
                cls
clus              0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 38 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      2    1
  MAP7 WILD-TYPE   38   21
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  FEMALE            2             38
  MALE              1             21
[1] 2 2
[1] FALSE
D94V7, binary
                cls
clus              0  1
  MAP7 MUTATED    0  1
  MAP7 WILD-TYPE  7 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      0    1
  MAP7 WILD-TYPE    7   26
                        clus
vv                       MAP7 MUTATED MAP7 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(95) Variable = PTX4 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2             0  1
  PTX4 MUTATED    0  3
  PTX4 WILD-TYPE 40 18
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             58 
  PTX4 MUTATED PTX4 WILD-TYPE 
             3             18 
$`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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        49.22        22.03         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       43.30        28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       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         42.905 
[1] "5.2 - 30.3 (18.1)"  "4.1 - 153.6 (42.9)"
[1] "hr=" "9.3"
D95V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTX4 MUTATED         0        0         0        3
  PTX4 WILD-TYPE       6       28        14        8
D95V3, multiclass
           clus
vv          PTX4 MUTATED PTX4 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             28
  STAGE III            0             14
  STAGE IV             3              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
  PTX4 MUTATED    0  0  0  3
  PTX4 WILD-TYPE  6 32  7 11
D95V4, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  T1            0              6
  T2            0             32
  T3            0              7
  T4            3             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"
D95V5, binary
                cls
clus              0  1
  PTX4 MUTATED    3  0
  PTX4 WILD-TYPE 50  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      3    0
  PTX4 WILD-TYPE   50    6
   clus
vv  PTX4 MUTATED PTX4 WILD-TYPE
  0            3             50
  1            0              6
[1] 2 2
[1] FALSE
D95V6, binary
                cls
clus              0  1
  PTX4 MUTATED    2  1
  PTX4 WILD-TYPE 38 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      2    1
  PTX4 WILD-TYPE   38   21
        clus
vv       PTX4 MUTATED PTX4 WILD-TYPE
  FEMALE            2             38
  MALE              1             21
[1] 2 2
[1] FALSE
D95V7, binary
                cls
clus              0  1
  PTX4 MUTATED    0  1
  PTX4 WILD-TYPE  7 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      0    1
  PTX4 WILD-TYPE    7   26
                        clus
vv                       PTX4 MUTATED PTX4 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(96) Variable = LRP11 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2              0  1
  LRP11 MUTATED    4  2
  LRP11 WILD-TYPE 36 19
  LRP11 MUTATED LRP11 WILD-TYPE 
              6              55 
  LRP11 MUTATED LRP11 WILD-TYPE 
              2              19 
$`LRP11 MUTATED`
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5L1 TCGA-OR-A5L6 TCGA-P6-A5OF TCGA-PK-A5HB 
       24.62        11.31        58.55        28.31         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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KO 
       18.15        32.68        22.98         8.32        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       44.84         4.11        60.89       152.15        31.79        43.30 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       73.05        53.03        69.11        61.05        28.04        15.45 
TCGA-PK-A5H8 
      106.52 

  LRP11 MUTATED LRP11 WILD-TYPE 
           6.81            4.11 
  LRP11 MUTATED LRP11 WILD-TYPE 
          58.55          153.63 
  LRP11 MUTATED LRP11 WILD-TYPE 
         26.465          43.300 
[1] "6.8 - 58.5 (26.5)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "1.5"
D96V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRP11 MUTATED         0        4         1        0
  LRP11 WILD-TYPE       6       24        13       11
D96V3, multiclass
           clus
vv          LRP11 MUTATED LRP11 WILD-TYPE
  STAGE I               0               6
  STAGE II              4              24
  STAGE III             1              13
  STAGE IV              0              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
  LRP11 MUTATED    0  4  0  1
  LRP11 WILD-TYPE  6 28  7 13
D96V4, multiclass
    clus
vv   LRP11 MUTATED LRP11 WILD-TYPE
  T1             0               6
  T2             4              28
  T3             0               7
  T4             1              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
  LRP11 MUTATED    5  0
  LRP11 WILD-TYPE 48  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      5    0
  LRP11 WILD-TYPE   48    6
   clus
vv  LRP11 MUTATED LRP11 WILD-TYPE
  0             5              48
  1             0               6
[1] 2 2
[1] FALSE
D96V6, binary
                 cls
clus               0  1
  LRP11 MUTATED    3  3
  LRP11 WILD-TYPE 37 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      3    3
  LRP11 WILD-TYPE   37   19
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  FEMALE             3              37
  MALE               3              19
[1] 2 2
[1] FALSE
D96V7, binary
                 cls
clus               0  1
  LRP11 MUTATED    0  4
  LRP11 WILD-TYPE  7 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      0    4
  LRP11 WILD-TYPE    7   23
                        clus
vv                       LRP11 MUTATED LRP11 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             4              23
[1] 2 2
[1] FALSE

Clustering(97) Variable = PDCD6 MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2              0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 38 20
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              58 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              1              20 
$`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        68.75        12.00        88.87        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 
       69.37        46.82        49.22         4.90        36.26        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       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           41.95 
[1] "15.4 - 121.2 (22.0)" "4.1 - 153.6 (42.0)" 
[1] "hr=" "1.1"
D97V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PDCD6 MUTATED         2        0         0        1
  PDCD6 WILD-TYPE       4       28        14       10
D97V3, multiclass
           clus
vv          PDCD6 MUTATED PDCD6 WILD-TYPE
  STAGE I               2               4
  STAGE II              0              28
  STAGE III             0              14
  STAGE IV              1              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
  PDCD6 MUTATED    2  0  1  0
  PDCD6 WILD-TYPE  4 32  6 14
D97V4, multiclass
    clus
vv   PDCD6 MUTATED PDCD6 WILD-TYPE
  T1             2               4
  T2             0              32
  T3             1               6
  T4             0              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
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 51  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      2    1
  PDCD6 WILD-TYPE   51    5
   clus
vv  PDCD6 MUTATED PDCD6 WILD-TYPE
  0             2              51
  1             1               5
[1] 2 2
[1] FALSE
D97V6, binary
                 cls
clus               0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 38 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      2    1
  PDCD6 WILD-TYPE   38   21
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  FEMALE             2              38
  MALE               1              21
[1] 2 2
[1] FALSE
D97V7, binary
                 cls
clus               0  1
  PDCD6 MUTATED    1  0
  PDCD6 WILD-TYPE  6 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      1    0
  PDCD6 WILD-TYPE    6   27
                        clus
vv                       PDCD6 MUTATED PDCD6 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             0              27
[1] 2 2
[1] FALSE

Clustering(98) Variable = SHOX2 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2              0  1
  SHOX2 MUTATED    3  0
  SHOX2 WILD-TYPE 37 21
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              3              58 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              0              21 
$`SHOX2 MUTATED`
TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5LK 
       24.36       127.50        73.05 

$`SHOX2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
       46.49        91.30        83.80        95.18       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        36.33        53.03        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  SHOX2 MUTATED SHOX2 WILD-TYPE 
          24.36            4.11 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
         127.50          153.63 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
         73.050          40.485 
[1] "24.4 - 127.5 (73.0)" "4.1 - 153.6 (40.5)" 
[1] "hr="     "7.4e+07"
D98V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SHOX2 MUTATED         0        2         1        0
  SHOX2 WILD-TYPE       6       26        13       11
D98V3, multiclass
           clus
vv          SHOX2 MUTATED SHOX2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              0              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
  SHOX2 MUTATED    0  3  0  0
  SHOX2 WILD-TYPE  6 29  7 14
D98V4, multiclass
    clus
vv   SHOX2 MUTATED SHOX2 WILD-TYPE
  T1             0               6
  T2             3              29
  T3             0               7
  T4             0              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
  SHOX2 MUTATED    2  1
  SHOX2 WILD-TYPE 51  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      2    1
  SHOX2 WILD-TYPE   51    5
   clus
vv  SHOX2 MUTATED SHOX2 WILD-TYPE
  0             2              51
  1             1               5
[1] 2 2
[1] FALSE
D98V6, binary
                 cls
clus               0  1
  SHOX2 MUTATED    2  1
  SHOX2 WILD-TYPE 38 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      2    1
  SHOX2 WILD-TYPE   38   21
        clus
vv       SHOX2 MUTATED SHOX2 WILD-TYPE
  FEMALE             2              38
  MALE               1              21
[1] 2 2
[1] FALSE
D98V7, binary
                 cls
clus               0  1
  SHOX2 MUTATED    0  2
  SHOX2 WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      0    2
  SHOX2 WILD-TYPE    7   25
                        clus
vv                       SHOX2 MUTATED SHOX2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(99) Variable = UQCRFS1 MUTATION ANALYSIS
D99V1, survival
                   sevent
clus2                0  1
  UQCRFS1 MUTATED    2  3
  UQCRFS1 WILD-TYPE 38 18
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                56 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                3                18 
$`UQCRFS1 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5JI TCGA-OR-A5LD TCGA-P6-A5OF 
       68.75        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        88.87        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        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        22.03         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ 
       28.31        28.64        23.64        39.58         5.23        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       73.05        53.03        69.11        61.05        28.04        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
             6.81              4.11 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            68.75            153.63 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            39.35             41.95 
[1] "6.8 - 68.8 (39.4)"  "4.1 - 153.6 (42.0)"
[1] "hr=" "2.3"
D99V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  UQCRFS1 MUTATED         1        0         3        1
  UQCRFS1 WILD-TYPE       5       28        11       10
D99V3, multiclass
           clus
vv          UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                0                28
  STAGE III               3                11
  STAGE IV                1                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
  UQCRFS1 MUTATED    1  0  2  2
  UQCRFS1 WILD-TYPE  5 32  5 12
D99V4, multiclass
    clus
vv   UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  T1               1                 5
  T2               0                32
  T3               2                 5
  T4               2                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
  UQCRFS1 MUTATED    4  1
  UQCRFS1 WILD-TYPE 49  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      4    1
  UQCRFS1 WILD-TYPE   49    5
   clus
vv  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  0               4                49
  1               1                 5
[1] 2 2
[1] FALSE
D99V6, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    3  2
  UQCRFS1 WILD-TYPE 37 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      3    2
  UQCRFS1 WILD-TYPE   37   20
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  FEMALE               3                37
  MALE                 2                20
[1] 2 2
[1] FALSE
D99V7, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    2  2
  UQCRFS1 WILD-TYPE  5 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      2    2
  UQCRFS1 WILD-TYPE    5   25
                        clus
vv                       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(100) Variable = CTBP2 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2              0  1
  CTBP2 MUTATED    2  1
  CTBP2 WILD-TYPE 38 20
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              3              58 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              1              20 
$`CTBP2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5L1 TCGA-OR-A5L5 
       19.04        58.55        43.30 

$`CTBP2 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        44.84         4.11        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  CTBP2 MUTATED CTBP2 WILD-TYPE 
          19.04            4.11 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
          58.55          153.63 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
         43.300          40.485 
[1] "19.0 - 58.5 (43.3)" "4.1 - 153.6 (40.5)"
[1] "hr=" "1.1"
D100V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CTBP2 MUTATED         1        1         1        0
  CTBP2 WILD-TYPE       5       27        13       11
D100V3, multiclass
           clus
vv          CTBP2 MUTATED CTBP2 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              27
  STAGE III             1              13
  STAGE IV              0              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
  CTBP2 MUTATED    1  1  1  0
  CTBP2 WILD-TYPE  5 31  6 14
D100V4, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  T1             1               5
  T2             1              31
  T3             1               6
  T4             0              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"
D100V5, binary
                 cls
clus               0  1
  CTBP2 MUTATED    3  0
  CTBP2 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      3    0
  CTBP2 WILD-TYPE   50    6
   clus
vv  CTBP2 MUTATED CTBP2 WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D100V6, binary
                 cls
clus               0  1
  CTBP2 MUTATED    2  1
  CTBP2 WILD-TYPE 38 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      2    1
  CTBP2 WILD-TYPE   38   21
        clus
vv       CTBP2 MUTATED CTBP2 WILD-TYPE
  FEMALE             2              38
  MALE               1              21
[1] 2 2
[1] FALSE
D100V7, binary
                 cls
clus               0  1
  CTBP2 MUTATED    1  2
  CTBP2 WILD-TYPE  6 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      1    2
  CTBP2 WILD-TYPE    6   25
                        clus
vv                       CTBP2 MUTATED CTBP2 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(101) Variable = PRKAR1A MUTATION ANALYSIS
D101V1, survival
                   sevent
clus2                0  1
  PRKAR1A MUTATED    4  2
  PRKAR1A WILD-TYPE 36 19
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                55 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                2                19 
$`PRKAR1A MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JL TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5LO 
       68.75        30.31        22.03        18.15        95.18        69.11 

$`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        88.87        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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       66.51        72.39        31.23        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        91.30        83.80 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        39.58         5.23        39.35        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       53.03        61.05        28.04         6.81        15.45       106.52 
TCGA-PK-A5HB 
       42.51 

  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            18.15              4.11 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            95.18            153.63 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            49.53             41.39 
[1] "18.1 - 95.2 (49.5)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.2"
D101V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PRKAR1A MUTATED         2        1         1        2
  PRKAR1A WILD-TYPE       4       27        13        9
D101V3, multiclass
           clus
vv          PRKAR1A MUTATED PRKAR1A WILD-TYPE
  STAGE I                 2                 4
  STAGE II                1                27
  STAGE III               1                13
  STAGE IV                2                 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
  PRKAR1A MUTATED    2  1  1  2
  PRKAR1A WILD-TYPE  4 31  6 12
D101V4, multiclass
    clus
vv   PRKAR1A MUTATED PRKAR1A WILD-TYPE
  T1               2                 4
  T2               1                31
  T3               1                 6
  T4               2                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"
D101V5, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    5  1
  PRKAR1A WILD-TYPE 48  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      5    1
  PRKAR1A WILD-TYPE   48    5
   clus
vv  PRKAR1A MUTATED PRKAR1A WILD-TYPE
  0               5                48
  1               1                 5
[1] 2 2
[1] FALSE
D101V6, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    6  0
  PRKAR1A WILD-TYPE 34 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      6    0
  PRKAR1A WILD-TYPE   34   22
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  FEMALE               6                34
  MALE                 0                22
[1] 2 2
[1] FALSE
D101V7, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    1  1
  PRKAR1A WILD-TYPE  6 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      1    1
  PRKAR1A WILD-TYPE    6   26
                        clus
vv                       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(102) Variable = JMJD4 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2              0  1
  JMJD4 MUTATED    2  1
  JMJD4 WILD-TYPE 38 20
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              3              58 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              1              20 
$`JMJD4 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JP TCGA-OR-A5KS 
       16.11         4.90        83.80 

$`JMJD4 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  JMJD4 MUTATED JMJD4 WILD-TYPE 
           4.90            4.11 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
          83.80          153.63 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
          16.11           41.95 
[1] "4.9 - 83.8 (16.1)"  "4.1 - 153.6 (42.0)"
[1] "hr=" "1.4"
D102V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  JMJD4 MUTATED         0        2         1        0
  JMJD4 WILD-TYPE       6       26        13       11
D102V3, multiclass
           clus
vv          JMJD4 MUTATED JMJD4 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              0              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
  JMJD4 MUTATED    0  2  1  0
  JMJD4 WILD-TYPE  6 30  6 14
D102V4, multiclass
    clus
vv   JMJD4 MUTATED JMJD4 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             1               6
  T4             0              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"
D102V5, binary
                 cls
clus               0  1
  JMJD4 MUTATED    3  0
  JMJD4 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      3    0
  JMJD4 WILD-TYPE   50    6
   clus
vv  JMJD4 MUTATED JMJD4 WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D102V6, binary
                 cls
clus               0  1
  JMJD4 MUTATED    1  2
  JMJD4 WILD-TYPE 39 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      1    2
  JMJD4 WILD-TYPE   39   20
        clus
vv       JMJD4 MUTATED JMJD4 WILD-TYPE
  FEMALE             1              39
  MALE               2              20
[1] 2 2
[1] FALSE
D102V7, binary
                 cls
clus               0  1
  JMJD4 MUTATED    1  1
  JMJD4 WILD-TYPE  6 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      1    1
  JMJD4 WILD-TYPE    6   26
                        clus
vv                       JMJD4 MUTATED JMJD4 WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(103) Variable = HSD17B1 MUTATION ANALYSIS
D103V1, survival
                   sevent
clus2                0  1
  HSD17B1 MUTATED    3  1
  HSD17B1 WILD-TYPE 37 20
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                57 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                1                20 
$`HSD17B1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K4 TCGA-OR-A5KT TCGA-OR-A5LP 
       19.04        22.98        95.18        61.05 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        83.80       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            19.04              4.11 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            95.18            153.63 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
           42.015            41.390 
[1] "19.0 - 95.2 (42.0)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.6"
D103V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  HSD17B1 MUTATED         1        1         2        0
  HSD17B1 WILD-TYPE       5       27        12       11
D103V3, multiclass
           clus
vv          HSD17B1 MUTATED HSD17B1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                27
  STAGE III               2                12
  STAGE IV                0                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
  HSD17B1 MUTATED    1  1  1  1
  HSD17B1 WILD-TYPE  5 31  6 13
D103V4, multiclass
    clus
vv   HSD17B1 MUTATED HSD17B1 WILD-TYPE
  T1               1                 5
  T2               1                31
  T3               1                 6
  T4               1                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"
D103V5, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    4  0
  HSD17B1 WILD-TYPE 49  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      4    0
  HSD17B1 WILD-TYPE   49    6
   clus
vv  HSD17B1 MUTATED HSD17B1 WILD-TYPE
  0               4                49
  1               0                 6
[1] 2 2
[1] FALSE
D103V6, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    3  1
  HSD17B1 WILD-TYPE 37 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      3    1
  HSD17B1 WILD-TYPE   37   21
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  FEMALE               3                37
  MALE                 1                21
[1] 2 2
[1] FALSE
D103V7, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    1  1
  HSD17B1 WILD-TYPE  6 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      1    1
  HSD17B1 WILD-TYPE    6   26
                        clus
vv                       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(104) Variable = COQ2 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2             0  1
  COQ2 MUTATED    3  2
  COQ2 WILD-TYPE 37 19
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             56 
  COQ2 MUTATED COQ2 WILD-TYPE 
             2             19 
$`COQ2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5L2 TCGA-OR-A5LK 
       30.31        41.39        22.03        60.89        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        68.75        15.45        12.00        88.87 
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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        49.22         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       66.51        72.39        31.23        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55       152.15        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        39.58         5.23        39.35        36.33 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      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 
        41.390         41.045 
[1] "22.0 - 73.0 (41.4)" "4.1 - 153.6 (41.0)"
[1] "hr=" "1"  
D104V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  COQ2 MUTATED         1        3         0        1
  COQ2 WILD-TYPE       5       25        14       10
D104V3, multiclass
           clus
vv          COQ2 MUTATED COQ2 WILD-TYPE
  STAGE I              1              5
  STAGE II             3             25
  STAGE III            0             14
  STAGE IV             1             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
  COQ2 MUTATED    1  3  0  1
  COQ2 WILD-TYPE  5 29  7 13
D104V4, multiclass
    clus
vv   COQ2 MUTATED COQ2 WILD-TYPE
  T1            1              5
  T2            3             29
  T3            0              7
  T4            1             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"
D104V5, binary
                cls
clus              0  1
  COQ2 MUTATED    5  0
  COQ2 WILD-TYPE 48  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      5    0
  COQ2 WILD-TYPE   48    6
   clus
vv  COQ2 MUTATED COQ2 WILD-TYPE
  0            5             48
  1            0              6
[1] 2 2
[1] FALSE
D104V6, binary
                cls
clus              0  1
  COQ2 MUTATED    4  1
  COQ2 WILD-TYPE 36 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      4    1
  COQ2 WILD-TYPE   36   21
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  FEMALE            4             36
  MALE              1             21
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus              0  1
  COQ2 MUTATED    0  1
  COQ2 WILD-TYPE  7 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      0    1
  COQ2 WILD-TYPE    7   26
                        clus
vv                       COQ2 MUTATED COQ2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            1             26
[1] 2 2
[1] FALSE

Clustering(105) Variable = FEZ2 MUTATION ANALYSIS
D105V1, survival
                sevent
clus2             0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 38 20
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             58 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             1             20 
$`FEZ2 MUTATED`
TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LJ 
       28.31        23.64        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC 
      152.15        31.79        43.30        28.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  FEZ2 MUTATED FEZ2 WILD-TYPE 
         23.64           4.11 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
         36.33         153.63 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
        28.310         42.905 
[1] "23.6 - 36.3 (28.3)" "4.1 - 153.6 (42.9)"
[1] "hr=" "1.5"
D105V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FEZ2 MUTATED         0        2         0        1
  FEZ2 WILD-TYPE       6       26        14       10
D105V3, multiclass
           clus
vv          FEZ2 MUTATED FEZ2 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             26
  STAGE III            0             14
  STAGE IV             1             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
  FEZ2 MUTATED    0  3  0  0
  FEZ2 WILD-TYPE  6 29  7 14
D105V4, multiclass
    clus
vv   FEZ2 MUTATED FEZ2 WILD-TYPE
  T1            0              6
  T2            3             29
  T3            0              7
  T4            0             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"
D105V5, binary
                cls
clus              0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 51  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      2    1
  FEZ2 WILD-TYPE   51    5
   clus
vv  FEZ2 MUTATED FEZ2 WILD-TYPE
  0            2             51
  1            1              5
[1] 2 2
[1] FALSE
D105V6, binary
                cls
clus              0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 38 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      2    1
  FEZ2 WILD-TYPE   38   21
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  FEMALE            2             38
  MALE              1             21
[1] 2 2
[1] FALSE
D105V7, binary
                cls
clus              0  1
  FEZ2 MUTATED    0  3
  FEZ2 WILD-TYPE  7 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      0    3
  FEZ2 WILD-TYPE    7   24
                        clus
vv                       FEZ2 MUTATED FEZ2 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(106) Variable = DLEU7 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2              0  1
  DLEU7 MUTATED    2  0
  DLEU7 WILD-TYPE 38 21
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              2              59 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              0              21 
$`DLEU7 MUTATED`
TCGA-OR-A5K8 TCGA-OR-A5KB 
       24.62        24.36 

$`DLEU7 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        32.68        22.98         8.32        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       28.04         6.81        15.45       106.52        42.51 

  DLEU7 MUTATED DLEU7 WILD-TYPE 
          24.36            4.11 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
          24.62          153.63 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
          24.49           42.51 
[1] "24.4 - 24.6 (24.5)" "4.1 - 153.6 (42.5)"
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
D106V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DLEU7 MUTATED         0        2         0        1
  DLEU7 WILD-TYPE       6       26        14       10
D106V3, multiclass
           clus
vv          DLEU7 MUTATED DLEU7 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             0              14
  STAGE IV              1              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
  DLEU7 MUTATED    0  2  0  1
  DLEU7 WILD-TYPE  6 30  7 13
D106V4, multiclass
    clus
vv   DLEU7 MUTATED DLEU7 WILD-TYPE
  T1             0               6
  T2             2              30
  T3             0               7
  T4             1              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"
D106V5, binary
                 cls
clus               0  1
  DLEU7 MUTATED    3  0
  DLEU7 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      3    0
  DLEU7 WILD-TYPE   50    6
   clus
vv  DLEU7 MUTATED DLEU7 WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D106V6, binary
                 cls
clus               0  1
  DLEU7 MUTATED    2  1
  DLEU7 WILD-TYPE 38 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      2    1
  DLEU7 WILD-TYPE   38   21
        clus
vv       DLEU7 MUTATED DLEU7 WILD-TYPE
  FEMALE             2              38
  MALE               1              21
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus               0  1
  DLEU7 MUTATED    0  3
  DLEU7 WILD-TYPE  7 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      0    3
  DLEU7 WILD-TYPE    7   24
                        clus
vv                       DLEU7 MUTATED DLEU7 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              24
[1] 2 2
[1] FALSE

Clustering(107) Variable = RNF135 MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2               0  1
  RNF135 MUTATED    3  0
  RNF135 WILD-TYPE 37 21
  RNF135 MUTATED RNF135 WILD-TYPE 
               3               58 
  RNF135 MUTATED RNF135 WILD-TYPE 
               0               21 
$`RNF135 MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5KS TCGA-OR-A5L9 
       88.87        83.80        28.64 

$`RNF135 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        68.75        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  RNF135 MUTATED RNF135 WILD-TYPE 
           28.64             4.11 
  RNF135 MUTATED RNF135 WILD-TYPE 
           88.87           153.63 
  RNF135 MUTATED RNF135 WILD-TYPE 
          83.800           40.485 
[1] "28.6 - 88.9 (83.8)" "4.1 - 153.6 (40.5)"
[1] "hr="     "7.4e+07"
D107V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF135 MUTATED         0        3         0        0
  RNF135 WILD-TYPE       6       25        14       11
D107V3, multiclass
           clus
vv          RNF135 MUTATED RNF135 WILD-TYPE
  STAGE I                0                6
  STAGE II               3               25
  STAGE III              0               14
  STAGE IV               0               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
  RNF135 MUTATED    0  3  0  0
  RNF135 WILD-TYPE  6 29  7 14
D107V4, multiclass
    clus
vv   RNF135 MUTATED RNF135 WILD-TYPE
  T1              0                6
  T2              3               29
  T3              0                7
  T4              0               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"
D107V5, binary
                  cls
clus                0  1
  RNF135 MUTATED    3  0
  RNF135 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      3    0
  RNF135 WILD-TYPE   50    6
   clus
vv  RNF135 MUTATED RNF135 WILD-TYPE
  0              3               50
  1              0                6
[1] 2 2
[1] FALSE
D107V6, binary
                  cls
clus                0  1
  RNF135 MUTATED    2  1
  RNF135 WILD-TYPE 38 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      2    1
  RNF135 WILD-TYPE   38   21
        clus
vv       RNF135 MUTATED RNF135 WILD-TYPE
  FEMALE              2               38
  MALE                1               21
[1] 2 2
[1] FALSE
D107V7, binary
                  cls
clus                0  1
  RNF135 MUTATED    1  2
  RNF135 WILD-TYPE  6 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      1    2
  RNF135 WILD-TYPE    6   25
                        clus
vv                       RNF135 MUTATED RNF135 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              2               25
[1] 2 2
[1] FALSE

Clustering(108) Variable = SPIRE2 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2               0  1
  SPIRE2 MUTATED    2  1
  SPIRE2 WILD-TYPE 38 20
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               58 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               1               20 
$`SPIRE2 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JL TCGA-OR-A5LP 
       16.11        22.03        61.05 

$`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        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        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        69.11        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           16.11             4.11 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           61.05           153.63 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           22.03            41.95 
[1] "16.1 - 61.0 (22.0)" "4.1 - 153.6 (42.0)"
[1] "hr=" "1.1"
D108V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SPIRE2 MUTATED         1        1         1        0
  SPIRE2 WILD-TYPE       5       27        13       11
D108V3, multiclass
           clus
vv          SPIRE2 MUTATED SPIRE2 WILD-TYPE
  STAGE I                1                5
  STAGE II               1               27
  STAGE III              1               13
  STAGE IV               0               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
  SPIRE2 MUTATED    1  1  1  0
  SPIRE2 WILD-TYPE  5 31  6 14
D108V4, multiclass
    clus
vv   SPIRE2 MUTATED SPIRE2 WILD-TYPE
  T1              1                5
  T2              1               31
  T3              1                6
  T4              0               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
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   50    6
   clus
vv  SPIRE2 MUTATED SPIRE2 WILD-TYPE
  0              3               50
  1              0                6
[1] 2 2
[1] FALSE
D108V6, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 37 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   37   22
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  FEMALE              3               37
  MALE                0               22
[1] 2 2
[1] FALSE
D108V7, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    1  0
  SPIRE2 WILD-TYPE  6 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      1    0
  SPIRE2 WILD-TYPE    6   27
                        clus
vv                       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              0               27
[1] 2 2
[1] FALSE

Clustering(109) Variable = KRTAP5-5 MUTATION ANALYSIS
D109V1, survival
                    sevent
clus2                 0  1
  KRTAP5-5 MUTATED    1  2
  KRTAP5-5 WILD-TYPE 39 19
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 58 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 19 
$`KRTAP5-5 MUTATED`
TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5LB 
       11.31        83.80        39.58 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB 
       18.15        32.68        22.98         8.32        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        28.64        23.64         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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             11.31               4.11 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             83.80             153.63 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             39.58              41.95 
[1] "11.3 - 83.8 (39.6)" "4.1 - 153.6 (42.0)"
[1] "hr=" "2.1"
D109V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP5-5 MUTATED         0        2         0        1
  KRTAP5-5 WILD-TYPE       6       26        14       10
D109V3, multiclass
           clus
vv          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 2                 26
  STAGE III                0                 14
  STAGE IV                 1                 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  2  0  1
  KRTAP5-5 WILD-TYPE  6 30  7 13
D109V4, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  T1                0                  6
  T2                2                 30
  T3                0                  7
  T4                1                 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"
D109V5, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    3  0
  KRTAP5-5 WILD-TYPE 50  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      3    0
  KRTAP5-5 WILD-TYPE   50    6
   clus
vv  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  0                3                 50
  1                0                  6
[1] 2 2
[1] FALSE
D109V6, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    1  2
  KRTAP5-5 WILD-TYPE 39 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      1    2
  KRTAP5-5 WILD-TYPE   39   20
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                1                 39
  MALE                  2                 20
[1] 2 2
[1] FALSE
D109V7, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    0  2
  KRTAP5-5 WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      0    2
  KRTAP5-5 WILD-TYPE    7   25
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(110) Variable = SGK223 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2               0  1
  SGK223 MUTATED    2  1
  SGK223 WILD-TYPE 38 20
  SGK223 MUTATED SGK223 WILD-TYPE 
               3               58 
  SGK223 MUTATED SGK223 WILD-TYPE 
               1               20 
$`SGK223 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5K4 TCGA-OR-A5L2 
       68.75        22.98        60.89 

$`SGK223 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        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       44.84         4.11        58.55       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  SGK223 MUTATED SGK223 WILD-TYPE 
           22.98             4.11 
  SGK223 MUTATED SGK223 WILD-TYPE 
           68.75           153.63 
  SGK223 MUTATED SGK223 WILD-TYPE 
          60.890           40.485 
[1] "23.0 - 68.8 (60.9)" "4.1 - 153.6 (40.5)"
[1] "hr=" "1.4"
D110V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SGK223 MUTATED         0        1         2        0
  SGK223 WILD-TYPE       6       27        12       11
D110V3, multiclass
           clus
vv          SGK223 MUTATED SGK223 WILD-TYPE
  STAGE I                0                6
  STAGE II               1               27
  STAGE III              2               12
  STAGE IV               0               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
  SGK223 MUTATED    0  1  1  1
  SGK223 WILD-TYPE  6 31  6 13
D110V4, multiclass
    clus
vv   SGK223 MUTATED SGK223 WILD-TYPE
  T1              0                6
  T2              1               31
  T3              1                6
  T4              1               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
  SGK223 MUTATED    3  0
  SGK223 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK223 MUTATED      3    0
  SGK223 WILD-TYPE   50    6
   clus
vv  SGK223 MUTATED SGK223 WILD-TYPE
  0              3               50
  1              0                6
[1] 2 2
[1] FALSE
D110V6, binary
                  cls
clus                0  1
  SGK223 MUTATED    3  0
  SGK223 WILD-TYPE 37 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK223 MUTATED      3    0
  SGK223 WILD-TYPE   37   22
        clus
vv       SGK223 MUTATED SGK223 WILD-TYPE
  FEMALE              3               37
  MALE                0               22
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                0  1
  SGK223 MUTATED    1  1
  SGK223 WILD-TYPE  6 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK223 MUTATED      1    1
  SGK223 WILD-TYPE    6   26
                        clus
vv                       SGK223 MUTATED SGK223 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              1               26
[1] 2 2
[1] FALSE

Clustering(111) Variable = C9ORF66 MUTATION ANALYSIS
D111V1, survival
                   sevent
clus2                0  1
  C9ORF66 MUTATED    2  3
  C9ORF66 WILD-TYPE 38 18
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                56 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                3                18 
$`C9ORF66 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JF TCGA-OR-A5JR TCGA-OR-A5K9 
       12.00        19.04        41.39       121.25        11.31 

$`C9ORF66 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        15.45        88.87        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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        22.03         4.90        36.26        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       72.39        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        24.36        46.49        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
            11.31              4.11 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
           121.25            153.63 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
           19.040            42.905 
[1] "11.3 - 121.2 (19.0)" "4.1 - 153.6 (42.9)" 
[1] "hr=" "2.5"
D111V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C9ORF66 MUTATED         1        2         2        0
  C9ORF66 WILD-TYPE       5       26        12       11
D111V3, multiclass
           clus
vv          C9ORF66 MUTATED C9ORF66 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                2                26
  STAGE III               2                12
  STAGE IV                0                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
  C9ORF66 MUTATED    1  2  1  1
  C9ORF66 WILD-TYPE  5 30  6 13
D111V4, multiclass
    clus
vv   C9ORF66 MUTATED C9ORF66 WILD-TYPE
  T1               1                 5
  T2               2                30
  T3               1                 6
  T4               1                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"
D111V5, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    5  0
  C9ORF66 WILD-TYPE 48  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      5    0
  C9ORF66 WILD-TYPE   48    6
   clus
vv  C9ORF66 MUTATED C9ORF66 WILD-TYPE
  0               5                48
  1               0                 6
[1] 2 2
[1] FALSE
D111V6, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    2  3
  C9ORF66 WILD-TYPE 38 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      2    3
  C9ORF66 WILD-TYPE   38   19
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  FEMALE               2                38
  MALE                 3                19
[1] 2 2
[1] FALSE
D111V7, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    2  0
  C9ORF66 WILD-TYPE  5 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      2    0
  C9ORF66 WILD-TYPE    5   27
                        clus
vv                       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               0                27
[1] 2 2
[1] FALSE

Clustering(112) Variable = AQP7 MUTATION ANALYSIS
D112V1, survival
                sevent
clus2             0  1
  AQP7 MUTATED    2  1
  AQP7 WILD-TYPE 38 20
  AQP7 MUTATED AQP7 WILD-TYPE 
             3             58 
  AQP7 MUTATED AQP7 WILD-TYPE 
             1             20 
$`AQP7 MUTATED`
TCGA-OR-A5KS TCGA-OR-A5L2 TCGA-OR-A5L9 
       83.80        60.89        28.64 

$`AQP7 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        91.30        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        44.84         4.11        58.55       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  AQP7 MUTATED AQP7 WILD-TYPE 
         28.64           4.11 
  AQP7 MUTATED AQP7 WILD-TYPE 
         83.80         153.63 
  AQP7 MUTATED AQP7 WILD-TYPE 
        60.890         40.485 
[1] "28.6 - 83.8 (60.9)" "4.1 - 153.6 (40.5)"
[1] "hr=" "1.4"
D112V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  AQP7 MUTATED         0        3         0        0
  AQP7 WILD-TYPE       6       25        14       11
D112V3, multiclass
           clus
vv          AQP7 MUTATED AQP7 WILD-TYPE
  STAGE I              0              6
  STAGE II             3             25
  STAGE III            0             14
  STAGE IV             0             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
  AQP7 MUTATED    0  3  0  0
  AQP7 WILD-TYPE  6 29  7 14
D112V4, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  T1            0              6
  T2            3             29
  T3            0              7
  T4            0             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"
D112V5, binary
                cls
clus              0  1
  AQP7 MUTATED    3  0
  AQP7 WILD-TYPE 50  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      3    0
  AQP7 WILD-TYPE   50    6
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            3             50
  1            0              6
[1] 2 2
[1] FALSE
D112V6, binary
                cls
clus              0  1
  AQP7 MUTATED    2  1
  AQP7 WILD-TYPE 38 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      2    1
  AQP7 WILD-TYPE   38   21
        clus
vv       AQP7 MUTATED AQP7 WILD-TYPE
  FEMALE            2             38
  MALE              1             21
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus              0  1
  AQP7 MUTATED    0  3
  AQP7 WILD-TYPE  7 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      0    3
  AQP7 WILD-TYPE    7   24
                        clus
vv                       AQP7 MUTATED AQP7 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(113) Variable = ADAMTS7 MUTATION ANALYSIS
D113V1, survival
                   sevent
clus2                0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 36 21
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                57 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                0                21 
$`ADAMTS7 MUTATED`
TCGA-OR-A5JT TCGA-OR-A5KU TCGA-OR-A5L5 TCGA-OR-A5LK 
       29.82       153.63        43.30        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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26       121.25        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        91.30        83.80        95.18       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
            29.82              4.11 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           153.63            152.15 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           58.175            39.580 
[1] "29.8 - 153.6 (58.2)" "4.1 - 152.2 (39.6)" 
[1] "hr="     "7.5e+07"
D113V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ADAMTS7 MUTATED         1        3         0        0
  ADAMTS7 WILD-TYPE       5       25        14       11
D113V3, multiclass
           clus
vv          ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                3                25
  STAGE III               0                14
  STAGE IV                0                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
  ADAMTS7 MUTATED    1  3  0  0
  ADAMTS7 WILD-TYPE  5 29  7 14
D113V4, multiclass
    clus
vv   ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  T1               1                 5
  T2               3                29
  T3               0                 7
  T4               0                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"
D113V5, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 49  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      4    0
  ADAMTS7 WILD-TYPE   49    6
   clus
vv  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  0               4                49
  1               0                 6
[1] 2 2
[1] FALSE
D113V6, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    3  1
  ADAMTS7 WILD-TYPE 37 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      3    1
  ADAMTS7 WILD-TYPE   37   21
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  FEMALE               3                37
  MALE                 1                21
[1] 2 2
[1] FALSE
D113V7, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    0  2
  ADAMTS7 WILD-TYPE  7 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      0    2
  ADAMTS7 WILD-TYPE    7   25
                        clus
vv                       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(114) Variable = PCDHB13 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                0  1
  PCDHB13 MUTATED    3  2
  PCDHB13 WILD-TYPE 37 19
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                56 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                2                19 
$`PCDHB13 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JI TCGA-OR-A5KB 
       68.75        12.00        30.31        46.82        24.36 

$`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        88.87        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        69.37        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       72.39        31.23        18.15        32.68        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        11.31        46.49        91.30        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        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-PA-A5YG 
       53.03        69.11        61.05        28.04         6.81        15.45 
TCGA-PK-A5H8 TCGA-PK-A5HB 
      106.52        42.51 

  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            12.00              4.11 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            68.75            153.63 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            30.31             41.95 
[1] "12.0 - 68.8 (30.3)" "4.1 - 153.6 (42.0)"
[1] "hr=" "1.4"
D114V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PCDHB13 MUTATED         1        1         2        1
  PCDHB13 WILD-TYPE       5       27        12       10
D114V3, multiclass
           clus
vv          PCDHB13 MUTATED PCDHB13 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                27
  STAGE III               2                12
  STAGE IV                1                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
  PCDHB13 MUTATED    1  1  1  2
  PCDHB13 WILD-TYPE  5 31  6 12
D114V4, multiclass
    clus
vv   PCDHB13 MUTATED PCDHB13 WILD-TYPE
  T1               1                 5
  T2               1                31
  T3               1                 6
  T4               2                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"
D114V5, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    5  0
  PCDHB13 WILD-TYPE 48  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      5    0
  PCDHB13 WILD-TYPE   48    6
   clus
vv  PCDHB13 MUTATED PCDHB13 WILD-TYPE
  0               5                48
  1               0                 6
[1] 2 2
[1] FALSE
D114V6, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    3  2
  PCDHB13 WILD-TYPE 37 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      3    2
  PCDHB13 WILD-TYPE   37   20
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  FEMALE               3                37
  MALE                 2                20
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    2  1
  PCDHB13 WILD-TYPE  5 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      2    1
  PCDHB13 WILD-TYPE    5   26
                        clus
vv                       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(115) Variable = CSGALNACT2 MUTATION ANALYSIS
D115V1, survival
                      sevent
clus2                   0  1
  CSGALNACT2 MUTATED    2  1
  CSGALNACT2 WILD-TYPE 38 20
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   58 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   20 
$`CSGALNACT2 MUTATED`
TCGA-OR-A5LC TCGA-OR-A5LP TCGA-OR-A5LR 
        5.23        61.05        28.04 

$`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        68.75        15.45        12.00        88.87 
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        69.37        46.82        49.22        22.03         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       18.15        32.68        22.98         8.32        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        91.30        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        28.31        28.64        23.64 
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        69.11 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                5.23                 4.11 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               61.05               153.63 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               28.04                41.95 
[1] "5.2 - 61.0 (28.0)"  "4.1 - 153.6 (42.0)"
[1] "hr=" "1.2"
D115V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         0        2         0        1
  CSGALNACT2 WILD-TYPE       6       26        14       10
D115V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    0                    6
  STAGE II                   2                   26
  STAGE III                  0                   14
  STAGE IV                   1                   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
  CSGALNACT2 MUTATED    0  2  0  1
  CSGALNACT2 WILD-TYPE  6 30  7 13
D115V4, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                  0                    6
  T2                  2                   30
  T3                  0                    7
  T4                  1                   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"
D115V5, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 50  6
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   50    6
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  3                   50
  1                  0                    6
[1] 2 2
[1] FALSE
D115V6, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 37 22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   37   22
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  3                   37
  MALE                    0                   22
[1] 2 2
[1] FALSE
D115V7, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    0  1
  CSGALNACT2 WILD-TYPE  7 26
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    1
  CSGALNACT2 WILD-TYPE    7   26
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                    7
  NOT HISPANIC OR LATINO                  1                   26
[1] 2 2
[1] FALSE

Clustering(116) Variable = HLA-A MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2              0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 37 21
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              58 
  HLA-A MUTATED HLA-A WILD-TYPE 
              0              21 
$`HLA-A MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JP TCGA-OR-A5JX 
       88.87         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        68.75        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 
       69.37        46.82        49.22        22.03        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 
       29.82        66.51        72.39        18.15        32.68        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
        8.32        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  HLA-A MUTATED HLA-A WILD-TYPE 
           4.90            4.11 
  HLA-A MUTATED HLA-A WILD-TYPE 
          88.87          153.63 
  HLA-A MUTATED HLA-A WILD-TYPE 
          31.23           41.95 
[1] "4.9 - 88.9 (31.2)"  "4.1 - 153.6 (42.0)"
[1] "hr="     "2.6e+07"
D116V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-A MUTATED         0        2         1        0
  HLA-A WILD-TYPE       6       26        13       11
D116V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             1              13
  STAGE IV              0              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-A MUTATED    0  2  1  0
  HLA-A WILD-TYPE  6 30  6 14
D116V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0               6
  T2             2              30
  T3             1               6
  T4             0              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"
D116V5, binary
                 cls
clus               0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3    0
  HLA-A WILD-TYPE   50    6
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D116V6, binary
                 cls
clus               0  1
  HLA-A MUTATED    1  2
  HLA-A WILD-TYPE 39 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    2
  HLA-A WILD-TYPE   39   20
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             1              39
  MALE               2              20
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus               0  1
  HLA-A MUTATED    1  0
  HLA-A WILD-TYPE  6 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    0
  HLA-A WILD-TYPE    6   27
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 1               6
  NOT HISPANIC OR LATINO             0              27
[1] 2 2
[1] FALSE

Clustering(117) Variable = MTFMT MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2              0  1
  MTFMT MUTATED    2  1
  MTFMT WILD-TYPE 38 20
  MTFMT MUTATED MTFMT WILD-TYPE 
              3              58 
  MTFMT MUTATED MTFMT WILD-TYPE 
              1              20 
$`MTFMT MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JP TCGA-OR-A5KS 
       18.12         4.90        83.80 

$`MTFMT WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        28.64        23.64        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        69.11        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
        6.81        15.45       106.52        42.51 

  MTFMT MUTATED MTFMT WILD-TYPE 
           4.90            4.11 
  MTFMT MUTATED MTFMT WILD-TYPE 
          83.80          153.63 
  MTFMT MUTATED MTFMT WILD-TYPE 
          18.12           41.95 
[1] "4.9 - 83.8 (18.1)"  "4.1 - 153.6 (42.0)"
[1] "hr=" "1.3"
D117V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MTFMT MUTATED         0        2         0        1
  MTFMT WILD-TYPE       6       26        14       10
D117V3, multiclass
           clus
vv          MTFMT MUTATED MTFMT WILD-TYPE
  STAGE I               0               6
  STAGE II              2              26
  STAGE III             0              14
  STAGE IV              1              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
  MTFMT MUTATED    0  2  0  1
  MTFMT WILD-TYPE  6 30  7 13
D117V4, multiclass
    clus
vv   MTFMT MUTATED MTFMT WILD-TYPE
  T1             0               6
  T2             2              30
  T3             0               7
  T4             1              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
  MTFMT MUTATED    3  0
  MTFMT WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTFMT MUTATED      3    0
  MTFMT WILD-TYPE   50    6
   clus
vv  MTFMT MUTATED MTFMT WILD-TYPE
  0             3              50
  1             0               6
[1] 2 2
[1] FALSE
D117V6, binary
                 cls
clus               0  1
  MTFMT MUTATED    0  3
  MTFMT WILD-TYPE 40 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTFMT MUTATED      0    3
  MTFMT WILD-TYPE   40   19
        clus
vv       MTFMT MUTATED MTFMT WILD-TYPE
  FEMALE             0              40
  MALE               3              19
[1] 2 2
[1] FALSE
D117V7, binary
                 cls
clus               0  1
  MTFMT MUTATED    0  1
  MTFMT WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTFMT MUTATED      0    1
  MTFMT WILD-TYPE    7   26
                        clus
vv                       MTFMT MUTATED MTFMT WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(118) Variable = NLRP5 MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2              0  1
  NLRP5 MUTATED    3  1
  NLRP5 WILD-TYPE 37 20
  NLRP5 MUTATED NLRP5 WILD-TYPE 
              4              57 
  NLRP5 MUTATED NLRP5 WILD-TYPE 
              1              20 
$`NLRP5 MUTATED`
TCGA-OR-A5JB TCGA-OR-A5K4 TCGA-OR-A5KB TCGA-OR-A5L5 
       18.12        22.98        24.36        43.30 

$`NLRP5 WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        15.45        12.00        88.87 
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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
       32.68         8.32        24.62        11.31        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.64        23.64        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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       106.52        42.51 

  NLRP5 MUTATED NLRP5 WILD-TYPE 
          18.12            4.11 
  NLRP5 MUTATED NLRP5 WILD-TYPE 
          43.30          153.63 
  NLRP5 MUTATED NLRP5 WILD-TYPE 
          23.67           42.51 
[1] "18.1 - 43.3 (23.7)" "4.1 - 153.6 (42.5)"
[1] "hr=" "1.1"
D118V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NLRP5 MUTATED         1        1         1        1
  NLRP5 WILD-TYPE       5       27        13       10
D118V3, multiclass
           clus
vv          NLRP5 MUTATED NLRP5 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              27
  STAGE III             1              13
  STAGE IV              1              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
  NLRP5 MUTATED    1  1  0  2
  NLRP5 WILD-TYPE  5 31  7 12
D118V4, multiclass
    clus
vv   NLRP5 MUTATED NLRP5 WILD-TYPE
  T1             1               5
  T2             1              31
  T3             0               7
  T4             2              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"
D118V5, binary
                 cls
clus               0  1
  NLRP5 MUTATED    4  0
  NLRP5 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP5 MUTATED      4    0
  NLRP5 WILD-TYPE   49    6
   clus
vv  NLRP5 MUTATED NLRP5 WILD-TYPE
  0             4              49
  1             0               6
[1] 2 2
[1] FALSE
D118V6, binary
                 cls
clus               0  1
  NLRP5 MUTATED    3  1
  NLRP5 WILD-TYPE 37 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP5 MUTATED      3    1
  NLRP5 WILD-TYPE   37   21
        clus
vv       NLRP5 MUTATED NLRP5 WILD-TYPE
  FEMALE             3              37
  MALE               1              21
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus               0  1
  NLRP5 MUTATED    0  2
  NLRP5 WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP5 MUTATED      0    2
  NLRP5 WILD-TYPE    7   25
                        clus
vv                       NLRP5 MUTATED NLRP5 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(119) Variable = KCNJ11 MUTATION ANALYSIS
D119V1, survival
                  sevent
clus2               0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 38 19
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               4               57 
  KCNJ11 MUTATED KCNJ11 WILD-TYPE 
               2               19 
$`KCNJ11 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5LB 
       12.00        50.14        44.84        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        68.75        15.45        88.87        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 
       69.37        46.82        49.22        22.03         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        22.98         8.32        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        83.80        95.18       153.63       127.50 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       28.31        28.64        23.64         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        69.11        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HB 
       15.45       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 
           42.21            41.39 
[1] "12.0 - 50.1 (42.2)" "4.1 - 153.6 (41.4)"
[1] "hr=" "1.7"
D119V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KCNJ11 MUTATED         0        0         3        1
  KCNJ11 WILD-TYPE       6       28        11       10
D119V3, multiclass
           clus
vv          KCNJ11 MUTATED KCNJ11 WILD-TYPE
  STAGE I                0                6
  STAGE II               0               28
  STAGE III              3               11
  STAGE IV               1               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
  KCNJ11 MUTATED    0  2  0  2
  KCNJ11 WILD-TYPE  6 30  7 12
D119V4, multiclass
    clus
vv   KCNJ11 MUTATED KCNJ11 WILD-TYPE
  T1              0                6
  T2              2               30
  T3              0                7
  T4              2               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"
D119V5, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 51  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      2    2
  KCNJ11 WILD-TYPE   51    4
   clus
vv  KCNJ11 MUTATED KCNJ11 WILD-TYPE
  0              2               51
  1              2                4
[1] 2 2
[1] FALSE
D119V6, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    2  2
  KCNJ11 WILD-TYPE 38 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      2    2
  KCNJ11 WILD-TYPE   38   20
        clus
vv       KCNJ11 MUTATED KCNJ11 WILD-TYPE
  FEMALE              2               38
  MALE                2               20
[1] 2 2
[1] FALSE
D119V7, binary
                  cls
clus                0  1
  KCNJ11 MUTATED    1  3
  KCNJ11 WILD-TYPE  6 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ11 MUTATED      1    3
  KCNJ11 WILD-TYPE    6   24
                        clus
vv                       KCNJ11 MUTATED KCNJ11 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              3               24
[1] 2 2
[1] FALSE
