[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/22489368/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22573897/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 121 to 116."
[1] 116  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] "TOR3A MUTATION ANALYSIS"
[1] 3
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              50 
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              50 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            13             49 
  TP53 MUTATED TP53 WILD-TYPE 
            13             49 
[1] "CLDN23 MUTATION ANALYSIS"
[1] 3
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               52 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               52 
[1] "GDF1 MUTATION ANALYSIS"
[1] 3
  GDF1 MUTATED GDF1 WILD-TYPE 
             5             57 
  GDF1 MUTATED GDF1 WILD-TYPE 
             5             57 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              56 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              56 
[1] "ANKRD43 MUTATION ANALYSIS"
[1] 3
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
               19                43 
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
               19                43 
[1] "KCNK17 MUTATION ANALYSIS"
[1] 3
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               53 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               53 
[1] "RINL MUTATION ANALYSIS"
[1] 3
  RINL MUTATED RINL WILD-TYPE 
             8             54 
  RINL MUTATED RINL WILD-TYPE 
             8             54 
[1] "ZAR1 MUTATION ANALYSIS"
[1] 3
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             51 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             51 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8               54 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8               54 
[1] "APOE MUTATION ANALYSIS"
[1] 3
  APOE MUTATED APOE WILD-TYPE 
             7             55 
  APOE MUTATED APOE WILD-TYPE 
             7             55 
[1] "GPRIN2 MUTATION ANALYSIS"
[1] 3
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               8               54 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               8               54 
[1] "ASPDH MUTATION ANALYSIS"
[1] 3
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              54 
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              54 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              52 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              52 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             8             54 
  IDUA MUTATED IDUA WILD-TYPE 
             8             54 
[1] "C1ORF106 MUTATION ANALYSIS"
[1] 3
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 53 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 53 
[1] "C10ORF95 MUTATION ANALYSIS"
[1] 3
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 56 
  C10ORF95 MUTATED C10ORF95 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] "THEM4 MUTATION ANALYSIS"
[1] 3
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              57 
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              57 
[1] "TSC22D2 MUTATION ANALYSIS"
[1] 3
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                54 
  TSC22D2 MUTATED TSC22D2 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] "PLIN5 MUTATION ANALYSIS"
[1] 3
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              57 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              57 
[1] "LRIG1 MUTATION ANALYSIS"
[1] 3
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             16              46 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             16              46 
[1] "HHIPL1 MUTATION ANALYSIS"
[1] 3
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               56 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               56 
[1] "CCDC105 MUTATION ANALYSIS"
[1] 3
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                56 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                56 
[1] "C19ORF10 MUTATION ANALYSIS"
[1] 3
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 55 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 55 
[1] "OPRD1 MUTATION ANALYSIS"
[1] 3
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             12              50 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             12              50 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              52 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              52 
[1] "AATK MUTATION ANALYSIS"
[1] 3
  AATK MUTATED AATK WILD-TYPE 
             6             56 
  AATK MUTATED AATK WILD-TYPE 
             6             56 
[1] "ZNF628 MUTATION ANALYSIS"
[1] 3
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               7               55 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               7               55 
[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] "NOXA1 MUTATION ANALYSIS"
[1] 3
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              5              57 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              5              57 
[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] "IRX3 MUTATION ANALYSIS"
[1] 3
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             57 
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             57 
[1] "WDR34 MUTATION ANALYSIS"
[1] 3
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              57 
  WDR34 MUTATED WDR34 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] "PANK2 MUTATION ANALYSIS"
[1] 3
  PANK2 MUTATED PANK2 WILD-TYPE 
              5              57 
  PANK2 MUTATED PANK2 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] "GLTPD2 MUTATION ANALYSIS"
[1] 3
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               56 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               56 
[1] "TNIP2 MUTATION ANALYSIS"
[1] 3
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              57 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              57 
[1] "AKAP2 MUTATION ANALYSIS"
[1] 3
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              6              56 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              6              56 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              57 
  RREB1 MUTATED RREB1 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] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              44 
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              44 
[1] "SNED1 MUTATION ANALYSIS"
[1] 3
  SNED1 MUTATED SNED1 WILD-TYPE 
              5              57 
  SNED1 MUTATED SNED1 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] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               56 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               56 
[1] "RNF149 MUTATION ANALYSIS"
[1] 3
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               58 
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               58 
[1] "KIAA1984 MUTATION ANALYSIS"
[1] 3
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 58 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 58 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                58 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                58 
[1] "FAM18B2 MUTATION ANALYSIS"
[1] 3
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                4                58 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                4                58 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              40 
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              40 
[1] "PTPLA MUTATION ANALYSIS"
[1] 3
  PTPLA MUTATED PTPLA WILD-TYPE 
              4              58 
  PTPLA MUTATED PTPLA 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] "GARS MUTATION ANALYSIS"
[1] 3
  GARS MUTATED GARS WILD-TYPE 
            19             43 
  GARS MUTATED GARS WILD-TYPE 
            19             43 
[1] "PRSS27 MUTATION ANALYSIS"
[1] 3
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               59 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               59 
[1] "SEMA5B MUTATION ANALYSIS"
[1] 3
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               54 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               54 
[1] "CD320 MUTATION ANALYSIS"
[1] 3
  CD320 MUTATED CD320 WILD-TYPE 
              4              58 
  CD320 MUTATED CD320 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] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6             56 
  NEFH MUTATED NEFH WILD-TYPE 
             6             56 
[1] "DMKN MUTATION ANALYSIS"
[1] 3
  DMKN MUTATED DMKN WILD-TYPE 
             3             59 
  DMKN MUTATED DMKN WILD-TYPE 
             3             59 
[1] "NPTX1 MUTATION ANALYSIS"
[1] 3
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              59 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              59 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               57 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               57 
[1] "RNF39 MUTATION ANALYSIS"
[1] 3
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              57 
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              57 
[1] "KBTBD13 MUTATION ANALYSIS"
[1] 3
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                53 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                53 
[1] "IER5 MUTATION ANALYSIS"
[1] 3
  IER5 MUTATED IER5 WILD-TYPE 
             3             59 
  IER5 MUTATED IER5 WILD-TYPE 
             3             59 
[1] "SCRT1 MUTATION ANALYSIS"
[1] 3
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              59 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              59 
[1] "KNDC1 MUTATION ANALYSIS"
[1] 3
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              53 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              53 
[1] "MAP1S MUTATION ANALYSIS"
[1] 3
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              57 
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              57 
[1] "RGMB MUTATION ANALYSIS"
[1] 3
  RGMB MUTATED RGMB WILD-TYPE 
             6             56 
  RGMB MUTATED RGMB WILD-TYPE 
             6             56 
[1] "LRP11 MUTATION ANALYSIS"
[1] 3
  LRP11 MUTATED LRP11 WILD-TYPE 
              6              56 
  LRP11 MUTATED LRP11 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] "VARS MUTATION ANALYSIS"
[1] 3
  VARS MUTATED VARS WILD-TYPE 
             6             56 
  VARS MUTATED VARS WILD-TYPE 
             6             56 
[1] "SEZ6L2 MUTATION ANALYSIS"
[1] 3
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               54 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               54 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               58 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               58 
[1] "FANK1 MUTATION ANALYSIS"
[1] 3
  FANK1 MUTATED FANK1 WILD-TYPE 
              3              59 
  FANK1 MUTATED FANK1 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] "ADAD2 MUTATION ANALYSIS"
[1] 3
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              58 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              58 
[1] "CLIC6 MUTATION ANALYSIS"
[1] 3
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              57 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              57 
[1] "PCDHB13 MUTATION ANALYSIS"
[1] 3
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                57 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                57 
[1] "PLEC MUTATION ANALYSIS"
[1] 3
  PLEC MUTATED PLEC WILD-TYPE 
            13             49 
  PLEC MUTATED PLEC WILD-TYPE 
            13             49 
[1] "AMDHD1 MUTATION ANALYSIS"
[1] 3
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               52 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               52 
[1] "DSPP MUTATION ANALYSIS"
[1] 3
  DSPP MUTATED DSPP WILD-TYPE 
             9             53 
  DSPP MUTATED DSPP WILD-TYPE 
             9             53 
[1] "TMEM189 MUTATION ANALYSIS"
[1] 3
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                59 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                59 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               52 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               52 
[1] "PDCD6 MUTATION ANALYSIS"
[1] 3
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              59 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              59 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             59 
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             59 
[1] "NOM1 MUTATION ANALYSIS"
[1] 3
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             56 
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             56 
[1] "SHOX2 MUTATION ANALYSIS"
[1] 3
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              3              59 
  SHOX2 MUTATED SHOX2 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] "PRKAR1A MUTATION ANALYSIS"
[1] 3
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                56 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                56 
[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] "DLEU7 MUTATION ANALYSIS"
[1] 3
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              3              59 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              3              59 
[1] "FEZ2 MUTATION ANALYSIS"
[1] 3
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             59 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             59 
[1] "RASIP1 MUTATION ANALYSIS"
[1] 3
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               6               56 
  RASIP1 MUTATED RASIP1 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] "COQ2 MUTATION ANALYSIS"
[1] 3
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             57 
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             57 
[1] "UQCRFS1 MUTATION ANALYSIS"
[1] 3
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                57 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                57 
[1] "C9ORF66 MUTATION ANALYSIS"
[1] 3
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                57 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                57 
[1] "POLRMT MUTATION ANALYSIS"
[1] 3
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               58 
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               58 
[1] "ADAMTS7 MUTATION ANALYSIS"
[1] 3
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                58 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                58 
[1] "BTNL9 MUTATION ANALYSIS"
[1] 3
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              4              58 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              4              58 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            7            55 
  NF1 MUTATED NF1 WILD-TYPE 
            7            55 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               59 
  ZNF814 MUTATED ZNF814 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] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   59 
  CSGALNACT2 MUTATED CSGALNACT2 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] "CYP4A22 MUTATION ANALYSIS"
[1] 3
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                4                58 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                4                58 
[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] "GLI3 MUTATION ANALYSIS"
[1] 3
  GLI3 MUTATED GLI3 WILD-TYPE 
             5             57 
  GLI3 MUTATED GLI3 WILD-TYPE 
             5             57 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 62 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE excluded in the analysis because there is no case of (both >= 3) in the table below"
              BLACK OR AFRICAN AMERICAN WHITE  
freq.values   "1"                       "55"   
freq.contrast "55"                      "1"    
both >= 3     "FALSE"                   "FALSE"
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 62 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "GENDER"                "RADIATION_THERAPY"    
 [7] "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES"
[10] "ETHNICITY"            
YEARS_TO_BIRTH, nv=42, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 33  7 14 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 33  7 14 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 6 33  7 14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 33  7 14 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=4, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = ZFPM1 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  ZFPM1 MUTATED   14 10
  ZFPM1 WILD-TYPE 25 13
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             24              38 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
             10              13 
$`ZFPM1 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       42.51        55.13        68.75        16.11        30.31        18.12 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       69.37        49.22        67.59       121.25        29.82        66.51 
TCGA-OR-A5JY TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KW 
       18.15        24.62        11.31        24.36       127.50        68.25 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LL TCGA-P6-A5OH 
        4.11        28.31        23.64         5.23        53.03         0.00 

$`ZFPM1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 
       91.30        43.30        39.58        44.55        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI 
       88.87        19.04        57.53        99.88        66.25        76.64 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 
       15.25        36.26        72.39        31.23        32.68        35.57 
TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX 
       16.37        46.49        83.80        95.18       153.63        44.84 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LD 
       58.55        60.89       152.15        31.79        28.64        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        90.08        79.07        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
           0.00            6.81 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
         127.50          153.63 
  ZFPM1 MUTATED ZFPM1 WILD-TYPE 
         30.065          44.695 
[1] "0.0 - 127.5 (30.1)" "6.8 - 153.6 (44.7)"
[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       19        10        4
D1V3, multiclass
           clus
vv          ZFPM1 MUTATED ZFPM1 WILD-TYPE
  STAGE I               2               4
  STAGE II             10              19
  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 21  4  8
D1V4, multiclass
    clus
vv   ZFPM1 MUTATED ZFPM1 WILD-TYPE
  T1             2               4
  T2            12              21
  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 34  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     20    3
  ZFPM1 WILD-TYPE   34    3
   clus
vv  ZFPM1 MUTATED ZFPM1 WILD-TYPE
  0            20              34
  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   17  6
  ZFPM1 WILD-TYPE 29  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED     17    6
  ZFPM1 WILD-TYPE   29    8
     clus
vv    ZFPM1 MUTATED ZFPM1 WILD-TYPE
  NO             17              29
  YES             6               8
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZFPM1 MUTATED                                       0
  ZFPM1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZFPM1 MUTATED                                          1
  ZFPM1 WILD-TYPE                                        2
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZFPM1 MUTATED                                     23
  ZFPM1 WILD-TYPE                                   35
D1V8, multiclass
                                          clus
vv                                         ZFPM1 MUTATED ZFPM1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             1               2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                23              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  ZFPM1 MUTATED   14  3  5  1
  ZFPM1 WILD-TYPE 30  1  3  3
D1V9, multiclass
    clus
vv   ZFPM1 MUTATED ZFPM1 WILD-TYPE
  R0            14              30
  R1             3               1
  R2             5               3
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, 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 27 16
  LACTB MUTATED LACTB WILD-TYPE 
             19              43 
  LACTB MUTATED LACTB WILD-TYPE 
              7              16 
$`LACTB MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC 
       43.30        12.00        88.87        19.04        18.12        57.53 
TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5K9 
       76.64        67.59        36.26        29.82        72.39        11.31 
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 
       24.36        83.80       153.63        68.25         4.11       152.15 
TCGA-OR-A5LJ 
       36.33 

$`LACTB WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       13.91        16.11        30.31        99.88        66.25        69.37 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       49.22        15.25       121.25        66.51        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        35.57        16.37        24.62        46.49        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 
      127.50        44.84        58.55        60.89        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64         5.23        39.35        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04         6.81         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  LACTB MUTATED LACTB WILD-TYPE 
           4.11            0.00 
  LACTB MUTATED LACTB WILD-TYPE 
         153.63          127.50 
  LACTB MUTATED LACTB WILD-TYPE 
          43.30           42.51 
[1] "4.1 - 153.6 (43.3)" "0.0 - 127.5 (42.5)"
[1] "hr=" "1"  
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LACTB MUTATED         4        9         3        2
  LACTB WILD-TYPE       2       20        11        9
D2V3, multiclass
           clus
vv          LACTB MUTATED LACTB WILD-TYPE
  STAGE I               4               2
  STAGE II              9              20
  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 22  6 12
D2V4, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  T1             4               2
  T2            11              22
  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 38  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     16    2
  LACTB WILD-TYPE   38    4
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0            16              38
  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   13  4
  LACTB WILD-TYPE 33 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED     13    4
  LACTB WILD-TYPE   33   10
     clus
vv    LACTB MUTATED LACTB WILD-TYPE
  NO             13              33
  YES             4              10
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  LACTB MUTATED                                       1
  LACTB WILD-TYPE                                     0
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  LACTB MUTATED                                          0
  LACTB WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  LACTB MUTATED                                     18
  LACTB WILD-TYPE                                   40
D2V8, multiclass
                                          clus
vv                                         LACTB MUTATED LACTB WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                1               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                18              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  LACTB MUTATED   14  1  2  1
  LACTB WILD-TYPE 30  3  6  3
D2V9, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  R0            14              30
  R1             1               3
  R2             2               6
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, 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 25 20
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                17                 45 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
                 3                 20 
$`CCDC102A MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       55.13        76.64        67.59        15.25        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        35.57        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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        69.37        49.22 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 
       29.82        66.51        18.15        32.68        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       24.36       127.50        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LJ 
       60.89       152.15        31.79        28.31        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  CCDC102A MUTATED CCDC102A WILD-TYPE 
              5.23               0.00 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
            153.63             152.15 
  CCDC102A MUTATED CCDC102A WILD-TYPE 
             46.49              42.51 
[1] "5.2 - 153.6 (46.5)" "0.0 - 152.2 (42.5)"
[1] "hr=" "2.6"
D3V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  CCDC102A MUTATED         4        8         2        3
  CCDC102A WILD-TYPE       2       21        12        8
D3V3, multiclass
           clus
vv          CCDC102A MUTATED CCDC102A WILD-TYPE
  STAGE I                  4                  2
  STAGE II                 8                 21
  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 25  5 11
D3V4, multiclass
    clus
vv   CCDC102A MUTATED CCDC102A WILD-TYPE
  T1                4                  2
  T2                8                 25
  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 37  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     17    0
  CCDC102A WILD-TYPE   37    6
   clus
vv  CCDC102A MUTATED CCDC102A WILD-TYPE
  0               17                 37
  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   14  3
  CCDC102A WILD-TYPE 32 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED     14    3
  CCDC102A WILD-TYPE   32   11
     clus
vv    CCDC102A MUTATED CCDC102A WILD-TYPE
  NO                14                 32
  YES                3                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CCDC102A MUTATED                                       1
  CCDC102A WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CCDC102A MUTATED                                          0
  CCDC102A WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CCDC102A MUTATED                                     16
  CCDC102A WILD-TYPE                                   42
D3V8, multiclass
                                          clus
vv                                         CCDC102A MUTATED CCDC102A WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   16                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  CCDC102A MUTATED   14  1  2  0
  CCDC102A WILD-TYPE 30  3  6  4
D3V9, multiclass
    clus
vv   CCDC102A MUTATED CCDC102A WILD-TYPE
  R0               14                 30
  R1                1                  3
  R2                2                  6
  RX                0                  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"
D3V10, continuous
D3V11, 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  4
  ZNF517 WILD-TYPE 30 19
  ZNF517 MUTATED ZNF517 WILD-TYPE 
              13               49 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
               4               19 
$`ZNF517 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5K4 TCGA-OR-A5K5 
       42.51        18.12        66.25        69.37        35.57        16.37 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KV TCGA-OR-A5L6 TCGA-OR-A5LA 
       11.31        24.36        83.80       127.50        28.31        23.64 
TCGA-P6-A5OH 
        0.00 

$`ZNF517 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       57.53        99.88        76.64        49.22        67.59        15.25 
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-A5K8 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       18.15        32.68        24.62        46.49        95.18       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       31.79        28.64         5.23        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        79.07        61.05        28.04         6.81        24.85 
TCGA-PK-A5H8 
      119.11 

  ZNF517 MUTATED ZNF517 WILD-TYPE 
            0.00             4.11 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
          127.50           153.63 
  ZNF517 MUTATED ZNF517 WILD-TYPE 
           28.31            44.84 
[1] "0.0 - 127.5 (28.3)" "4.1 - 153.6 (44.8)"
[1] "hr=" "1"  
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF517 MUTATED         0        7         3        2
  ZNF517 WILD-TYPE       6       22        11        9
D4V3, multiclass
           clus
vv          ZNF517 MUTATED ZNF517 WILD-TYPE
  STAGE I                0                6
  STAGE II               7               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
  ZNF517 MUTATED    0  8  1  3
  ZNF517 WILD-TYPE  6 25  6 11
D4V4, multiclass
    clus
vv   ZNF517 MUTATED ZNF517 WILD-TYPE
  T1              0                6
  T2              8               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"
D4V5, binary
                  cls
clus                0  1
  ZNF517 MUTATED   11  1
  ZNF517 WILD-TYPE 43  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED     11    1
  ZNF517 WILD-TYPE   43    5
   clus
vv  ZNF517 MUTATED ZNF517 WILD-TYPE
  0             11               43
  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    7  5
  ZNF517 WILD-TYPE 39  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      7    5
  ZNF517 WILD-TYPE   39    9
     clus
vv    ZNF517 MUTATED ZNF517 WILD-TYPE
  NO               7               39
  YES              5                9
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZNF517 MUTATED                                       0
  ZNF517 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZNF517 MUTATED                                          1
  ZNF517 WILD-TYPE                                        2
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZNF517 MUTATED                                     12
  ZNF517 WILD-TYPE                                   46
D4V8, multiclass
                                          clus
vv                                         ZNF517 MUTATED ZNF517 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              1                2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 12               46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  ZNF517 MUTATED    9  2  1  0
  ZNF517 WILD-TYPE 35  2  7  4
D4V9, multiclass
    clus
vv   ZNF517 MUTATED ZNF517 WILD-TYPE
  R0              9               35
  R1              2                2
  R2              1                7
  RX              0                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"
D4V10, continuous
D4V11, 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 31 20
  MAL2 MUTATED MAL2 WILD-TYPE 
            11             51 
  MAL2 MUTATED MAL2 WILD-TYPE 
             3             20 
$`MAL2 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5JF TCGA-OR-A5JT TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       91.30        66.25        29.82        16.37        11.31        24.36 
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-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25        36.26       121.25        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO 
       31.23        18.15        32.68        35.57        24.62        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63       127.50        68.25         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD 
       60.89       152.15        31.79        28.31         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  MAL2 MUTATED MAL2 WILD-TYPE 
         11.31           0.00 
  MAL2 MUTATED MAL2 WILD-TYPE 
         91.30         153.63 
  MAL2 MUTATED MAL2 WILD-TYPE 
         29.82          44.55 
[1] "11.3 - 91.3 (29.8)" "0.0 - 153.6 (44.5)"
[1] "hr=" "1.2"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAL2 MUTATED         0        8         2        1
  MAL2 WILD-TYPE       6       21        12       10
D5V3, multiclass
           clus
vv          MAL2 MUTATED MAL2 WILD-TYPE
  STAGE I              0              6
  STAGE II             8             21
  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 23  6 14
D5V4, multiclass
    clus
vv   MAL2 MUTATED MAL2 WILD-TYPE
  T1            0              6
  T2           10             23
  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 45  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      9    2
  MAL2 WILD-TYPE   45    4
   clus
vv  MAL2 MUTATED MAL2 WILD-TYPE
  0            9             45
  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    8  3
  MAL2 WILD-TYPE 38 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      8    3
  MAL2 WILD-TYPE   38   11
     clus
vv    MAL2 MUTATED MAL2 WILD-TYPE
  NO             8             38
  YES            3             11
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  MAL2 MUTATED                                       0
  MAL2 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  MAL2 MUTATED                                          0
  MAL2 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  MAL2 MUTATED                                     11
  MAL2 WILD-TYPE                                   47
D5V8, multiclass
                                          clus
vv                                         MAL2 MUTATED MAL2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               11             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  MAL2 MUTATED   10  0  1  0
  MAL2 WILD-TYPE 34  4  7  4
D5V9, multiclass
    clus
vv   MAL2 MUTATED MAL2 WILD-TYPE
  R0           10             34
  R1            0              4
  R2            1              7
  RX            0              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"
D5V10, continuous
D5V11, 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 = TOR3A MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  TOR3A MUTATED    9  3
  TOR3A WILD-TYPE 30 20
  TOR3A MUTATED TOR3A WILD-TYPE 
             12              50 
  TOR3A MUTATED TOR3A WILD-TYPE 
              3              20 
$`TOR3A MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JL TCGA-OR-A5JR 
       42.51        88.87        30.31        18.12        67.59       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5L6 TCGA-P6-A5OF 
       29.82        66.51        24.36        95.18        28.31         6.81 

$`TOR3A WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD 
       13.91        12.00        16.11        19.04        57.53        99.88 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       66.25        69.37        76.64        49.22        15.25        36.26 
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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV 
       24.62        11.31        46.49        83.80       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        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-A5OH 
       90.08        53.03        79.07        61.05        28.04         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  TOR3A MUTATED TOR3A WILD-TYPE 
           6.81            0.00 
  TOR3A MUTATED TOR3A WILD-TYPE 
         121.25          153.63 
  TOR3A MUTATED TOR3A WILD-TYPE 
         36.410          43.925 
[1] "6.8 - 121.2 (36.4)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.6"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TOR3A MUTATED         3        5         1        2
  TOR3A WILD-TYPE       3       24        13        9
D6V3, multiclass
           clus
vv          TOR3A MUTATED TOR3A WILD-TYPE
  STAGE I               3               3
  STAGE II              5              24
  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 28  7 11
D6V4, multiclass
    clus
vv   TOR3A MUTATED TOR3A WILD-TYPE
  T1             3               3
  T2             5              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"
D6V5, binary
                 cls
clus               0  1
  TOR3A MUTATED   11  0
  TOR3A WILD-TYPE 43  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED     11    0
  TOR3A WILD-TYPE   43    6
   clus
vv  TOR3A MUTATED TOR3A WILD-TYPE
  0            11              43
  1             0               6
[1] 2 2
[1] FALSE
D6V6, 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
D6V7, binary
                 cls
clus               0  1
  TOR3A MUTATED    9  2
  TOR3A WILD-TYPE 37 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      9    2
  TOR3A WILD-TYPE   37   12
     clus
vv    TOR3A MUTATED TOR3A WILD-TYPE
  NO              9              37
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TOR3A MUTATED                                       0
  TOR3A WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TOR3A MUTATED                                          0
  TOR3A WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TOR3A MUTATED                                     12
  TOR3A WILD-TYPE                                   46
D6V8, multiclass
                                          clus
vv                                         TOR3A MUTATED TOR3A WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                12              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  TOR3A MUTATED    8  2  0  1
  TOR3A WILD-TYPE 36  2  8  3
D6V9, multiclass
    clus
vv   TOR3A MUTATED TOR3A WILD-TYPE
  R0             8              36
  R1             2               2
  R2             0               8
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, 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(7) Variable = TP53 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    6  7
  TP53 WILD-TYPE 33 16
  TP53 MUTATED TP53 WILD-TYPE 
            13             49 
  TP53 MUTATED TP53 WILD-TYPE 
             7             16 
$`TP53 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       42.51        55.13        12.00        19.04        30.31        18.12 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5K4 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KZ 
       67.59        15.25        35.57        24.36        46.49         4.11 
TCGA-OR-A5LJ 
       36.33 

$`TP53 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        44.55        68.75        13.91 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       88.87        16.11        57.53        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       76.64        49.22        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        18.15        32.68        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64         5.23        39.35        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04         6.81         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  TP53 MUTATED TP53 WILD-TYPE 
          4.11           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
         67.59         153.63 
  TP53 MUTATED TP53 WILD-TYPE 
         30.31          49.22 
[1] "4.1 - 67.6 (30.3)"  "0.0 - 153.6 (49.2)"
[1] "hr=" "2.6"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         1        3         3        5
  TP53 WILD-TYPE       5       26        11        6
D7V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              1              5
  STAGE II             3             26
  STAGE III            3             11
  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  2  5
  TP53 WILD-TYPE  5 29  5  9
D7V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            1              5
  T2            4             29
  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"
D7V5, binary
                cls
clus              0  1
  TP53 MUTATED   11  1
  TP53 WILD-TYPE 43  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     11    1
  TP53 WILD-TYPE   43    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           11             43
  1            1              5
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus              0  1
  TP53 MUTATED    7  6
  TP53 WILD-TYPE 33 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7    6
  TP53 WILD-TYPE   33   16
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            7             33
  MALE              6             16
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus              0  1
  TP53 MUTATED    9  3
  TP53 WILD-TYPE 37 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9    3
  TP53 WILD-TYPE   37   11
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             9             37
  YES            3             11
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TP53 MUTATED                                       0
  TP53 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TP53 MUTATED                                          0
  TP53 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TP53 MUTATED                                     13
  TP53 WILD-TYPE                                   45
D7V8, multiclass
                                          clus
vv                                         TP53 MUTATED TP53 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               13             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED    5  3  3  1
  TP53 WILD-TYPE 39  1  5  3
D7V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0            5             39
  R1            3              1
  R2            3              5
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, binary
                cls
clus              0  1
  TP53 MUTATED    3  4
  TP53 WILD-TYPE  4 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    4
  TP53 WILD-TYPE    4   23
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                3              4
  NOT HISPANIC OR LATINO            4             23
[1] 2 2
[1] FALSE

Clustering(8) Variable = CLDN23 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  CLDN23 MUTATED    7  3
  CLDN23 WILD-TYPE 32 20
  CLDN23 MUTATED CLDN23 WILD-TYPE 
              10               52 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
               3               20 
$`CLDN23 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JY TCGA-OR-A5L4 TCGA-OR-A5L9 
       76.64        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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
       28.31         5.23        39.35        90.08        79.07        61.05 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  CLDN23 MUTATED CLDN23 WILD-TYPE 
           18.15             0.00 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
           76.64           153.63 
  CLDN23 MUTATED CLDN23 WILD-TYPE 
          34.025           44.695 
[1] "18.1 - 76.6 (34.0)" "0.0 - 153.6 (44.7)"
[1] "hr=" "1"  
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CLDN23 MUTATED         1        5         1        3
  CLDN23 WILD-TYPE       5       24        13        8
D8V3, multiclass
           clus
vv          CLDN23 MUTATED CLDN23 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               24
  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 27  7 11
D8V4, multiclass
    clus
vv   CLDN23 MUTATED CLDN23 WILD-TYPE
  T1              1                5
  T2              6               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"
D8V5, binary
                  cls
clus                0  1
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 46  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   46    4
   clus
vv  CLDN23 MUTATED CLDN23 WILD-TYPE
  0              8               46
  1              2                4
[1] 2 2
[1] FALSE
D8V6, 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
D8V7, binary
                  cls
clus                0  1
  CLDN23 MUTATED    8  2
  CLDN23 WILD-TYPE 38 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      8    2
  CLDN23 WILD-TYPE   38   12
     clus
vv    CLDN23 MUTATED CLDN23 WILD-TYPE
  NO               8               38
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CLDN23 MUTATED                                       1
  CLDN23 WILD-TYPE                                     0
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CLDN23 MUTATED                                          0
  CLDN23 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CLDN23 MUTATED                                      9
  CLDN23 WILD-TYPE                                   49
D8V8, multiclass
                                          clus
vv                                         CLDN23 MUTATED CLDN23 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 1                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  9               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  CLDN23 MUTATED    6  0  3  1
  CLDN23 WILD-TYPE 38  4  5  3
D8V9, multiclass
    clus
vv   CLDN23 MUTATED CLDN23 WILD-TYPE
  R0              6               38
  R1              0                4
  R2              3                5
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, 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(9) Variable = GDF1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  GDF1 MUTATED    5  0
  GDF1 WILD-TYPE 34 23
  GDF1 MUTATED GDF1 WILD-TYPE 
             5             57 
  GDF1 MUTATED GDF1 WILD-TYPE 
             0             23 
$`GDF1 MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5JW TCGA-OR-A5KU TCGA-OR-A5L9 
       91.30        42.51        72.39       153.63        28.64 

$`GDF1 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        39.58        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       11.31        24.36        46.49        83.80        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        28.31        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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  GDF1 MUTATED GDF1 WILD-TYPE 
         28.64           0.00 
  GDF1 MUTATED GDF1 WILD-TYPE 
        153.63         152.15 
  GDF1 MUTATED GDF1 WILD-TYPE 
         72.39          39.58 
[1] "28.6 - 153.6 (72.4)" "0.0 - 152.2 (39.6)" 
[1] "hr="     "7.9e+07"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GDF1 MUTATED         0        4         0        0
  GDF1 WILD-TYPE       6       25        14       11
D9V3, multiclass
           clus
vv          GDF1 MUTATED GDF1 WILD-TYPE
  STAGE I              0              6
  STAGE II             4             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
  GDF1 MUTATED    0  4  0  0
  GDF1 WILD-TYPE  6 29  7 14
D9V4, multiclass
    clus
vv   GDF1 MUTATED GDF1 WILD-TYPE
  T1            0              6
  T2            4             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"
D9V5, binary
                cls
clus              0  1
  GDF1 MUTATED    4  0
  GDF1 WILD-TYPE 50  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      4    0
  GDF1 WILD-TYPE   50    6
   clus
vv  GDF1 MUTATED GDF1 WILD-TYPE
  0            4             50
  1            0              6
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus              0  1
  GDF1 MUTATED    3  2
  GDF1 WILD-TYPE 37 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      3    2
  GDF1 WILD-TYPE   37   20
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  FEMALE            3             37
  MALE              2             20
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus              0  1
  GDF1 MUTATED    3  2
  GDF1 WILD-TYPE 43 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      3    2
  GDF1 WILD-TYPE   43   12
     clus
vv    GDF1 MUTATED GDF1 WILD-TYPE
  NO             3             43
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  GDF1 MUTATED                                       0
  GDF1 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  GDF1 MUTATED                                          0
  GDF1 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  GDF1 MUTATED                                      5
  GDF1 WILD-TYPE                                   53
D9V8, multiclass
                                          clus
vv                                         GDF1 MUTATED GDF1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  GDF1 MUTATED    4  0  0  0
  GDF1 WILD-TYPE 40  4  8  4
D9V9, multiclass
    clus
vv   GDF1 MUTATED GDF1 WILD-TYPE
  R0            4             40
  R1            0              4
  R2            0              8
  RX            0              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"
D9V10, continuous
D9V11, binary
                cls
clus              0  1
  GDF1 MUTATED    0  3
  GDF1 WILD-TYPE  7 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      0    3
  GDF1 WILD-TYPE    7   24
                        clus
vv                       GDF1 MUTATED GDF1 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3             24
[1] 2 2
[1] FALSE

Clustering(10) Variable = LZTR1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  LZTR1 MUTATED    3  3
  LZTR1 WILD-TYPE 36 20
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              6              56 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              3              20 
$`LZTR1 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV 
       91.30        39.58        19.04        11.31        24.36       127.50 

$`LZTR1 WILD-TYPE`
TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        42.51        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       12.00        88.87        16.11        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        83.80        95.18       153.63        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64         5.23        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  LZTR1 MUTATED LZTR1 WILD-TYPE 
          11.31            0.00 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
         127.50          153.63 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
         31.970          43.925 
[1] "11.3 - 127.5 (32.0)" "0.0 - 153.6 (43.9)" 
[1] "hr=" "1.5"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LZTR1 MUTATED         0        3         2        1
  LZTR1 WILD-TYPE       6       26        12       10
D10V3, multiclass
           clus
vv          LZTR1 MUTATED LZTR1 WILD-TYPE
  STAGE I               0               6
  STAGE II              3              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
  LZTR1 MUTATED    0  4  1  1
  LZTR1 WILD-TYPE  6 29  6 13
D10V4, multiclass
    clus
vv   LZTR1 MUTATED LZTR1 WILD-TYPE
  T1             0               6
  T2             4              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"
D10V5, binary
                 cls
clus               0  1
  LZTR1 MUTATED    5  1
  LZTR1 WILD-TYPE 49  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      5    1
  LZTR1 WILD-TYPE   49    5
   clus
vv  LZTR1 MUTATED LZTR1 WILD-TYPE
  0             5              49
  1             1               5
[1] 2 2
[1] FALSE
D10V6, 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
D10V7, binary
                 cls
clus               0  1
  LZTR1 MUTATED    3  3
  LZTR1 WILD-TYPE 43 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      3    3
  LZTR1 WILD-TYPE   43   11
     clus
vv    LZTR1 MUTATED LZTR1 WILD-TYPE
  NO              3              43
  YES             3              11
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  LZTR1 MUTATED                                       0
  LZTR1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  LZTR1 MUTATED                                          0
  LZTR1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  LZTR1 MUTATED                                      6
  LZTR1 WILD-TYPE                                   52
D10V8, multiclass
                                          clus
vv                                         LZTR1 MUTATED LZTR1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 6              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  LZTR1 MUTATED    6  0  0  0
  LZTR1 WILD-TYPE 38  4  8  4
D10V9, multiclass
    clus
vv   LZTR1 MUTATED LZTR1 WILD-TYPE
  R0             6              38
  R1             0               4
  R2             0               8
  RX             0               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"
D10V10, continuous
D10V11, 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(11) Variable = ANKRD43 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  ANKRD43 MUTATED   10  9
  ANKRD43 WILD-TYPE 29 14
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
               19                43 
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
                9                14 
$`ANKRD43 MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       91.30        42.51        68.75        13.91        12.00        16.11 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JR TCGA-OR-A5K4 
       30.31        57.53        99.88        66.25       121.25        35.57 
TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LD 
       11.31       153.63       127.50        58.55        60.89        39.35 
TCGA-OR-A5LJ 
       36.33 

$`ANKRD43 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 
       43.30        39.58        44.55        55.13        88.87        19.04 
TCGA-OR-A5JB TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       18.12        69.37        76.64        49.22        67.59        15.25 
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-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       32.68        16.37        24.62        24.36        46.49        83.80 
TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       95.18        68.25        44.84         4.11       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LK TCGA-OR-A5LL 
       28.31        28.64        23.64         5.23        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04         6.81         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
            11.31              0.00 
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
           153.63            152.15 
  ANKRD43 MUTATED ANKRD43 WILD-TYPE 
            57.53             39.58 
[1] "11.3 - 153.6 (57.5)" "0.0 - 152.2 (39.6)" 
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ANKRD43 MUTATED         1        7         6        3
  ANKRD43 WILD-TYPE       5       22         8        8
D11V3, multiclass
           clus
vv          ANKRD43 MUTATED ANKRD43 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                7                22
  STAGE III               6                 8
  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
  ANKRD43 MUTATED    1  9  3  4
  ANKRD43 WILD-TYPE  5 24  4 10
D11V4, multiclass
    clus
vv   ANKRD43 MUTATED ANKRD43 WILD-TYPE
  T1               1                 5
  T2               9                24
  T3               3                 4
  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
  ANKRD43 MUTATED   14  3
  ANKRD43 WILD-TYPE 40  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD43 MUTATED     14    3
  ANKRD43 WILD-TYPE   40    3
   clus
vv  ANKRD43 MUTATED ANKRD43 WILD-TYPE
  0              14                40
  1               3                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  ANKRD43 MUTATED   14  5
  ANKRD43 WILD-TYPE 26 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD43 MUTATED     14    5
  ANKRD43 WILD-TYPE   26   17
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  FEMALE              14                26
  MALE                 5                17
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  ANKRD43 MUTATED   14  4
  ANKRD43 WILD-TYPE 32 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD43 MUTATED     14    4
  ANKRD43 WILD-TYPE   32   10
     clus
vv    ANKRD43 MUTATED ANKRD43 WILD-TYPE
  NO               14                32
  YES               4                10
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ANKRD43 MUTATED                                       0
  ANKRD43 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ANKRD43 MUTATED                                          1
  ANKRD43 WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ANKRD43 MUTATED                                     18
  ANKRD43 WILD-TYPE                                   40
D11V8, multiclass
                                          clus
vv                                         ANKRD43 MUTATED ANKRD43 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  18                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  ANKRD43 MUTATED   10  3  3  1
  ANKRD43 WILD-TYPE 34  1  5  3
D11V9, multiclass
    clus
vv   ANKRD43 MUTATED ANKRD43 WILD-TYPE
  R0              10                34
  R1               3                 1
  R2               3                 5
  RX               1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, binary
                   cls
clus                 0  1
  ANKRD43 MUTATED    4  7
  ANKRD43 WILD-TYPE  3 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD43 MUTATED      4    7
  ANKRD43 WILD-TYPE    3   20
                        clus
vv                       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO               7                20
[1] 2 2
[1] FALSE

Clustering(12) Variable = KCNK17 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2               0  1
  KCNK17 MUTATED    6  3
  KCNK17 WILD-TYPE 33 20
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               9               53 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
               3               20 
$`KCNK17 MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JI 
       91.30        42.51        68.75        19.04        30.31        76.64 
TCGA-OR-A5JW TCGA-OR-A5KO TCGA-OR-A5LO 
       72.39        46.49        79.07 

$`KCNK17 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        39.58        44.55        55.13        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       88.87        16.11        18.12        57.53        99.88        66.25 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        24.62        11.31        24.36        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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
        5.23        39.35        36.33        90.08        53.03        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  KCNK17 MUTATED KCNK17 WILD-TYPE 
           19.04             0.00 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
           91.30           153.63 
  KCNK17 MUTATED KCNK17 WILD-TYPE 
           68.75            39.35 
[1] "19.0 - 91.3 (68.8)" "0.0 - 153.6 (39.4)"
[1] "hr=" "1.5"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KCNK17 MUTATED         1        3         2        2
  KCNK17 WILD-TYPE       5       26        12        9
D12V3, multiclass
           clus
vv          KCNK17 MUTATED KCNK17 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               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
  KCNK17 MUTATED    1  3  2  2
  KCNK17 WILD-TYPE  5 30  5 12
D12V4, multiclass
    clus
vv   KCNK17 MUTATED KCNK17 WILD-TYPE
  T1              1                5
  T2              3               30
  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"
D12V5, binary
                  cls
clus                0  1
  KCNK17 MUTATED    8  0
  KCNK17 WILD-TYPE 46  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      8    0
  KCNK17 WILD-TYPE   46    6
   clus
vv  KCNK17 MUTATED KCNK17 WILD-TYPE
  0              8               46
  1              0                6
[1] 2 2
[1] FALSE
D12V6, 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
D12V7, binary
                  cls
clus                0  1
  KCNK17 MUTATED    6  3
  KCNK17 WILD-TYPE 40 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      6    3
  KCNK17 WILD-TYPE   40   11
     clus
vv    KCNK17 MUTATED KCNK17 WILD-TYPE
  NO               6               40
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KCNK17 MUTATED                                       0
  KCNK17 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KCNK17 MUTATED                                          0
  KCNK17 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KCNK17 MUTATED                                      9
  KCNK17 WILD-TYPE                                   49
D12V8, multiclass
                                          clus
vv                                         KCNK17 MUTATED KCNK17 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  9               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  KCNK17 MUTATED    7  1  0  0
  KCNK17 WILD-TYPE 37  3  8  4
D12V9, multiclass
    clus
vv   KCNK17 MUTATED KCNK17 WILD-TYPE
  R0              7               37
  R1              1                3
  R2              0                8
  RX              0                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"
D12V10, continuous
D12V11, 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(13) Variable = RINL MUTATION ANALYSIS
D13V1, survival
                sevent
clus2             0  1
  RINL MUTATED    4  4
  RINL WILD-TYPE 35 19
  RINL MUTATED RINL WILD-TYPE 
             8             54 
  RINL MUTATED RINL WILD-TYPE 
             4             19 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX 
       67.59        15.25        36.26       121.25        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       18.15        35.57        16.37        24.62        11.31        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       23.64        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  RINL MUTATED RINL WILD-TYPE 
          5.23           0.00 
  RINL MUTATED RINL WILD-TYPE 
        127.50         153.63 
  RINL MUTATED RINL WILD-TYPE 
        31.250         43.925 
[1] "5.2 - 127.5 (31.2)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.6"
D13V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RINL MUTATED         0        3         3        2
  RINL WILD-TYPE       6       26        11        9
D13V3, multiclass
           clus
vv          RINL MUTATED RINL WILD-TYPE
  STAGE I              0              6
  STAGE II             3             26
  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 29  5 12
D13V4, multiclass
    clus
vv   RINL MUTATED RINL WILD-TYPE
  T1            0              6
  T2            4             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
  RINL MUTATED    7  1
  RINL WILD-TYPE 47  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      7    1
  RINL WILD-TYPE   47    5
   clus
vv  RINL MUTATED RINL WILD-TYPE
  0            7             47
  1            1              5
[1] 2 2
[1] FALSE
D13V6, 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
D13V7, binary
                cls
clus              0  1
  RINL MUTATED    3  5
  RINL WILD-TYPE 43  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      3    5
  RINL WILD-TYPE   43    9
     clus
vv    RINL MUTATED RINL WILD-TYPE
  NO             3             43
  YES            5              9
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RINL MUTATED                                       0
  RINL WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RINL MUTATED                                          0
  RINL WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RINL MUTATED                                      8
  RINL WILD-TYPE                                   50
D13V8, multiclass
                                          clus
vv                                         RINL MUTATED RINL WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                8             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  RINL MUTATED    6  0  2  0
  RINL WILD-TYPE 38  4  6  4
D13V9, multiclass
    clus
vv   RINL MUTATED RINL WILD-TYPE
  R0            6             38
  R1            0              4
  R2            2              6
  RX            0              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"
D13V10, continuous
D13V11, 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(14) Variable = ZAR1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  ZAR1 MUTATED    6  5
  ZAR1 WILD-TYPE 33 18
  ZAR1 MUTATED ZAR1 WILD-TYPE 
            11             51 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
             5             18 
$`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 TCGA-P6-A5OH 
       68.25        28.64        23.64        90.08         0.00 

$`ZAR1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       31.23        35.57        16.37        24.62        24.36        46.49 
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-A5L6 TCGA-OR-A5LC 
       58.55        60.89       152.15        31.79        28.31         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        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  ZAR1 MUTATED ZAR1 WILD-TYPE 
          0.00           4.11 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
         90.08         153.63 
  ZAR1 MUTATED ZAR1 WILD-TYPE 
         30.31          44.84 
[1] "0.0 - 90.1 (30.3)"  "4.1 - 153.6 (44.8)"
[1] "hr=" "1.7"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ZAR1 MUTATED         0        6         2        3
  ZAR1 WILD-TYPE       6       23        12        8
D14V3, multiclass
           clus
vv          ZAR1 MUTATED ZAR1 WILD-TYPE
  STAGE I              0              6
  STAGE II             6             23
  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 26  7 10
D14V4, multiclass
    clus
vv   ZAR1 MUTATED ZAR1 WILD-TYPE
  T1            0              6
  T2            7             26
  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"
D14V5, binary
                cls
clus              0  1
  ZAR1 MUTATED    9  2
  ZAR1 WILD-TYPE 45  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      9    2
  ZAR1 WILD-TYPE   45    4
   clus
vv  ZAR1 MUTATED ZAR1 WILD-TYPE
  0            9             45
  1            2              4
[1] 2 2
[1] FALSE
D14V6, 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
D14V7, binary
                cls
clus              0  1
  ZAR1 MUTATED    8  3
  ZAR1 WILD-TYPE 38 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      8    3
  ZAR1 WILD-TYPE   38   11
     clus
vv    ZAR1 MUTATED ZAR1 WILD-TYPE
  NO             8             38
  YES            3             11
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZAR1 MUTATED                                       1
  ZAR1 WILD-TYPE                                     0
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZAR1 MUTATED                                          2
  ZAR1 WILD-TYPE                                        1
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZAR1 MUTATED                                      8
  ZAR1 WILD-TYPE                                   50
D14V8, multiclass
                                          clus
vv                                         ZAR1 MUTATED ZAR1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               1              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            2              1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                8             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  ZAR1 MUTATED    8  1  2  0
  ZAR1 WILD-TYPE 36  3  6  4
D14V9, multiclass
    clus
vv   ZAR1 MUTATED ZAR1 WILD-TYPE
  R0            8             36
  R1            1              3
  R2            2              6
  RX            0              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"
D14V10, continuous
D14V11, 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(15) Variable = CTNNB1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED    3  5
  CTNNB1 WILD-TYPE 36 18
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8               54 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               5               18 
$`CTNNB1 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JY TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5L1 
       55.13        18.15        16.37        11.31       153.63        58.55 
TCGA-OR-A5L3 TCGA-OR-A5LJ 
      152.15        36.33 

$`CTNNB1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 
       66.51        72.39        31.23        32.68        35.57        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       24.36        46.49        83.80        95.18       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       44.84         4.11        60.89        31.79        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       23.64         5.23        39.35        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           11.31             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          153.63           127.50 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          45.730           42.905 
[1] "11.3 - 153.6 (45.7)" "0.0 - 127.5 (42.9)" 
[1] "hr=" "1.9"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CTNNB1 MUTATED         1        3         1        3
  CTNNB1 WILD-TYPE       5       26        13        8
D15V3, multiclass
           clus
vv          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               26
  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
  CTNNB1 MUTATED    1  4  2  1
  CTNNB1 WILD-TYPE  5 29  5 13
D15V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              1                5
  T2              4               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"
D15V5, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    6  2
  CTNNB1 WILD-TYPE 48  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6    2
  CTNNB1 WILD-TYPE   48    4
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0              6               48
  1              2                4
[1] 2 2
[1] FALSE
D15V6, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    8  0
  CTNNB1 WILD-TYPE 32 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      8    0
  CTNNB1 WILD-TYPE   32   22
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              8               32
  MALE                0               22
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    6  2
  CTNNB1 WILD-TYPE 40 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6    2
  CTNNB1 WILD-TYPE   40   12
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               6               40
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CTNNB1 MUTATED                                       0
  CTNNB1 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CTNNB1 MUTATED                                          0
  CTNNB1 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CTNNB1 MUTATED                                      8
  CTNNB1 WILD-TYPE                                   50
D15V8, multiclass
                                          clus
vv                                         CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  8               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  CTNNB1 MUTATED    5  0  3  0
  CTNNB1 WILD-TYPE 39  4  5  4
D15V9, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              5               39
  R1              0                4
  R2              3                5
  RX              0                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"
D15V10, continuous
D15V11, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    1  4
  CTNNB1 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1    4
  CTNNB1 WILD-TYPE    6   23
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  1                6
  NOT HISPANIC OR LATINO              4               23
[1] 2 2
[1] FALSE

Clustering(16) Variable = APOE MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  APOE MUTATED    5  2
  APOE WILD-TYPE 34 21
  APOE MUTATED APOE WILD-TYPE 
             7             55 
  APOE MUTATED APOE WILD-TYPE 
             2             21 
$`APOE MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 
       42.51        18.12        72.39        35.57        24.62        11.31 
TCGA-OR-A5KS 
       83.80 

$`APOE WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KO 
       31.23        18.15        32.68        16.37        24.36        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        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        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04         6.81         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  APOE MUTATED APOE WILD-TYPE 
         11.31           0.00 
  APOE MUTATED APOE WILD-TYPE 
         83.80         153.63 
  APOE MUTATED APOE WILD-TYPE 
         35.57          44.55 
[1] "11.3 - 83.8 (35.6)" "0.0 - 153.6 (44.5)"
[1] "hr=" "1.2"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  APOE MUTATED         0        4         1        1
  APOE WILD-TYPE       6       25        13       10
D16V3, multiclass
           clus
vv          APOE MUTATED APOE WILD-TYPE
  STAGE I              0              6
  STAGE II             4             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
  APOE MUTATED    0  4  0  2
  APOE WILD-TYPE  6 29  7 12
D16V4, multiclass
    clus
vv   APOE MUTATED APOE WILD-TYPE
  T1            0              6
  T2            4             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"
D16V5, binary
                cls
clus              0  1
  APOE MUTATED    6  0
  APOE WILD-TYPE 48  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      6    0
  APOE WILD-TYPE   48    6
   clus
vv  APOE MUTATED APOE WILD-TYPE
  0            6             48
  1            0              6
[1] 2 2
[1] FALSE
D16V6, 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
D16V7, binary
                cls
clus              0  1
  APOE MUTATED    3  3
  APOE WILD-TYPE 43 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      3    3
  APOE WILD-TYPE   43   11
     clus
vv    APOE MUTATED APOE WILD-TYPE
  NO             3             43
  YES            3             11
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  APOE MUTATED                                       0
  APOE WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  APOE MUTATED                                          0
  APOE WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  APOE MUTATED                                      7
  APOE WILD-TYPE                                   51
D16V8, multiclass
                                          clus
vv                                         APOE MUTATED APOE WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                7             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  APOE MUTATED    4  2  0  0
  APOE WILD-TYPE 40  2  8  4
D16V9, multiclass
    clus
vv   APOE MUTATED APOE WILD-TYPE
  R0            4             40
  R1            2              2
  R2            0              8
  RX            0              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"
D16V10, continuous
D16V11, 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(17) Variable = GPRIN2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2               0  1
  GPRIN2 MUTATED    5  3
  GPRIN2 WILD-TYPE 34 20
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               8               54 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               3               20 
$`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 TCGA-P6-A5OH 
       23.64         0.00 

$`GPRIN2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       49.22        67.59        15.25        36.26       121.25        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       31.23        18.15        35.57        16.37        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        83.80        95.18       127.50        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64         5.23        39.35        36.33        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       79.07        61.05        28.04         6.81        24.85       119.11 

  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
            0.00             4.11 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          153.63           152.15 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          27.220           44.695 
[1] "0.0 - 153.6 (27.2)" "4.1 - 152.2 (44.7)"
[1] "hr=" "1.4"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GPRIN2 MUTATED         0        5         2        1
  GPRIN2 WILD-TYPE       6       24        12       10
D17V3, multiclass
           clus
vv          GPRIN2 MUTATED GPRIN2 WILD-TYPE
  STAGE I                0                6
  STAGE II               5               24
  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 28  7 11
D17V4, multiclass
    clus
vv   GPRIN2 MUTATED GPRIN2 WILD-TYPE
  T1              0                6
  T2              5               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"
D17V5, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    8  0
  GPRIN2 WILD-TYPE 46  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      8    0
  GPRIN2 WILD-TYPE   46    6
   clus
vv  GPRIN2 MUTATED GPRIN2 WILD-TYPE
  0              8               46
  1              0                6
[1] 2 2
[1] FALSE
D17V6, 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
D17V7, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    5  3
  GPRIN2 WILD-TYPE 41 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      5    3
  GPRIN2 WILD-TYPE   41   11
     clus
vv    GPRIN2 MUTATED GPRIN2 WILD-TYPE
  NO               5               41
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  GPRIN2 MUTATED                                       0
  GPRIN2 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  GPRIN2 MUTATED                                          0
  GPRIN2 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  GPRIN2 MUTATED                                      8
  GPRIN2 WILD-TYPE                                   50
D17V8, multiclass
                                          clus
vv                                         GPRIN2 MUTATED GPRIN2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  8               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  GPRIN2 MUTATED    6  0  2  0
  GPRIN2 WILD-TYPE 38  4  6  4
D17V9, multiclass
    clus
vv   GPRIN2 MUTATED GPRIN2 WILD-TYPE
  R0              6               38
  R1              0                4
  R2              2                6
  RX              0                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"
D17V10, continuous
D17V11, 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(18) Variable = ASPDH MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  ASPDH MUTATED    4  4
  ASPDH WILD-TYPE 35 19
  ASPDH MUTATED ASPDH WILD-TYPE 
              8              54 
  ASPDH MUTATED ASPDH WILD-TYPE 
              4              19 
$`ASPDH MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       42.51        30.31        57.53        32.68        35.57        16.37 
TCGA-OR-A5KW TCGA-OR-A5KX 
       68.25        44.84 

$`ASPDH WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       31.23        18.15        24.62        11.31        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80        95.18       153.63       127.50         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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  ASPDH MUTATED ASPDH WILD-TYPE 
          16.37            0.00 
  ASPDH MUTATED ASPDH WILD-TYPE 
          68.25          153.63 
  ASPDH MUTATED ASPDH WILD-TYPE 
         39.040          43.925 
[1] "16.4 - 68.2 (39.0)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.6"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASPDH MUTATED         0        0         5        1
  ASPDH WILD-TYPE       6       29         9       10
D18V3, multiclass
           clus
vv          ASPDH MUTATED ASPDH WILD-TYPE
  STAGE I               0               6
  STAGE II              0              29
  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 31  6 11
D18V4, multiclass
    clus
vv   ASPDH MUTATED ASPDH WILD-TYPE
  T1             0               6
  T2             2              31
  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"
D18V5, binary
                 cls
clus               0  1
  ASPDH MUTATED    4  2
  ASPDH WILD-TYPE 50  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      4    2
  ASPDH WILD-TYPE   50    4
   clus
vv  ASPDH MUTATED ASPDH WILD-TYPE
  0             4              50
  1             2               4
[1] 2 2
[1] FALSE
D18V6, 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
D18V7, binary
                 cls
clus               0  1
  ASPDH MUTATED    2  5
  ASPDH WILD-TYPE 44  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      2    5
  ASPDH WILD-TYPE   44    9
     clus
vv    ASPDH MUTATED ASPDH WILD-TYPE
  NO              2              44
  YES             5               9
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ASPDH MUTATED                                       0
  ASPDH WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ASPDH MUTATED                                          0
  ASPDH WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ASPDH MUTATED                                      8
  ASPDH WILD-TYPE                                   50
D18V8, multiclass
                                          clus
vv                                         ASPDH MUTATED ASPDH WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 8              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  ASPDH MUTATED    4  2  0  0
  ASPDH WILD-TYPE 40  2  8  4
D18V9, multiclass
    clus
vv   ASPDH MUTATED ASPDH WILD-TYPE
  R0             4              40
  R1             2               2
  R2             0               8
  RX             0               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"
D18V10, continuous
D18V11, 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(19) Variable = ERCC2 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  ERCC2 MUTATED    5  5
  ERCC2 WILD-TYPE 34 18
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10              52 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
              5              18 
$`ERCC2 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 
       68.75        15.25       121.25        72.39        32.68        16.37 
TCGA-OR-A5K9 TCGA-OR-A5KW TCGA-OR-A5LJ TCGA-OR-A5LO 
       11.31        68.25        36.33        79.07 

$`ERCC2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        67.59        36.26        29.82        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       18.15        35.57        24.62        24.36        46.49        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR 
        5.23        39.35        90.08        53.03        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  ERCC2 MUTATED ERCC2 WILD-TYPE 
          11.31            0.00 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         121.25          153.63 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         52.290          42.905 
[1] "11.3 - 121.2 (52.3)" "0.0 - 153.6 (42.9)" 
[1] "hr=" "1.4"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         1        4         4        1
  ERCC2 WILD-TYPE       5       25        10       10
D19V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               1               5
  STAGE II              4              25
  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 27  5 13
D19V4, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  T1             1               5
  T2             6              27
  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"
D19V5, binary
                 cls
clus               0  1
  ERCC2 MUTATED    8  2
  ERCC2 WILD-TYPE 46  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      8    2
  ERCC2 WILD-TYPE   46    4
   clus
vv  ERCC2 MUTATED ERCC2 WILD-TYPE
  0             8              46
  1             2               4
[1] 2 2
[1] FALSE
D19V6, 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
D19V7, binary
                 cls
clus               0  1
  ERCC2 MUTATED    6  4
  ERCC2 WILD-TYPE 40 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      6    4
  ERCC2 WILD-TYPE   40   10
     clus
vv    ERCC2 MUTATED ERCC2 WILD-TYPE
  NO              6              40
  YES             4              10
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ERCC2 MUTATED                                       0
  ERCC2 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ERCC2 MUTATED                                          0
  ERCC2 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ERCC2 MUTATED                                     10
  ERCC2 WILD-TYPE                                   48
D19V8, multiclass
                                          clus
vv                                         ERCC2 MUTATED ERCC2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                10              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  ERCC2 MUTATED    9  0  1  0
  ERCC2 WILD-TYPE 35  4  7  4
D19V9, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  R0             9              35
  R1             0               4
  R2             1               7
  RX             0               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"
D19V10, continuous
D19V11, 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(20) Variable = IDUA MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  IDUA MUTATED    6  2
  IDUA WILD-TYPE 33 21
  IDUA MUTATED IDUA WILD-TYPE 
             8             54 
  IDUA MUTATED IDUA WILD-TYPE 
             2             21 
$`IDUA MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5JP TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5L3 
       91.30        42.51        15.25        11.31       153.63       152.15 
TCGA-OR-A5LK TCGA-OR-A5LO 
       90.08        79.07 

$`IDUA WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        39.58        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        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        35.57        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       24.36        46.49        83.80        95.18       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84         4.11        58.55        60.89        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL 
       28.64        23.64         5.23        39.35        36.33        53.03 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  IDUA MUTATED IDUA WILD-TYPE 
         11.31           0.00 
  IDUA MUTATED IDUA WILD-TYPE 
        153.63         127.50 
  IDUA MUTATED IDUA WILD-TYPE 
        84.575         39.465 
[1] "11.3 - 153.6 (84.6)" "0.0 - 127.5 (39.5)" 
[1] "hr=" "2.1"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         1        6         0        0
  IDUA WILD-TYPE       5       23        14       11
D20V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              1              5
  STAGE II             6             23
  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 27  7 14
D20V4, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  T1            1              5
  T2            6             27
  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"
D20V5, binary
                cls
clus              0  1
  IDUA MUTATED    7  0
  IDUA WILD-TYPE 47  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      7    0
  IDUA WILD-TYPE   47    6
   clus
vv  IDUA MUTATED IDUA WILD-TYPE
  0            7             47
  1            0              6
[1] 2 2
[1] FALSE
D20V6, 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
D20V7, binary
                cls
clus              0  1
  IDUA MUTATED    7  1
  IDUA WILD-TYPE 39 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      7    1
  IDUA WILD-TYPE   39   13
     clus
vv    IDUA MUTATED IDUA WILD-TYPE
  NO             7             39
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  IDUA MUTATED                                       0
  IDUA WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  IDUA MUTATED                                          1
  IDUA WILD-TYPE                                        2
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  IDUA MUTATED                                      7
  IDUA WILD-TYPE                                   51
D20V8, multiclass
                                          clus
vv                                         IDUA MUTATED IDUA WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            1              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                7             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  IDUA MUTATED    7  0  0  0
  IDUA WILD-TYPE 37  4  8  4
D20V9, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  R0            7             37
  R1            0              4
  R2            0              8
  RX            0              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"
D20V10, continuous
D20V11, 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(21) Variable = C1ORF106 MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  C1ORF106 MUTATED    7  2
  C1ORF106 WILD-TYPE 32 21
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 9                 53 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
                 2                 21 
$`C1ORF106 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5KU 
       91.30        67.59        15.25        18.15        95.18       153.63 
TCGA-OR-A5KX TCGA-OR-A5LA TCGA-OR-A5LO 
       44.84        23.64        79.07 

$`C1ORF106 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
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-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ 
       24.36        46.49        83.80       127.50        68.25         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        28.31        28.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
        5.23        39.35        36.33        90.08        53.03        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
             15.25               0.00 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
            153.63             152.15 
  C1ORF106 MUTATED C1ORF106 WILD-TYPE 
             67.59              39.58 
[1] "15.2 - 153.6 (67.6)" "0.0 - 152.2 (39.6)" 
[1] "hr=" "2.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C1ORF106 MUTATED         2        5         1        1
  C1ORF106 WILD-TYPE       4       24        13       10
D21V3, multiclass
           clus
vv          C1ORF106 MUTATED C1ORF106 WILD-TYPE
  STAGE I                  2                  4
  STAGE II                 5                 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
  C1ORF106 MUTATED    2  6  0  1
  C1ORF106 WILD-TYPE  4 27  7 13
D21V4, multiclass
    clus
vv   C1ORF106 MUTATED C1ORF106 WILD-TYPE
  T1                2                  4
  T2                6                 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"
D21V5, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    7  2
  C1ORF106 WILD-TYPE 47  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      7    2
  C1ORF106 WILD-TYPE   47    4
   clus
vv  C1ORF106 MUTATED C1ORF106 WILD-TYPE
  0                7                 47
  1                2                  4
[1] 2 2
[1] FALSE
D21V6, 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
D21V7, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    8  1
  C1ORF106 WILD-TYPE 38 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      8    1
  C1ORF106 WILD-TYPE   38   13
     clus
vv    C1ORF106 MUTATED C1ORF106 WILD-TYPE
  NO                 8                 38
  YES                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  C1ORF106 MUTATED                                       0
  C1ORF106 WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  C1ORF106 MUTATED                                          0
  C1ORF106 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  C1ORF106 MUTATED                                      9
  C1ORF106 WILD-TYPE                                   49
D21V8, multiclass
                                          clus
vv                                         C1ORF106 MUTATED C1ORF106 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    9                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  C1ORF106 MUTATED    8  0  1  0
  C1ORF106 WILD-TYPE 36  4  7  4
D21V9, multiclass
    clus
vv   C1ORF106 MUTATED C1ORF106 WILD-TYPE
  R0                8                 36
  R1                0                  4
  R2                1                  7
  RX                0                  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"
D21V10, continuous
D21V11, 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(22) Variable = C10ORF95 MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  C10ORF95 MUTATED    3  3
  C10ORF95 WILD-TYPE 36 20
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 6                 56 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 3                 20 
$`C10ORF95 MUTATED`
TCGA-OR-A5LB TCGA-OR-A5JQ TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5LO TCGA-PK-A5H8 
       39.58        36.26        11.31        24.36        79.07       119.11 

$`C10ORF95 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        15.25       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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.62        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        90.08        53.03        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG 
        0.00        24.85 

  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
             11.31               0.00 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
            119.11             153.63 
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
            37.920             43.925 
[1] "11.3 - 119.1 (37.9)" "0.0 - 153.6 (43.9)" 
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C10ORF95 MUTATED         0        5         0        1
  C10ORF95 WILD-TYPE       6       24        14       10
D22V3, multiclass
           clus
vv          C10ORF95 MUTATED C10ORF95 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 5                 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  5  0  1
  C10ORF95 WILD-TYPE  6 28  7 13
D22V4, multiclass
    clus
vv   C10ORF95 MUTATED C10ORF95 WILD-TYPE
  T1                0                  6
  T2                5                 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"
D22V5, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    6  0
  C10ORF95 WILD-TYPE 48  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      6    0
  C10ORF95 WILD-TYPE   48    6
   clus
vv  C10ORF95 MUTATED C10ORF95 WILD-TYPE
  0                6                 48
  1                0                  6
[1] 2 2
[1] FALSE
D22V6, 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
D22V7, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    5  1
  C10ORF95 WILD-TYPE 41 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      5    1
  C10ORF95 WILD-TYPE   41   13
     clus
vv    C10ORF95 MUTATED C10ORF95 WILD-TYPE
  NO                 5                 41
  YES                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  C10ORF95 MUTATED                                       1
  C10ORF95 WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  C10ORF95 MUTATED                                          0
  C10ORF95 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  C10ORF95 MUTATED                                      5
  C10ORF95 WILD-TYPE                                   53
D22V8, multiclass
                                          clus
vv                                         C10ORF95 MUTATED C10ORF95 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  C10ORF95 MUTATED    6  0  0  0
  C10ORF95 WILD-TYPE 38  4  8  4
D22V9, multiclass
    clus
vv   C10ORF95 MUTATED C10ORF95 WILD-TYPE
  R0                6                 38
  R1                0                  4
  R2                0                  8
  RX                0                  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"
D22V10, continuous
[1] "Remove cluster labels:" "C10ORF95 MUTATED"      
clus
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 2                 18 
        TCGA-OR-A5KP         TCGA-OR-A5J2         TCGA-OR-A5J3 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J7         TCGA-OR-A5J8 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JX 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5JY         TCGA-OR-A5K2         TCGA-OR-A5K5 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LL         TCGA-OR-A5LP 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
D22V11, 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(23) Variable = RGS9BP MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2               0  1
  RGS9BP MUTATED    5  3
  RGS9BP WILD-TYPE 34 20
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8               54 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               3               20 
$`RGS9BP MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5JR TCGA-OR-A5JX TCGA-OR-A5K5 TCGA-OR-A5K8 
       42.51        13.91       121.25        31.23        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5LA 
       11.31        23.64 

$`RGS9BP WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25        36.26        29.82        66.51        72.39 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       18.15        32.68        35.57        24.36        46.49        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        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        28.31        28.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  RGS9BP MUTATED RGS9BP WILD-TYPE 
           11.31             0.00 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
          121.25           153.63 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
          24.130           45.665 
[1] "11.3 - 121.2 (24.1)" "0.0 - 153.6 (45.7)" 
[1] "hr=" "1.6"
D23V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RGS9BP MUTATED         1        3         2        1
  RGS9BP WILD-TYPE       5       26        12       10
D23V3, multiclass
           clus
vv          RGS9BP MUTATED RGS9BP WILD-TYPE
  STAGE I                1                5
  STAGE II               3               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
  RGS9BP MUTATED    1  3  3  0
  RGS9BP WILD-TYPE  5 30  4 14
D23V4, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  T1              1                5
  T2              3               30
  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"
D23V5, binary
                  cls
clus                0  1
  RGS9BP MUTATED    6  1
  RGS9BP WILD-TYPE 48  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      6    1
  RGS9BP WILD-TYPE   48    5
   clus
vv  RGS9BP MUTATED RGS9BP WILD-TYPE
  0              6               48
  1              1                5
[1] 2 2
[1] FALSE
D23V6, 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
D23V7, binary
                  cls
clus                0  1
  RGS9BP MUTATED    5  3
  RGS9BP WILD-TYPE 41 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      5    3
  RGS9BP WILD-TYPE   41   11
     clus
vv    RGS9BP MUTATED RGS9BP WILD-TYPE
  NO               5               41
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RGS9BP MUTATED                                       0
  RGS9BP WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RGS9BP MUTATED                                          0
  RGS9BP WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RGS9BP MUTATED                                      8
  RGS9BP WILD-TYPE                                   50
D23V8, multiclass
                                          clus
vv                                         RGS9BP MUTATED RGS9BP WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  8               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  RGS9BP MUTATED    6  0  1  0
  RGS9BP WILD-TYPE 38  4  7  4
D23V9, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  R0              6               38
  R1              0                4
  R2              1                7
  RX              0                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"
D23V10, continuous
D23V11, 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(24) Variable = THEM4 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2              0  1
  THEM4 MUTATED    3  2
  THEM4 WILD-TYPE 36 21
  THEM4 MUTATED THEM4 WILD-TYPE 
              5              57 
  THEM4 MUTATED THEM4 WILD-TYPE 
              2              21 
$`THEM4 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5LJ 
       42.51        67.59        11.31        24.36        36.33 

$`THEM4 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        15.25        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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.62        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  THEM4 MUTATED THEM4 WILD-TYPE 
          11.31            0.00 
  THEM4 MUTATED THEM4 WILD-TYPE 
          67.59          153.63 
  THEM4 MUTATED THEM4 WILD-TYPE 
          36.33           44.55 
[1] "11.3 - 67.6 (36.3)" "0.0 - 153.6 (44.5)"
[1] "hr=" "1.4"
D24V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  THEM4 MUTATED         1        2         0        1
  THEM4 WILD-TYPE       5       27        14       10
D24V3, multiclass
           clus
vv          THEM4 MUTATED THEM4 WILD-TYPE
  STAGE I               1               5
  STAGE II              2              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
  THEM4 MUTATED    1  3  0  0
  THEM4 WILD-TYPE  5 30  7 14
D24V4, multiclass
    clus
vv   THEM4 MUTATED THEM4 WILD-TYPE
  T1             1               5
  T2             3              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"
D24V5, binary
                 cls
clus               0  1
  THEM4 MUTATED    3  1
  THEM4 WILD-TYPE 51  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      3    1
  THEM4 WILD-TYPE   51    5
   clus
vv  THEM4 MUTATED THEM4 WILD-TYPE
  0             3              51
  1             1               5
[1] 2 2
[1] FALSE
D24V6, 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
D24V7, binary
                 cls
clus               0  1
  THEM4 MUTATED    4  1
  THEM4 WILD-TYPE 42 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      4    1
  THEM4 WILD-TYPE   42   13
     clus
vv    THEM4 MUTATED THEM4 WILD-TYPE
  NO              4              42
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  THEM4 MUTATED                                       0
  THEM4 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  THEM4 MUTATED                                          0
  THEM4 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  THEM4 MUTATED                                      5
  THEM4 WILD-TYPE                                   53
D24V8, multiclass
                                          clus
vv                                         THEM4 MUTATED THEM4 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  THEM4 MUTATED    3  0  1  0
  THEM4 WILD-TYPE 41  4  7  4
D24V9, multiclass
    clus
vv   THEM4 MUTATED THEM4 WILD-TYPE
  R0             3              41
  R1             0               4
  R2             1               7
  RX             0               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"
D24V10, continuous
[1] "Remove cluster labels:" "THEM4 MUTATED"         
clus
  THEM4 MUTATED THEM4 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
D24V11, 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(25) Variable = TSC22D2 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                0  1
  TSC22D2 MUTATED    3  5
  TSC22D2 WILD-TYPE 36 18
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                8                54 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
                5                18 
$`TSC22D2 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JQ TCGA-OR-A5K2 TCGA-OR-A5LC 
       42.51        19.04        30.31        36.26        32.68         5.23 
TCGA-OR-A5LP TCGA-P6-A5OH 
       61.05         0.00 

$`TSC22D2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       15.25       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-A5KB 
       18.15        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.31        28.64        23.64        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       53.03        79.07        28.04         6.81        24.85       119.11 

  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
             0.00              4.11 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
            61.05            153.63 
  TSC22D2 MUTATED TSC22D2 WILD-TYPE 
           31.495            45.665 
[1] "0.0 - 61.0 (31.5)"  "4.1 - 153.6 (45.7)"
[1] "hr=" "3.1"
D25V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TSC22D2 MUTATED         0        2         2        3
  TSC22D2 WILD-TYPE       6       27        12        8
D25V3, multiclass
           clus
vv          TSC22D2 MUTATED TSC22D2 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                27
  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 31  6 10
D25V4, multiclass
    clus
vv   TSC22D2 MUTATED TSC22D2 WILD-TYPE
  T1               0                 6
  T2               2                31
  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"
D25V5, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    7  0
  TSC22D2 WILD-TYPE 47  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      7    0
  TSC22D2 WILD-TYPE   47    6
   clus
vv  TSC22D2 MUTATED TSC22D2 WILD-TYPE
  0               7                47
  1               0                 6
[1] 2 2
[1] FALSE
D25V6, 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
D25V7, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    5  3
  TSC22D2 WILD-TYPE 41 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      5    3
  TSC22D2 WILD-TYPE   41   11
     clus
vv    TSC22D2 MUTATED TSC22D2 WILD-TYPE
  NO                5                41
  YES               3                11
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TSC22D2 MUTATED                                       1
  TSC22D2 WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TSC22D2 MUTATED                                          0
  TSC22D2 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TSC22D2 MUTATED                                      7
  TSC22D2 WILD-TYPE                                   51
D25V8, multiclass
                                          clus
vv                                         TSC22D2 MUTATED TSC22D2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   7                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  TSC22D2 MUTATED    4  1  2  0
  TSC22D2 WILD-TYPE 40  3  6  4
D25V9, multiclass
    clus
vv   TSC22D2 MUTATED TSC22D2 WILD-TYPE
  R0               4                40
  R1               1                 3
  R2               2                 6
  RX               0                 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"
D25V10, continuous
D25V11, 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(26) Variable = SYT8 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2             0  1
  SYT8 MUTATED    6  2
  SYT8 WILD-TYPE 33 21
  SYT8 MUTATED SYT8 WILD-TYPE 
             8             54 
  SYT8 MUTATED SYT8 WILD-TYPE 
             2             21 
$`SYT8 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5JF TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5LO 
       91.30        39.58        66.25        46.49        83.80        79.07 
TCGA-OR-A5LR TCGA-PA-A5YG 
       28.04        24.85 

$`SYT8 WILD-TYPE`
TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        42.51        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       57.53        99.88        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        24.36        95.18       153.63       127.50        68.25 
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-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-P6-A5OF TCGA-P6-A5OH TCGA-PK-A5H8 
       90.08        53.03        61.05         6.81         0.00       119.11 

  SYT8 MUTATED SYT8 WILD-TYPE 
         24.85           0.00 
  SYT8 MUTATED SYT8 WILD-TYPE 
         91.30         153.63 
  SYT8 MUTATED SYT8 WILD-TYPE 
         56.37          40.93 
[1] "24.9 - 91.3 (56.4)" "0.0 - 153.6 (40.9)"
[1] "hr=" "2"  
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SYT8 MUTATED         0        6         0        2
  SYT8 WILD-TYPE       6       23        14        9
D26V3, multiclass
           clus
vv          SYT8 MUTATED SYT8 WILD-TYPE
  STAGE I              0              6
  STAGE II             6             23
  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 27  7 12
D26V4, multiclass
    clus
vv   SYT8 MUTATED SYT8 WILD-TYPE
  T1            0              6
  T2            6             27
  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"
D26V5, binary
                cls
clus              0  1
  SYT8 MUTATED    8  0
  SYT8 WILD-TYPE 46  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      8    0
  SYT8 WILD-TYPE   46    6
   clus
vv  SYT8 MUTATED SYT8 WILD-TYPE
  0            8             46
  1            0              6
[1] 2 2
[1] FALSE
D26V6, 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
D26V7, binary
                cls
clus              0  1
  SYT8 MUTATED    6  2
  SYT8 WILD-TYPE 40 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      6    2
  SYT8 WILD-TYPE   40   12
     clus
vv    SYT8 MUTATED SYT8 WILD-TYPE
  NO             6             40
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SYT8 MUTATED                                       0
  SYT8 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SYT8 MUTATED                                          0
  SYT8 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SYT8 MUTATED                                      8
  SYT8 WILD-TYPE                                   50
D26V8, multiclass
                                          clus
vv                                         SYT8 MUTATED SYT8 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                8             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  SYT8 MUTATED    8  0  0  0
  SYT8 WILD-TYPE 36  4  8  4
D26V9, multiclass
    clus
vv   SYT8 MUTATED SYT8 WILD-TYPE
  R0            8             36
  R1            0              4
  R2            0              8
  RX            0              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"
D26V10, continuous
[1] "Remove cluster labels:" "SYT8 MUTATED"          
clus
  SYT8 MUTATED SYT8 WILD-TYPE 
             2             18 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J7 
"SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JX 
"SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" 
    TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5     TCGA-OR-A5KB 
"SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" "SYT8 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LP 
"SYT8 WILD-TYPE" "SYT8 WILD-TYPE" 
D26V11, 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(27) Variable = PLIN5 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2              0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 35 22
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              5              57 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
              1              22 
$`PLIN5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JF TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5L9 
       68.75        66.25        72.39        18.15        28.64 

$`PLIN5 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        28.31        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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  PLIN5 MUTATED PLIN5 WILD-TYPE 
          18.15            0.00 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
          72.39          153.63 
  PLIN5 MUTATED PLIN5 WILD-TYPE 
          66.25           42.51 
[1] "18.1 - 72.4 (66.2)" "0.0 - 153.6 (42.5)"
[1] "hr=" "2.2"
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PLIN5 MUTATED         0        3         1        1
  PLIN5 WILD-TYPE       6       26        13       10
D27V3, multiclass
           clus
vv          PLIN5 MUTATED PLIN5 WILD-TYPE
  STAGE I               0               6
  STAGE II              3              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
  PLIN5 MUTATED    0  3  1  1
  PLIN5 WILD-TYPE  6 30  6 13
D27V4, multiclass
    clus
vv   PLIN5 MUTATED PLIN5 WILD-TYPE
  T1             0               6
  T2             3              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"
D27V5, binary
                 cls
clus               0  1
  PLIN5 MUTATED    4  1
  PLIN5 WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      4    1
  PLIN5 WILD-TYPE   50    5
   clus
vv  PLIN5 MUTATED PLIN5 WILD-TYPE
  0             4              50
  1             1               5
[1] 2 2
[1] FALSE
D27V6, 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
D27V7, binary
                 cls
clus               0  1
  PLIN5 MUTATED    2  3
  PLIN5 WILD-TYPE 44 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      2    3
  PLIN5 WILD-TYPE   44   11
     clus
vv    PLIN5 MUTATED PLIN5 WILD-TYPE
  NO              2              44
  YES             3              11
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PLIN5 MUTATED                                       0
  PLIN5 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PLIN5 MUTATED                                          0
  PLIN5 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PLIN5 MUTATED                                      5
  PLIN5 WILD-TYPE                                   53
D27V8, multiclass
                                          clus
vv                                         PLIN5 MUTATED PLIN5 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  PLIN5 MUTATED    4  0  1  0
  PLIN5 WILD-TYPE 40  4  7  4
D27V9, multiclass
    clus
vv   PLIN5 MUTATED PLIN5 WILD-TYPE
  R0             4              40
  R1             0               4
  R2             1               7
  RX             0               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"
D27V10, continuous
D27V11, 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(28) Variable = LRIG1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2              0  1
  LRIG1 MUTATED   11  5
  LRIG1 WILD-TYPE 28 18
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             16              46 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
              5              18 
$`LRIG1 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL 
       42.51        13.91        66.25        69.37        76.64        67.59 
TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L4 
       16.37        24.36        83.80        44.84        60.89        31.79 
TCGA-OR-A5L9 TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-P6-A5OH 
       28.64        36.33        90.08         0.00 

$`LRIG1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       57.53        99.88        49.22        15.25        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-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       35.57        24.62        11.31        46.49        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L6 
      127.50        68.25         4.11        58.55       152.15        28.31 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       23.64         5.23        39.35        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        24.85       119.11 

  LRIG1 MUTATED LRIG1 WILD-TYPE 
           0.00            4.11 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          90.08          153.63 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
         43.675          41.440 
[1] "0.0 - 90.1 (43.7)"  "4.1 - 153.6 (41.4)"
[1] "hr=" "1.3"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRIG1 MUTATED         2        7         3        3
  LRIG1 WILD-TYPE       4       22        11        8
D28V3, multiclass
           clus
vv          LRIG1 MUTATED LRIG1 WILD-TYPE
  STAGE I               2               4
  STAGE II              7              22
  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 24  5 12
D28V4, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  T1             2               4
  T2             9              24
  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"
D28V5, binary
                 cls
clus               0  1
  LRIG1 MUTATED   12  3
  LRIG1 WILD-TYPE 42  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     12    3
  LRIG1 WILD-TYPE   42    3
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0            12              42
  1             3               3
[1] 2 2
[1] FALSE
D28V6, 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
D28V7, binary
                 cls
clus               0  1
  LRIG1 MUTATED   13  3
  LRIG1 WILD-TYPE 33 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     13    3
  LRIG1 WILD-TYPE   33   11
     clus
vv    LRIG1 MUTATED LRIG1 WILD-TYPE
  NO             13              33
  YES             3              11
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  LRIG1 MUTATED                                       0
  LRIG1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  LRIG1 MUTATED                                          2
  LRIG1 WILD-TYPE                                        1
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  LRIG1 MUTATED                                     14
  LRIG1 WILD-TYPE                                   44
D28V8, multiclass
                                          clus
vv                                         LRIG1 MUTATED LRIG1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             2               1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                14              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  LRIG1 MUTATED   11  0  3  1
  LRIG1 WILD-TYPE 33  4  5  3
D28V9, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  R0            11              33
  R1             0               4
  R2             3               5
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, 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(29) Variable = HHIPL1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  HHIPL1 MUTATED    4  2
  HHIPL1 WILD-TYPE 35 21
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               6               56 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               2               21 
$`HHIPL1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KZ 
       19.04        49.22        67.59        24.36       127.50         4.11 

$`HHIPL1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       68.75        13.91        12.00        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        99.88        66.25        69.37        76.64 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
       11.31        46.49        83.80        95.18       153.63        68.25 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84        58.55        60.89       152.15        31.79        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        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
            4.11             0.00 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          127.50           153.63 
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
          36.790           42.905 
[1] "4.1 - 127.5 (36.8)" "0.0 - 153.6 (42.9)"
[1] "hr=" "1"  
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HHIPL1 MUTATED         1        2         2        1
  HHIPL1 WILD-TYPE       5       27        12       10
D29V3, multiclass
           clus
vv          HHIPL1 MUTATED HHIPL1 WILD-TYPE
  STAGE I                1                5
  STAGE II               2               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
  HHIPL1 MUTATED    1  3  1  1
  HHIPL1 WILD-TYPE  5 30  6 13
D29V4, multiclass
    clus
vv   HHIPL1 MUTATED HHIPL1 WILD-TYPE
  T1              1                5
  T2              3               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"
D29V5, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    5  1
  HHIPL1 WILD-TYPE 49  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      5    1
  HHIPL1 WILD-TYPE   49    5
   clus
vv  HHIPL1 MUTATED HHIPL1 WILD-TYPE
  0              5               49
  1              1                5
[1] 2 2
[1] FALSE
D29V6, 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
D29V7, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    3  3
  HHIPL1 WILD-TYPE 43 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      3    3
  HHIPL1 WILD-TYPE   43   11
     clus
vv    HHIPL1 MUTATED HHIPL1 WILD-TYPE
  NO               3               43
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  HHIPL1 MUTATED                                       0
  HHIPL1 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  HHIPL1 MUTATED                                          0
  HHIPL1 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  HHIPL1 MUTATED                                      6
  HHIPL1 WILD-TYPE                                   52
D29V8, multiclass
                                          clus
vv                                         HHIPL1 MUTATED HHIPL1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  6               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  HHIPL1 MUTATED    4  0  1  1
  HHIPL1 WILD-TYPE 40  4  7  3
D29V9, multiclass
    clus
vv   HHIPL1 MUTATED HHIPL1 WILD-TYPE
  R0              4               40
  R1              0                4
  R2              1                7
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, 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(30) Variable = CCDC105 MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  CCDC105 MUTATED    3  3
  CCDC105 WILD-TYPE 36 20
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                6                56 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                3                20 
$`CCDC105 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J3 TCGA-OR-A5JL TCGA-OR-A5K9 TCGA-OR-A5LJ TCGA-OR-A5LL 
       43.30        68.75        67.59        11.31        36.33        53.03 

$`CCDC105 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 
       91.30        39.58        42.51        44.55        55.13        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       90.08        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  CCDC105 MUTATED CCDC105 WILD-TYPE 
            11.31              0.00 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
            68.75            153.63 
  CCDC105 MUTATED CCDC105 WILD-TYPE 
           48.165            41.045 
[1] "11.3 - 68.8 (48.2)" "0.0 - 153.6 (41.0)"
[1] "hr=" "1.4"
D30V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC105 MUTATED         2        2         1        1
  CCDC105 WILD-TYPE       4       27        13       10
D30V3, multiclass
           clus
vv          CCDC105 MUTATED CCDC105 WILD-TYPE
  STAGE I                 2                 4
  STAGE II                2                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
  CCDC105 MUTATED    2  3  1  0
  CCDC105 WILD-TYPE  4 30  6 14
D30V4, multiclass
    clus
vv   CCDC105 MUTATED CCDC105 WILD-TYPE
  T1               2                 4
  T2               3                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"
D30V5, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    5  1
  CCDC105 WILD-TYPE 49  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      5    1
  CCDC105 WILD-TYPE   49    5
   clus
vv  CCDC105 MUTATED CCDC105 WILD-TYPE
  0               5                49
  1               1                 5
[1] 2 2
[1] FALSE
D30V6, 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
D30V7, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    6  0
  CCDC105 WILD-TYPE 40 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      6    0
  CCDC105 WILD-TYPE   40   14
     clus
vv    CCDC105 MUTATED CCDC105 WILD-TYPE
  NO                6                40
  YES               0                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CCDC105 MUTATED                                       0
  CCDC105 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CCDC105 MUTATED                                          0
  CCDC105 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CCDC105 MUTATED                                      6
  CCDC105 WILD-TYPE                                   52
D30V8, multiclass
                                          clus
vv                                         CCDC105 MUTATED CCDC105 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  CCDC105 MUTATED    5  0  1  0
  CCDC105 WILD-TYPE 39  4  7  4
D30V9, multiclass
    clus
vv   CCDC105 MUTATED CCDC105 WILD-TYPE
  R0               5                39
  R1               0                 4
  R2               1                 7
  RX               0                 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"
D30V10, continuous
[1] "Remove cluster labels:" "CCDC105 MUTATED"       
clus
  CCDC105 MUTATED CCDC105 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J4        TCGA-OR-A5J7 
"CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" 
       TCGA-OR-A5J8        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9 
"CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP 
"CCDC105 WILD-TYPE" "CCDC105 WILD-TYPE" 
D30V11, 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(31) Variable = C19ORF10 MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  C19ORF10 MUTATED    4  3
  C19ORF10 WILD-TYPE 35 20
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 7                 55 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
                 3                 20 
$`C19ORF10 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JW TCGA-OR-A5K5 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5L2 
       68.75        72.39        16.37       153.63       127.50        60.89 
TCGA-P6-A5OF 
        6.81 

$`C19ORF10 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 
       66.51        31.23        18.15        32.68        35.57        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KW 
       11.31        24.36        46.49        83.80        95.18        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84         4.11        58.55       152.15        31.79        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        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH TCGA-PA-A5YG 
       53.03        79.07        61.05        28.04         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
              6.81               0.00 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
            153.63             152.15 
  C19ORF10 MUTATED C19ORF10 WILD-TYPE 
             68.75              39.58 
[1] "6.8 - 153.6 (68.8)" "0.0 - 152.2 (39.6)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C19ORF10 MUTATED         0        3         4        0
  C19ORF10 WILD-TYPE       6       26        10       11
D31V3, multiclass
           clus
vv          C19ORF10 MUTATED C19ORF10 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 3                 26
  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 29  5 13
D31V4, multiclass
    clus
vv   C19ORF10 MUTATED C19ORF10 WILD-TYPE
  T1                0                  6
  T2                4                 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"
D31V5, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    6  1
  C19ORF10 WILD-TYPE 48  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      6    1
  C19ORF10 WILD-TYPE   48    5
   clus
vv  C19ORF10 MUTATED C19ORF10 WILD-TYPE
  0                6                 48
  1                1                  5
[1] 2 2
[1] FALSE
D31V6, 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
D31V7, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    4  3
  C19ORF10 WILD-TYPE 42 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      4    3
  C19ORF10 WILD-TYPE   42   11
     clus
vv    C19ORF10 MUTATED C19ORF10 WILD-TYPE
  NO                 4                 42
  YES                3                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  C19ORF10 MUTATED                                       0
  C19ORF10 WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  C19ORF10 MUTATED                                          0
  C19ORF10 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  C19ORF10 MUTATED                                      7
  C19ORF10 WILD-TYPE                                   51
D31V8, multiclass
                                          clus
vv                                         C19ORF10 MUTATED C19ORF10 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  C19ORF10 MUTATED    6  0  0  1
  C19ORF10 WILD-TYPE 38  4  8  3
D31V9, multiclass
    clus
vv   C19ORF10 MUTATED C19ORF10 WILD-TYPE
  R0                6                 38
  R1                0                  4
  R2                0                  8
  RX                1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, 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(32) Variable = OPRD1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  OPRD1 MUTATED    8  4
  OPRD1 WILD-TYPE 31 19
  OPRD1 MUTATED OPRD1 WILD-TYPE 
             12              50 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
              4              19 
$`OPRD1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5K2 
       19.04        30.31        66.25        67.59        15.25        32.68 
TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH 
       24.62       153.63       127.50        61.05        28.04         0.00 

$`OPRD1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB 
       68.75        13.91        12.00        88.87        16.11        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ 
       57.53        99.88        69.37        76.64        49.22        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-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       35.57        16.37        11.31        24.36        46.49        83.80 
TCGA-OR-A5KT TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       95.18        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-P6-A5OF 
       39.35        36.33        90.08        53.03        79.07         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  OPRD1 MUTATED OPRD1 WILD-TYPE 
           0.00            4.11 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         153.63          152.15 
  OPRD1 MUTATED OPRD1 WILD-TYPE 
         31.495          43.925 
[1] "0.0 - 153.6 (31.5)" "4.1 - 152.2 (43.9)"
[1] "hr=" "1.1"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OPRD1 MUTATED         1        6         3        2
  OPRD1 WILD-TYPE       5       23        11        9
D32V3, multiclass
           clus
vv          OPRD1 MUTATED OPRD1 WILD-TYPE
  STAGE I               1               5
  STAGE II              6              23
  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 26  6 11
D32V4, multiclass
    clus
vv   OPRD1 MUTATED OPRD1 WILD-TYPE
  T1             1               5
  T2             7              26
  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 43  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED     11    1
  OPRD1 WILD-TYPE   43    5
   clus
vv  OPRD1 MUTATED OPRD1 WILD-TYPE
  0            11              43
  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    8  4
  OPRD1 WILD-TYPE 38 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      8    4
  OPRD1 WILD-TYPE   38   10
     clus
vv    OPRD1 MUTATED OPRD1 WILD-TYPE
  NO              8              38
  YES             4              10
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  OPRD1 MUTATED                                       0
  OPRD1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  OPRD1 MUTATED                                          0
  OPRD1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  OPRD1 MUTATED                                     12
  OPRD1 WILD-TYPE                                   46
D32V8, multiclass
                                          clus
vv                                         OPRD1 MUTATED OPRD1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                12              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  OPRD1 MUTATED   10  1  1  0
  OPRD1 WILD-TYPE 34  3  7  4
D32V9, multiclass
    clus
vv   OPRD1 MUTATED OPRD1 WILD-TYPE
  R0            10              34
  R1             1               3
  R2             1               7
  RX             0               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"
D32V10, continuous
D32V11, 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 = ATXN1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  ATXN1 MUTATED    6  4
  ATXN1 WILD-TYPE 33 19
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10              52 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              4              19 
$`ATXN1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.00        66.25        24.36        46.49       152.15        31.79 
TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        36.33        79.07        61.05 

$`ATXN1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.62        11.31        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-A5L6 
       68.25        44.84         4.11        58.55        60.89        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LR 
       28.64        23.64        39.35        90.08        53.03        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  ATXN1 MUTATED ATXN1 WILD-TYPE 
           5.23            0.00 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         152.15          153.63 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         41.410          42.905 
[1] "5.2 - 152.2 (41.4)" "0.0 - 153.6 (42.9)"
[1] "hr=" "1.1"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ATXN1 MUTATED         1        4         2        3
  ATXN1 WILD-TYPE       5       25        12        8
D33V3, multiclass
           clus
vv          ATXN1 MUTATED ATXN1 WILD-TYPE
  STAGE I               1               5
  STAGE II              4              25
  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 28  7 10
D33V4, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  T1             1               5
  T2             5              28
  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"
D33V5, binary
                 cls
clus               0  1
  ATXN1 MUTATED    9  1
  ATXN1 WILD-TYPE 45  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      9    1
  ATXN1 WILD-TYPE   45    5
   clus
vv  ATXN1 MUTATED ATXN1 WILD-TYPE
  0             9              45
  1             1               5
[1] 2 2
[1] FALSE
D33V6, 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
D33V7, binary
                 cls
clus               0  1
  ATXN1 MUTATED    9  1
  ATXN1 WILD-TYPE 37 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      9    1
  ATXN1 WILD-TYPE   37   13
     clus
vv    ATXN1 MUTATED ATXN1 WILD-TYPE
  NO              9              37
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ATXN1 MUTATED                                       0
  ATXN1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ATXN1 MUTATED                                          0
  ATXN1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ATXN1 MUTATED                                     10
  ATXN1 WILD-TYPE                                   48
D33V8, multiclass
                                          clus
vv                                         ATXN1 MUTATED ATXN1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                10              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  ATXN1 MUTATED    6  0  3  1
  ATXN1 WILD-TYPE 38  4  5  3
D33V9, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  R0             6              38
  R1             0               4
  R2             3               5
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, 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(34) Variable = AATK MUTATION ANALYSIS
D34V1, survival
                sevent
clus2             0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 34 22
  AATK MUTATED AATK WILD-TYPE 
             6             56 
  AATK MUTATED AATK WILD-TYPE 
             1             22 
$`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        68.25        58.55        28.04 

$`AATK WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
      127.50        44.84         4.11        60.89       152.15        31.79 
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-P6-A5OF TCGA-P6-A5OH 
       90.08        53.03        79.07        61.05         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  AATK MUTATED AATK WILD-TYPE 
            12              0 
  AATK MUTATED AATK WILD-TYPE 
        153.63         152.15 
  AATK MUTATED AATK WILD-TYPE 
        63.400         41.045 
[1] "12.0 - 153.6 (63.4)" "0.0 - 152.2 (41.0)" 
[1] "hr=" "2.8"
D34V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  AATK MUTATED         0        4         2        0
  AATK WILD-TYPE       6       25        12       11
D34V3, multiclass
           clus
vv          AATK MUTATED AATK WILD-TYPE
  STAGE I              0              6
  STAGE II             4             25
  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 28  7 13
D34V4, multiclass
    clus
vv   AATK MUTATED AATK WILD-TYPE
  T1            0              6
  T2            5             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"
D34V5, binary
                cls
clus              0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 49  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      5    1
  AATK WILD-TYPE   49    5
   clus
vv  AATK MUTATED AATK WILD-TYPE
  0            5             49
  1            1              5
[1] 2 2
[1] FALSE
D34V6, 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
D34V7, binary
                cls
clus              0  1
  AATK MUTATED    5  1
  AATK WILD-TYPE 41 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      5    1
  AATK WILD-TYPE   41   13
     clus
vv    AATK MUTATED AATK WILD-TYPE
  NO             5             41
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AATK MUTATED                                       0
  AATK WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AATK MUTATED                                          1
  AATK WILD-TYPE                                        2
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AATK MUTATED                                      5
  AATK WILD-TYPE                                   53
D34V8, multiclass
                                          clus
vv                                         AATK MUTATED AATK WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            1              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  AATK MUTATED    5  0  1  0
  AATK WILD-TYPE 39  4  7  4
D34V9, multiclass
    clus
vv   AATK MUTATED AATK WILD-TYPE
  R0            5             39
  R1            0              4
  R2            1              7
  RX            0              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"
D34V10, continuous
[1] "Remove cluster labels:" "AATK MUTATED"          
clus
  AATK MUTATED AATK WILD-TYPE 
             2             18 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KV     TCGA-OR-A5L9     TCGA-OR-A5LL 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5LO     TCGA-OR-A5LP 
"AATK WILD-TYPE" "AATK WILD-TYPE" 
D34V11, 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(35) Variable = ZNF628 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2               0  1
  ZNF628 MUTATED    2  5
  ZNF628 WILD-TYPE 37 18
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               7               55 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               5               18 
$`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        16.37        11.31        58.55 
TCGA-P6-A5OH 
        0.00 

$`ZNF628 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB 
       31.23        18.15        32.68        35.57        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84         4.11        60.89       152.15        31.79        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        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        79.07        61.05        28.04         6.81        24.85 
TCGA-PK-A5H8 
      119.11 

  ZNF628 MUTATED ZNF628 WILD-TYPE 
            0.00             4.11 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
           72.39           153.63 
  ZNF628 MUTATED ZNF628 WILD-TYPE 
           18.12            43.30 
[1] "0.0 - 72.4 (18.1)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "3"  
D35V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF628 MUTATED         0        3         1        3
  ZNF628 WILD-TYPE       6       26        13        8
D35V3, multiclass
           clus
vv          ZNF628 MUTATED ZNF628 WILD-TYPE
  STAGE I                0                6
  STAGE II               3               26
  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 30  5 12
D35V4, multiclass
    clus
vv   ZNF628 MUTATED ZNF628 WILD-TYPE
  T1              0                6
  T2              3               30
  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"
D35V5, binary
                  cls
clus                0  1
  ZNF628 MUTATED    7  0
  ZNF628 WILD-TYPE 47  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      7    0
  ZNF628 WILD-TYPE   47    6
   clus
vv  ZNF628 MUTATED ZNF628 WILD-TYPE
  0              7               47
  1              0                6
[1] 2 2
[1] FALSE
D35V6, 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
D35V7, binary
                  cls
clus                0  1
  ZNF628 MUTATED    4  2
  ZNF628 WILD-TYPE 42 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      4    2
  ZNF628 WILD-TYPE   42   12
     clus
vv    ZNF628 MUTATED ZNF628 WILD-TYPE
  NO               4               42
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZNF628 MUTATED                                       0
  ZNF628 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZNF628 MUTATED                                          0
  ZNF628 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZNF628 MUTATED                                      7
  ZNF628 WILD-TYPE                                   51
D35V8, multiclass
                                          clus
vv                                         ZNF628 MUTATED ZNF628 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  7               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  ZNF628 MUTATED    4  1  2  0
  ZNF628 WILD-TYPE 40  3  6  4
D35V9, multiclass
    clus
vv   ZNF628 MUTATED ZNF628 WILD-TYPE
  R0              4               40
  R1              1                3
  R2              2                6
  RX              0                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"
D35V10, continuous
[1] "Remove cluster labels:" "ZNF628 MUTATED"        
clus
  ZNF628 MUTATED ZNF628 WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J3       TCGA-OR-A5J4       TCGA-OR-A5J7 
"ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JX 
"ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5KB       TCGA-OR-A5KU 
"ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9       TCGA-OR-A5LL 
"ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" 
      TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF628 WILD-TYPE" "ZNF628 WILD-TYPE" 
D35V11, 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(36) Variable = KRTAP4-5 MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  KRTAP4-5 MUTATED    5  0
  KRTAP4-5 WILD-TYPE 34 23
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                 57 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 0                 23 
$`KRTAP4-5 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JP TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L9 
       68.75        15.25        58.55       152.15        28.64 

$`KRTAP4-5 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        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        35.57        16.37 
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-A5L2 
      153.63       127.50        68.25        44.84         4.11        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        28.31        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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             15.25               0.00 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
            152.15             153.63 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             58.55              42.51 
[1] "15.2 - 152.2 (58.5)" "0.0 - 153.6 (42.5)" 
[1] "hr="     "7.6e+07"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP4-5 MUTATED         1        3         1        0
  KRTAP4-5 WILD-TYPE       5       26        13       11
D36V3, multiclass
           clus
vv          KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  STAGE I                  1                  5
  STAGE II                 3                 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
  KRTAP4-5 MUTATED    1  3  1  0
  KRTAP4-5 WILD-TYPE  5 30  6 14
D36V4, multiclass
    clus
vv   KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  T1                1                  5
  T2                3                 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"
D36V5, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    5  0
  KRTAP4-5 WILD-TYPE 49  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      5    0
  KRTAP4-5 WILD-TYPE   49    6
   clus
vv  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  0                5                 49
  1                0                  6
[1] 2 2
[1] FALSE
D36V6, 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
D36V7, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    5  0
  KRTAP4-5 WILD-TYPE 41 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      5    0
  KRTAP4-5 WILD-TYPE   41   14
     clus
vv    KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  NO                 5                 41
  YES                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KRTAP4-5 MUTATED                                       0
  KRTAP4-5 WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KRTAP4-5 MUTATED                                          0
  KRTAP4-5 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KRTAP4-5 MUTATED                                      5
  KRTAP4-5 WILD-TYPE                                   53
D36V8, multiclass
                                          clus
vv                                         KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  KRTAP4-5 MUTATED    5  0  0  0
  KRTAP4-5 WILD-TYPE 39  4  8  4
D36V9, multiclass
    clus
vv   KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  R0                5                 39
  R1                0                  4
  R2                0                  8
  RX                0                  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"
D36V10, continuous
[1] "Remove cluster labels:" "KRTAP4-5 MUTATED"      
clus
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 2                 18 
        TCGA-OR-A5KP         TCGA-OR-A5J2         TCGA-OR-A5J4 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JT 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
D36V11, 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(37) Variable = NOXA1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2              0  1
  NOXA1 MUTATED    2  3
  NOXA1 WILD-TYPE 37 20
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              5              57 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              3              20 
$`NOXA1 MUTATED`
TCGA-OR-A5K2 TCGA-OR-A5KB TCGA-OR-A5KX TCGA-OR-A5LO TCGA-P6-A5OH 
       32.68        24.36        44.84        79.07         0.00 

$`NOXA1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        24.62        11.31        46.49        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      153.63       127.50        68.25         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        36.33        90.08        53.03        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  NOXA1 MUTATED NOXA1 WILD-TYPE 
           0.00            4.11 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          79.07          153.63 
  NOXA1 MUTATED NOXA1 WILD-TYPE 
          32.68           43.30 
[1] "0.0 - 79.1 (32.7)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "2.1"
D37V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NOXA1 MUTATED         0        2         2        1
  NOXA1 WILD-TYPE       6       27        12       10
D37V3, multiclass
           clus
vv          NOXA1 MUTATED NOXA1 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  NOXA1 MUTATED    0  3  0  2
  NOXA1 WILD-TYPE  6 30  7 12
D37V4, multiclass
    clus
vv   NOXA1 MUTATED NOXA1 WILD-TYPE
  T1             0               6
  T2             3              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"
D37V5, binary
                 cls
clus               0  1
  NOXA1 MUTATED    4  1
  NOXA1 WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      4    1
  NOXA1 WILD-TYPE   50    5
   clus
vv  NOXA1 MUTATED NOXA1 WILD-TYPE
  0             4              50
  1             1               5
[1] 2 2
[1] FALSE
D37V6, 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
D37V7, binary
                 cls
clus               0  1
  NOXA1 MUTATED    4  1
  NOXA1 WILD-TYPE 42 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      4    1
  NOXA1 WILD-TYPE   42   13
     clus
vv    NOXA1 MUTATED NOXA1 WILD-TYPE
  NO              4              42
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NOXA1 MUTATED                                       0
  NOXA1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NOXA1 MUTATED                                          0
  NOXA1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NOXA1 MUTATED                                      5
  NOXA1 WILD-TYPE                                   53
D37V8, multiclass
                                          clus
vv                                         NOXA1 MUTATED NOXA1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  NOXA1 MUTATED    4  0  1  0
  NOXA1 WILD-TYPE 40  4  7  4
D37V9, multiclass
    clus
vv   NOXA1 MUTATED NOXA1 WILD-TYPE
  R0             4              40
  R1             0               4
  R2             1               7
  RX             0               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"
D37V10, continuous
D37V11, 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(38) Variable = TRIOBP MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2               0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 32 20
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              10               52 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               3               20 
$`TRIOBP MUTATED`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K4 
       91.30        43.30        13.91        66.51        32.68        35.57 
TCGA-OR-A5KV TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LJ 
      127.50        28.64        23.64        36.33 

$`TRIOBP WILD-TYPE`
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 
       39.58        42.51        44.55        55.13        68.75        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       88.87        16.11        19.04        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX 
       15.25        36.26       121.25        29.82        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       18.15        16.37        24.62        11.31        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80        95.18       153.63        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LC 
       58.55        60.89       152.15        31.79        28.31         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
           13.91             0.00 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          127.50           153.63 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          35.950           44.695 
[1] "13.9 - 127.5 (36.0)" "0.0 - 153.6 (44.7)" 
[1] "hr=" "1.2"
D38V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TRIOBP MUTATED         1        4         3        2
  TRIOBP WILD-TYPE       5       25        11        9
D38V3, multiclass
           clus
vv          TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                1                5
  STAGE II               4               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
  TRIOBP MUTATED    1  6  1  2
  TRIOBP WILD-TYPE  5 27  6 12
D38V4, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  T1              1                5
  T2              6               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"
D38V5, binary
                  cls
clus                0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 47  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      7    3
  TRIOBP WILD-TYPE   47    3
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0              7               47
  1              3                3
[1] 2 2
[1] FALSE
D38V6, 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
D38V7, binary
                  cls
clus                0  1
  TRIOBP MUTATED    7  3
  TRIOBP WILD-TYPE 39 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      7    3
  TRIOBP WILD-TYPE   39   11
     clus
vv    TRIOBP MUTATED TRIOBP WILD-TYPE
  NO               7               39
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TRIOBP MUTATED                                       0
  TRIOBP WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TRIOBP MUTATED                                          0
  TRIOBP WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TRIOBP MUTATED                                     10
  TRIOBP WILD-TYPE                                   48
D38V8, multiclass
                                          clus
vv                                         TRIOBP MUTATED TRIOBP WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 10               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  TRIOBP MUTATED    7  1  2  0
  TRIOBP WILD-TYPE 37  3  6  4
D38V9, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  R0              7               37
  R1              1                3
  R2              2                6
  RX              0                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"
D38V10, continuous
D38V11, 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(39) Variable = ZNF598 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2               0  1
  ZNF598 MUTATED    7  5
  ZNF598 WILD-TYPE 32 18
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              12               50 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               5               18 
$`ZNF598 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JP TCGA-OR-A5JT TCGA-OR-A5JV 
       42.51        12.00        19.04        15.25        29.82        66.51 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5LD TCGA-OR-A5LK TCGA-P6-A5OH 
       11.31        24.36        83.80        39.35        90.08         0.00 

$`ZNF598 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       13.91        88.87        16.11        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       36.26       121.25        72.39        31.23        18.15        32.68 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       35.57        16.37        24.62        46.49        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        53.03        79.07        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
            0.00             4.11 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           90.08           153.63 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          27.090           45.665 
[1] "0.0 - 90.1 (27.1)"  "4.1 - 153.6 (45.7)"
[1] "hr=" "1.6"
D39V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         0        7         3        1
  ZNF598 WILD-TYPE       6       22        11       10
D39V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                0                6
  STAGE II               7               22
  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 26  6 11
D39V4, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  T1              0                6
  T2              7               26
  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"
D39V5, binary
                  cls
clus                0  1
  ZNF598 MUTATED   11  0
  ZNF598 WILD-TYPE 43  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED     11    0
  ZNF598 WILD-TYPE   43    6
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0             11               43
  1              0                6
[1] 2 2
[1] FALSE
D39V6, 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
D39V7, binary
                  cls
clus                0  1
  ZNF598 MUTATED    9  3
  ZNF598 WILD-TYPE 37 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      9    3
  ZNF598 WILD-TYPE   37   11
     clus
vv    ZNF598 MUTATED ZNF598 WILD-TYPE
  NO               9               37
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZNF598 MUTATED                                       0
  ZNF598 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZNF598 MUTATED                                          1
  ZNF598 WILD-TYPE                                        2
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZNF598 MUTATED                                     11
  ZNF598 WILD-TYPE                                   47
D39V8, multiclass
                                          clus
vv                                         ZNF598 MUTATED ZNF598 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              1                2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 11               47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  ZNF598 MUTATED    8  0  2  1
  ZNF598 WILD-TYPE 36  4  6  3
D39V9, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  R0              8               36
  R1              0                4
  R2              2                6
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, 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(40) Variable = IRX3 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2             0  1
  IRX3 MUTATED    2  3
  IRX3 WILD-TYPE 37 20
  IRX3 MUTATED IRX3 WILD-TYPE 
             5             57 
  IRX3 MUTATED IRX3 WILD-TYPE 
             3             20 
$`IRX3 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5L3 TCGA-OR-A5LO 
       91.30        30.31        18.12       152.15        79.07 

$`IRX3 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        19.04        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       36.33        90.08        53.03        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  IRX3 MUTATED IRX3 WILD-TYPE 
         18.12           0.00 
  IRX3 MUTATED IRX3 WILD-TYPE 
        152.15         153.63 
  IRX3 MUTATED IRX3 WILD-TYPE 
         79.07          42.51 
[1] "18.1 - 152.2 (79.1)" "0.0 - 153.6 (42.5)" 
[1] "hr=" "1.3"
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IRX3 MUTATED         1        2         0        2
  IRX3 WILD-TYPE       5       27        14        9
D40V3, multiclass
           clus
vv          IRX3 MUTATED IRX3 WILD-TYPE
  STAGE I              1              5
  STAGE II             2             27
  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 31  7 12
D40V4, multiclass
    clus
vv   IRX3 MUTATED IRX3 WILD-TYPE
  T1            1              5
  T2            2             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"
D40V5, binary
                cls
clus              0  1
  IRX3 MUTATED    5  0
  IRX3 WILD-TYPE 49  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      5    0
  IRX3 WILD-TYPE   49    6
   clus
vv  IRX3 MUTATED IRX3 WILD-TYPE
  0            5             49
  1            0              6
[1] 2 2
[1] FALSE
D40V6, 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
D40V7, binary
                cls
clus              0  1
  IRX3 MUTATED    4  0
  IRX3 WILD-TYPE 42 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      4    0
  IRX3 WILD-TYPE   42   14
     clus
vv    IRX3 MUTATED IRX3 WILD-TYPE
  NO             4             42
  YES            0             14
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  IRX3 MUTATED                                       0
  IRX3 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  IRX3 MUTATED                                          0
  IRX3 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  IRX3 MUTATED                                      5
  IRX3 WILD-TYPE                                   53
D40V8, multiclass
                                          clus
vv                                         IRX3 MUTATED IRX3 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  IRX3 MUTATED    3  2  0  0
  IRX3 WILD-TYPE 41  2  8  4
D40V9, multiclass
    clus
vv   IRX3 MUTATED IRX3 WILD-TYPE
  R0            3             41
  R1            2              2
  R2            0              8
  RX            0              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"
D40V10, continuous
[1] "Remove cluster labels:" "IRX3 MUTATED"          
clus
  IRX3 MUTATED IRX3 WILD-TYPE 
             2             18 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J7 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JX 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5     TCGA-OR-A5KB 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LP 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
D40V11, 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(41) Variable = WDR34 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  WDR34 MUTATED    4  1
  WDR34 WILD-TYPE 35 22
  WDR34 MUTATED WDR34 WILD-TYPE 
              5              57 
  WDR34 MUTATED WDR34 WILD-TYPE 
              1              22 
$`WDR34 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5LD 
       42.51        99.88        49.22        15.25        39.35 

$`WDR34 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL 
       18.12        57.53        66.25        69.37        76.64        67.59 
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        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LJ 
       31.79        28.31        28.64        23.64         5.23        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  WDR34 MUTATED WDR34 WILD-TYPE 
          15.25            0.00 
  WDR34 MUTATED WDR34 WILD-TYPE 
          99.88          153.63 
  WDR34 MUTATED WDR34 WILD-TYPE 
          42.51           43.30 
[1] "15.2 - 99.9 (42.5)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.9"
D41V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  WDR34 MUTATED         0        2         1        1
  WDR34 WILD-TYPE       6       27        13       10
D41V3, multiclass
           clus
vv          WDR34 MUTATED WDR34 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  WDR34 MUTATED    0  2  0  2
  WDR34 WILD-TYPE  6 31  7 12
D41V4, multiclass
    clus
vv   WDR34 MUTATED WDR34 WILD-TYPE
  T1             0               6
  T2             2              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"
D41V5, binary
                 cls
clus               0  1
  WDR34 MUTATED    4  0
  WDR34 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      4    0
  WDR34 WILD-TYPE   50    6
   clus
vv  WDR34 MUTATED WDR34 WILD-TYPE
  0             4              50
  1             0               6
[1] 2 2
[1] FALSE
D41V6, 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
D41V7, binary
                 cls
clus               0  1
  WDR34 MUTATED    3  2
  WDR34 WILD-TYPE 43 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      3    2
  WDR34 WILD-TYPE   43   12
     clus
vv    WDR34 MUTATED WDR34 WILD-TYPE
  NO              3              43
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  WDR34 MUTATED                                       0
  WDR34 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  WDR34 MUTATED                                          1
  WDR34 WILD-TYPE                                        2
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  WDR34 MUTATED                                      4
  WDR34 WILD-TYPE                                   54
D41V8, multiclass
                                          clus
vv                                         WDR34 MUTATED WDR34 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             1               2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  WDR34 MUTATED    2  0  1  1
  WDR34 WILD-TYPE 42  4  7  3
D41V9, multiclass
    clus
vv   WDR34 MUTATED WDR34 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, 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(42) Variable = BHLHE22 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  BHLHE22 MUTATED    2  3
  BHLHE22 WILD-TYPE 37 20
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                5                57 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
                3                20 
$`BHLHE22 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5JT TCGA-OR-A5KW TCGA-OR-A5LJ 
       55.13        12.00        29.82        68.25        36.33 

$`BHLHE22 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25        36.26       121.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        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-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
               12                 0 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
            68.25            153.63 
  BHLHE22 MUTATED BHLHE22 WILD-TYPE 
            36.33             43.30 
[1] "12.0 - 68.2 (36.3)" "0.0 - 153.6 (43.3)"
[1] "hr=" "2"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  BHLHE22 MUTATED         0        1         2        2
  BHLHE22 WILD-TYPE       6       28        12        9
D42V3, multiclass
           clus
vv          BHLHE22 MUTATED BHLHE22 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                1                28
  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 30  6 13
D42V4, multiclass
    clus
vv   BHLHE22 MUTATED BHLHE22 WILD-TYPE
  T1               0                 6
  T2               3                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"
D42V5, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    3  2
  BHLHE22 WILD-TYPE 51  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      3    2
  BHLHE22 WILD-TYPE   51    4
   clus
vv  BHLHE22 MUTATED BHLHE22 WILD-TYPE
  0               3                51
  1               2                 4
[1] 2 2
[1] FALSE
D42V6, 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
D42V7, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    3  2
  BHLHE22 WILD-TYPE 43 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      3    2
  BHLHE22 WILD-TYPE   43   12
     clus
vv    BHLHE22 MUTATED BHLHE22 WILD-TYPE
  NO                3                43
  YES               2                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  BHLHE22 MUTATED                                       0
  BHLHE22 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  BHLHE22 MUTATED                                          0
  BHLHE22 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  BHLHE22 MUTATED                                      5
  BHLHE22 WILD-TYPE                                   53
D42V8, multiclass
                                          clus
vv                                         BHLHE22 MUTATED BHLHE22 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  BHLHE22 MUTATED    2  0  3  0
  BHLHE22 WILD-TYPE 42  4  5  4
D42V9, multiclass
    clus
vv   BHLHE22 MUTATED BHLHE22 WILD-TYPE
  R0               2                42
  R1               0                 4
  R2               3                 5
  RX               0                 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"
D42V10, continuous
D42V11, 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(43) Variable = PANK2 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  PANK2 MUTATED    1  4
  PANK2 WILD-TYPE 38 19
  PANK2 MUTATED PANK2 WILD-TYPE 
              5              57 
  PANK2 MUTATED PANK2 WILD-TYPE 
              4              19 
$`PANK2 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5KS TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-P6-A5OH 
       19.04        83.80         4.11        39.35         0.00 

$`PANK2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       68.75        13.91        12.00        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        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       16.37        24.62        11.31        24.36        46.49        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 
      153.63       127.50        68.25        44.84        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  PANK2 MUTATED PANK2 WILD-TYPE 
           0.00            5.23 
  PANK2 MUTATED PANK2 WILD-TYPE 
          83.80          153.63 
  PANK2 MUTATED PANK2 WILD-TYPE 
          19.04           44.55 
[1] "0.0 - 83.8 (19.0)"  "5.2 - 153.6 (44.5)"
[1] "hr=" "3.8"
D43V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PANK2 MUTATED         0        2         2        1
  PANK2 WILD-TYPE       6       27        12       10
D43V3, multiclass
           clus
vv          PANK2 MUTATED PANK2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  PANK2 MUTATED    0  2  1  2
  PANK2 WILD-TYPE  6 31  6 12
D43V4, multiclass
    clus
vv   PANK2 MUTATED PANK2 WILD-TYPE
  T1             0               6
  T2             2              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"
D43V5, binary
                 cls
clus               0  1
  PANK2 MUTATED    5  0
  PANK2 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      5    0
  PANK2 WILD-TYPE   49    6
   clus
vv  PANK2 MUTATED PANK2 WILD-TYPE
  0             5              49
  1             0               6
[1] 2 2
[1] FALSE
D43V6, 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
D43V7, binary
                 cls
clus               0  1
  PANK2 MUTATED    4  1
  PANK2 WILD-TYPE 42 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      4    1
  PANK2 WILD-TYPE   42   13
     clus
vv    PANK2 MUTATED PANK2 WILD-TYPE
  NO              4              42
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PANK2 MUTATED                                       0
  PANK2 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PANK2 MUTATED                                          0
  PANK2 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PANK2 MUTATED                                      5
  PANK2 WILD-TYPE                                   53
D43V8, multiclass
                                          clus
vv                                         PANK2 MUTATED PANK2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  PANK2 MUTATED    2  0  1  2
  PANK2 WILD-TYPE 42  4  7  2
D43V9, multiclass
    clus
vv   PANK2 MUTATED PANK2 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             2               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
[1] "Remove cluster labels:" "PANK2 MUTATED"         
clus
  PANK2 MUTATED PANK2 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JX 
"PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"PANK2 WILD-TYPE" "PANK2 WILD-TYPE" "PANK2 WILD-TYPE" 
D43V11, 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(44) Variable = FPGS MUTATION ANALYSIS
D44V1, survival
                sevent
clus2             0  1
  FPGS MUTATED    2  3
  FPGS WILD-TYPE 37 20
  FPGS MUTATED FPGS WILD-TYPE 
             5             57 
  FPGS MUTATED FPGS WILD-TYPE 
             3             20 
$`FPGS MUTATED`
TCGA-OR-A5JR TCGA-OR-A5K5 TCGA-OR-A5L6 TCGA-OR-A5LJ TCGA-P6-A5OH 
      121.25        16.37        28.31        36.33         0.00 

$`FPGS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT 
       76.64        49.22        67.59        15.25        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        35.57 
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        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       60.89       152.15        31.79        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  FPGS MUTATED FPGS WILD-TYPE 
          0.00           4.11 
  FPGS MUTATED FPGS WILD-TYPE 
        121.25         153.63 
  FPGS MUTATED FPGS WILD-TYPE 
         28.31          44.55 
[1] "0.0 - 121.2 (28.3)" "4.1 - 153.6 (44.5)"
[1] "hr=" "2.5"
D44V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FPGS MUTATED         1        1         1        2
  FPGS WILD-TYPE       5       28        13        9
D44V3, multiclass
           clus
vv          FPGS MUTATED FPGS WILD-TYPE
  STAGE I              1              5
  STAGE II             1             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
  FPGS MUTATED    1  2  1  1
  FPGS WILD-TYPE  5 31  6 13
D44V4, multiclass
    clus
vv   FPGS MUTATED FPGS WILD-TYPE
  T1            1              5
  T2            2             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"
D44V5, binary
                cls
clus              0  1
  FPGS MUTATED    4  1
  FPGS WILD-TYPE 50  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      4    1
  FPGS WILD-TYPE   50    5
   clus
vv  FPGS MUTATED FPGS WILD-TYPE
  0            4             50
  1            1              5
[1] 2 2
[1] FALSE
D44V6, 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
D44V7, binary
                cls
clus              0  1
  FPGS MUTATED    4  1
  FPGS WILD-TYPE 42 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      4    1
  FPGS WILD-TYPE   42   13
     clus
vv    FPGS MUTATED FPGS WILD-TYPE
  NO             4             42
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  FPGS MUTATED                                       0
  FPGS WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  FPGS MUTATED                                          0
  FPGS WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  FPGS MUTATED                                      5
  FPGS WILD-TYPE                                   53
D44V8, multiclass
                                          clus
vv                                         FPGS MUTATED FPGS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  FPGS MUTATED    3  0  2  0
  FPGS WILD-TYPE 41  4  6  4
D44V9, multiclass
    clus
vv   FPGS MUTATED FPGS WILD-TYPE
  R0            3             41
  R1            0              4
  R2            2              6
  RX            0              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"
D44V10, continuous
[1] "Remove cluster labels:" "FPGS MUTATED"          
clus
  FPGS MUTATED FPGS WILD-TYPE 
             1             19 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5KB 
"FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"FPGS WILD-TYPE" "FPGS WILD-TYPE" "FPGS WILD-TYPE" 
D44V11, 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(45) Variable = GLTPD2 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 36 20
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               6               56 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               3               20 
$`GLTPD2 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5K9 
       42.51        19.04        30.31        99.88        49.22        11.31 

$`GLTPD2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        18.12        57.53 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ 
       66.25        69.37        76.64        67.59        15.25        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        35.57        16.37        24.62        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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64         5.23        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
           11.31             0.00 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
           99.88           153.63 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
          36.410           43.925 
[1] "11.3 - 99.9 (36.4)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.7"
D45V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GLTPD2 MUTATED         0        2         1        2
  GLTPD2 WILD-TYPE       6       27        13        9
D45V3, multiclass
           clus
vv          GLTPD2 MUTATED GLTPD2 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               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
  GLTPD2 MUTATED    0  2  1  2
  GLTPD2 WILD-TYPE  6 31  6 12
D45V4, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  T1              0                6
  T2              2               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"
D45V5, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    5  0
  GLTPD2 WILD-TYPE 49  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      5    0
  GLTPD2 WILD-TYPE   49    6
   clus
vv  GLTPD2 MUTATED GLTPD2 WILD-TYPE
  0              5               49
  1              0                6
[1] 2 2
[1] FALSE
D45V6, 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
D45V7, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    3  3
  GLTPD2 WILD-TYPE 43 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      3    3
  GLTPD2 WILD-TYPE   43   11
     clus
vv    GLTPD2 MUTATED GLTPD2 WILD-TYPE
  NO               3               43
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  GLTPD2 MUTATED                                       0
  GLTPD2 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  GLTPD2 MUTATED                                          1
  GLTPD2 WILD-TYPE                                        2
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  GLTPD2 MUTATED                                      5
  GLTPD2 WILD-TYPE                                   53
D45V8, multiclass
                                          clus
vv                                         GLTPD2 MUTATED GLTPD2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              1                2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  5               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  GLTPD2 MUTATED    3  1  1  0
  GLTPD2 WILD-TYPE 41  3  7  4
D45V9, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  R0              3               41
  R1              1                3
  R2              1                7
  RX              0                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"
D45V10, continuous
[1] "Remove cluster labels:" "GLTPD2 MUTATED"        
clus
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               1               19 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JX 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5       TCGA-OR-A5KB 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
D45V11, 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(46) Variable = TNIP2 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2              0  1
  TNIP2 MUTATED    4  1
  TNIP2 WILD-TYPE 35 22
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              5              57 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              1              22 
$`TNIP2 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JI TCGA-OR-A5KV TCGA-OR-A5KW TCGA-P6-A5OH 
       42.51        76.64       127.50        68.25         0.00 

$`TNIP2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        69.37        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      153.63        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  TNIP2 MUTATED TNIP2 WILD-TYPE 
           0.00            4.11 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
         127.50          153.63 
  TNIP2 MUTATED TNIP2 WILD-TYPE 
          68.25           39.58 
[1] "0.0 - 127.5 (68.2)" "4.1 - 153.6 (39.6)"
[1] "hr=" "2.2"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TNIP2 MUTATED         1        0         2        1
  TNIP2 WILD-TYPE       5       29        12       10
D46V3, multiclass
           clus
vv          TNIP2 MUTATED TNIP2 WILD-TYPE
  STAGE I               1               5
  STAGE II              0              29
  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 31  7 13
D46V4, multiclass
    clus
vv   TNIP2 MUTATED TNIP2 WILD-TYPE
  T1             1               5
  T2             2              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"
D46V5, binary
                 cls
clus               0  1
  TNIP2 MUTATED    2  2
  TNIP2 WILD-TYPE 52  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      2    2
  TNIP2 WILD-TYPE   52    4
   clus
vv  TNIP2 MUTATED TNIP2 WILD-TYPE
  0             2              52
  1             2               4
[1] 2 2
[1] FALSE
D46V6, 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
D46V7, binary
                 cls
clus               0  1
  TNIP2 MUTATED    2  3
  TNIP2 WILD-TYPE 44 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      2    3
  TNIP2 WILD-TYPE   44   11
     clus
vv    TNIP2 MUTATED TNIP2 WILD-TYPE
  NO              2              44
  YES             3              11
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TNIP2 MUTATED                                       0
  TNIP2 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TNIP2 MUTATED                                          0
  TNIP2 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TNIP2 MUTATED                                      5
  TNIP2 WILD-TYPE                                   53
D46V8, multiclass
                                          clus
vv                                         TNIP2 MUTATED TNIP2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  TNIP2 MUTATED    3  0  1  0
  TNIP2 WILD-TYPE 41  4  7  4
D46V9, multiclass
    clus
vv   TNIP2 MUTATED TNIP2 WILD-TYPE
  R0             3              41
  R1             0               4
  R2             1               7
  RX             0               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"
D46V10, continuous
[1] "Remove cluster labels:" "TNIP2 MUTATED"         
clus
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              2              18 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5KB      TCGA-OR-A5KU      TCGA-OR-A5L9      TCGA-OR-A5LL 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5LO      TCGA-OR-A5LP 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
D46V11, 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(47) Variable = AKAP2 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2              0  1
  AKAP2 MUTATED    3  3
  AKAP2 WILD-TYPE 36 20
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              6              56 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              3              20 
$`AKAP2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JW TCGA-OR-A5KZ TCGA-OR-A5LK TCGA-OR-A5LP 
       30.31        18.12        72.39         4.11        90.08        61.05 

$`AKAP2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        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        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      127.50        68.25        44.84        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       36.33        53.03        79.07        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  AKAP2 MUTATED AKAP2 WILD-TYPE 
           4.11            0.00 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
          90.08          153.63 
  AKAP2 MUTATED AKAP2 WILD-TYPE 
         45.680          42.905 
[1] "4.1 - 90.1 (45.7)"  "0.0 - 153.6 (42.9)"
[1] "hr=" "1.4"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  AKAP2 MUTATED         0        4         0        2
  AKAP2 WILD-TYPE       6       25        14        9
D47V3, multiclass
           clus
vv          AKAP2 MUTATED AKAP2 WILD-TYPE
  STAGE I               0               6
  STAGE II              4              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
  AKAP2 MUTATED    0  4  0  2
  AKAP2 WILD-TYPE  6 29  7 12
D47V4, multiclass
    clus
vv   AKAP2 MUTATED AKAP2 WILD-TYPE
  T1             0               6
  T2             4              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"
D47V5, binary
                 cls
clus               0  1
  AKAP2 MUTATED    6  0
  AKAP2 WILD-TYPE 48  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      6    0
  AKAP2 WILD-TYPE   48    6
   clus
vv  AKAP2 MUTATED AKAP2 WILD-TYPE
  0             6              48
  1             0               6
[1] 2 2
[1] FALSE
D47V6, binary
                 cls
clus               0  1
  AKAP2 MUTATED    2  4
  AKAP2 WILD-TYPE 38 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      2    4
  AKAP2 WILD-TYPE   38   18
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  FEMALE             2              38
  MALE               4              18
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus               0  1
  AKAP2 MUTATED    4  1
  AKAP2 WILD-TYPE 42 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      4    1
  AKAP2 WILD-TYPE   42   13
     clus
vv    AKAP2 MUTATED AKAP2 WILD-TYPE
  NO              4              42
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AKAP2 MUTATED                                       0
  AKAP2 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AKAP2 MUTATED                                          1
  AKAP2 WILD-TYPE                                        2
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AKAP2 MUTATED                                      5
  AKAP2 WILD-TYPE                                   53
D47V8, multiclass
                                          clus
vv                                         AKAP2 MUTATED AKAP2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             1               2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  AKAP2 MUTATED    3  2  0  1
  AKAP2 WILD-TYPE 41  2  8  3
D47V9, multiclass
    clus
vv   AKAP2 MUTATED AKAP2 WILD-TYPE
  R0             3              41
  R1             2               2
  R2             0               8
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
[1] "Remove cluster labels:" "AKAP2 MUTATED"         
clus
  AKAP2 MUTATED AKAP2 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" 
     TCGA-OR-A5KB      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" 
     TCGA-OR-A5L9      TCGA-OR-A5LL      TCGA-OR-A5LO 
"AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" "AKAP2 WILD-TYPE" 
D47V11, binary
                 cls
clus               0  1
  AKAP2 MUTATED    0  1
  AKAP2 WILD-TYPE  7 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      0    1
  AKAP2 WILD-TYPE    7   26
                        clus
vv                       AKAP2 MUTATED AKAP2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             1              26
[1] 2 2
[1] FALSE

Clustering(48) Variable = RREB1 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 36 21
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              57 
  RREB1 MUTATED RREB1 WILD-TYPE 
              2              21 
$`RREB1 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J4 TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       91.30        13.91        66.51        31.23        18.15 

$`RREB1 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JW 
       67.59        15.25        36.26       121.25        29.82        72.39 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  RREB1 MUTATED RREB1 WILD-TYPE 
          13.91            0.00 
  RREB1 MUTATED RREB1 WILD-TYPE 
          91.30          153.63 
  RREB1 MUTATED RREB1 WILD-TYPE 
          31.23           43.30 
[1] "13.9 - 91.3 (31.2)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.2"
D48V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RREB1 MUTATED         0        2         1        2
  RREB1 WILD-TYPE       6       27        13        9
D48V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  RREB1 MUTATED    0  2  2  1
  RREB1 WILD-TYPE  6 31  5 13
D48V4, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  T1             0               6
  T2             2              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"
D48V5, binary
                 cls
clus               0  1
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 51  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    2
  RREB1 WILD-TYPE   51    4
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             3              51
  1             2               4
[1] 2 2
[1] FALSE
D48V6, 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
D48V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    3  2
  RREB1 WILD-TYPE 43 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    2
  RREB1 WILD-TYPE   43   12
     clus
vv    RREB1 MUTATED RREB1 WILD-TYPE
  NO              3              43
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RREB1 MUTATED                                       0
  RREB1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RREB1 MUTATED                                          0
  RREB1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RREB1 MUTATED                                      5
  RREB1 WILD-TYPE                                   53
D48V8, multiclass
                                          clus
vv                                         RREB1 MUTATED RREB1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  RREB1 MUTATED    3  0  2  0
  RREB1 WILD-TYPE 41  4  6  4
D48V9, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  R0             3              41
  R1             0               4
  R2             2               6
  RX             0               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"
D48V10, continuous
D48V11, 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(49) Variable = TPO MUTATION ANALYSIS
D49V1, survival
               sevent
clus2            0  1
  TPO MUTATED    7  5
  TPO WILD-TYPE 32 18
  TPO MUTATED TPO WILD-TYPE 
           12            50 
  TPO MUTATED TPO WILD-TYPE 
            5            18 
$`TPO MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       91.30        19.04        18.12        66.25        69.37        76.64 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5LD TCGA-OR-A5LJ 
       11.31        24.36       127.50        68.25        39.35        36.33 

$`TPO WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        30.31        57.53 
TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       99.88        49.22        67.59        15.25        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-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       35.57        16.37        24.62        46.49        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      153.63        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LK 
       31.79        28.31        28.64        23.64         5.23        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  TPO MUTATED TPO WILD-TYPE 
        11.31          0.00 
  TPO MUTATED TPO WILD-TYPE 
       127.50        153.63 
  TPO MUTATED TPO WILD-TYPE 
       52.800        42.905 
[1] "11.3 - 127.5 (52.8)" "0.0 - 153.6 (42.9)" 
[1] "hr=" "1.1"
D49V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TPO MUTATED         1        5         4        2
  TPO WILD-TYPE       5       24        10        9
D49V3, multiclass
           clus
vv          TPO MUTATED TPO WILD-TYPE
  STAGE I             1             5
  STAGE II            5            24
  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 25  6 12
D49V4, multiclass
    clus
vv   TPO MUTATED TPO WILD-TYPE
  T1           1             5
  T2           8            25
  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"
D49V5, binary
               cls
clus             0  1
  TPO MUTATED    9  3
  TPO WILD-TYPE 45  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      9    3
  TPO WILD-TYPE   45    3
   clus
vv  TPO MUTATED TPO WILD-TYPE
  0           9            45
  1           3             3
[1] 2 2
[1] FALSE
D49V6, 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
D49V7, binary
               cls
clus             0  1
  TPO MUTATED    7  4
  TPO WILD-TYPE 39 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      7    4
  TPO WILD-TYPE   39   10
     clus
vv    TPO MUTATED TPO WILD-TYPE
  NO            7            39
  YES           4            10
[1] 2 2
[1] FALSE
               vv
clus            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TPO MUTATED                                       0
  TPO WILD-TYPE                                     1
               vv
clus            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TPO MUTATED                                          1
  TPO WILD-TYPE                                        2
               vv
clus            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TPO MUTATED                                     11
  TPO WILD-TYPE                                   47
D49V8, multiclass
                                          clus
vv                                         TPO MUTATED TPO WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE              0             1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE           1             2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE              11            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            R0 R1 R2 RX
  TPO MUTATED    9  1  1  1
  TPO WILD-TYPE 35  3  7  3
D49V9, multiclass
    clus
vv   TPO MUTATED TPO WILD-TYPE
  R0           9            35
  R1           1             3
  R2           1             7
  RX           1             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
D49V11, 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(50) Variable = OBSCN MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2              0  1
  OBSCN MUTATED   11  7
  OBSCN WILD-TYPE 28 16
  OBSCN MUTATED OBSCN WILD-TYPE 
             18              44 
  OBSCN MUTATED OBSCN WILD-TYPE 
              7              16 
$`OBSCN MUTATED`
TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF 
       43.30        42.51        68.75        19.04        18.12        66.25 
TCGA-OR-A5JI TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KB 
       76.64        66.51        18.15        35.57        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KV TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LP 
       46.49       127.50        60.89         5.23        36.33        61.05 

$`OBSCN WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 
       91.30        39.58        44.55        55.13        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       88.87        16.11        30.31        57.53        99.88        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KS 
       72.39        31.23        32.68        16.37        24.62        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63        68.25        44.84         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        28.31        28.64        23.64        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       90.08        53.03        79.07        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  OBSCN MUTATED OBSCN WILD-TYPE 
           5.23            0.00 
  OBSCN MUTATED OBSCN WILD-TYPE 
         127.50          153.63 
  OBSCN MUTATED OBSCN WILD-TYPE 
         42.905          42.065 
[1] "5.2 - 127.5 (42.9)" "0.0 - 153.6 (42.1)"
[1] "hr=" "1.1"
D50V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OBSCN MUTATED         2        6         4        5
  OBSCN WILD-TYPE       4       23        10        6
D50V3, multiclass
           clus
vv          OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I               2               4
  STAGE II              6              23
  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 25  5  9
D50V4, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  T1             2               4
  T2             8              25
  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"
D50V5, binary
                 cls
clus               0  1
  OBSCN MUTATED   14  3
  OBSCN WILD-TYPE 40  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     14    3
  OBSCN WILD-TYPE   40    3
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0            14              40
  1             3               3
[1] 2 2
[1] FALSE
D50V6, 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
D50V7, binary
                 cls
clus               0  1
  OBSCN MUTATED   11  6
  OBSCN WILD-TYPE 35  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     11    6
  OBSCN WILD-TYPE   35    8
     clus
vv    OBSCN MUTATED OBSCN WILD-TYPE
  NO             11              35
  YES             6               8
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  OBSCN MUTATED                                       0
  OBSCN WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  OBSCN MUTATED                                          0
  OBSCN WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  OBSCN MUTATED                                     18
  OBSCN WILD-TYPE                                   40
D50V8, multiclass
                                          clus
vv                                         OBSCN MUTATED OBSCN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                18              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  OBSCN MUTATED   12  2  3  0
  OBSCN WILD-TYPE 32  2  5  4
D50V9, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  R0            12              32
  R1             2               2
  R2             3               5
  RX             0               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"
D50V10, continuous
D50V11, 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(51) Variable = SNED1 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2              0  1
  SNED1 MUTATED    4  1
  SNED1 WILD-TYPE 35 22
  SNED1 MUTATED SNED1 WILD-TYPE 
              5              57 
  SNED1 MUTATED SNED1 WILD-TYPE 
              1              22 
$`SNED1 MUTATED`
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JY TCGA-OR-A5KV TCGA-OR-A5L3 
       66.25        76.64        18.15       127.50       152.15 

$`SNED1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK 
       30.31        18.12        57.53        99.88        69.37        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        32.68        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
       68.25        44.84         4.11        58.55        60.89        31.79 
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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  SNED1 MUTATED SNED1 WILD-TYPE 
          18.15            0.00 
  SNED1 MUTATED SNED1 WILD-TYPE 
         152.15          153.63 
  SNED1 MUTATED SNED1 WILD-TYPE 
          76.64           39.58 
[1] "18.1 - 152.2 (76.6)" "0.0 - 153.6 (39.6)" 
[1] "hr=" "2.8"
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SNED1 MUTATED         2        1         1        1
  SNED1 WILD-TYPE       4       28        13       10
D51V3, multiclass
           clus
vv          SNED1 MUTATED SNED1 WILD-TYPE
  STAGE I               2               4
  STAGE II              1              28
  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 31  7 13
D51V4, multiclass
    clus
vv   SNED1 MUTATED SNED1 WILD-TYPE
  T1             2               4
  T2             2              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"
D51V5, binary
                 cls
clus               0  1
  SNED1 MUTATED    3  2
  SNED1 WILD-TYPE 51  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      3    2
  SNED1 WILD-TYPE   51    4
   clus
vv  SNED1 MUTATED SNED1 WILD-TYPE
  0             3              51
  1             2               4
[1] 2 2
[1] FALSE
D51V6, 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
D51V7, binary
                 cls
clus               0  1
  SNED1 MUTATED    2  3
  SNED1 WILD-TYPE 44 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      2    3
  SNED1 WILD-TYPE   44   11
     clus
vv    SNED1 MUTATED SNED1 WILD-TYPE
  NO              2              44
  YES             3              11
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SNED1 MUTATED                                       0
  SNED1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SNED1 MUTATED                                          0
  SNED1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SNED1 MUTATED                                      5
  SNED1 WILD-TYPE                                   53
D51V8, multiclass
                                          clus
vv                                         SNED1 MUTATED SNED1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  SNED1 MUTATED    4  0  1  0
  SNED1 WILD-TYPE 40  4  7  4
D51V9, multiclass
    clus
vv   SNED1 MUTATED SNED1 WILD-TYPE
  R0             4              40
  R1             0               4
  R2             1               7
  RX             0               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"
D51V10, continuous
[1] "Remove cluster labels:" "SNED1 MUTATED"         
clus
  SNED1 MUTATED SNED1 WILD-TYPE 
              2              18 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5L9      TCGA-OR-A5LL 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5LO      TCGA-OR-A5LP 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
D51V11, 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(52) Variable = MEN1 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2             0  1
  MEN1 MUTATED    2  3
  MEN1 WILD-TYPE 37 20
  MEN1 MUTATED MEN1 WILD-TYPE 
             5             57 
  MEN1 MUTATED MEN1 WILD-TYPE 
             3             20 
$`MEN1 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5KW TCGA-P6-A5OF 
       42.51        12.00        30.31        68.25         6.81 

$`MEN1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC 
       13.91        88.87        16.11        19.04        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        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-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  MEN1 MUTATED MEN1 WILD-TYPE 
          6.81           0.00 
  MEN1 MUTATED MEN1 WILD-TYPE 
         68.25         153.63 
  MEN1 MUTATED MEN1 WILD-TYPE 
         30.31          44.55 
[1] "6.8 - 68.2 (30.3)"  "0.0 - 153.6 (44.5)"
[1] "hr=" "2.5"
D52V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MEN1 MUTATED         0        0         3        1
  MEN1 WILD-TYPE       6       29        11       10
D52V3, multiclass
           clus
vv          MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             29
  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 32  7 11
D52V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            0              6
  T2            1             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"
D52V5, binary
                cls
clus              0  1
  MEN1 MUTATED    3  1
  MEN1 WILD-TYPE 51  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    1
  MEN1 WILD-TYPE   51    5
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0            3             51
  1            1              5
[1] 2 2
[1] FALSE
D52V6, 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
D52V7, binary
                cls
clus              0  1
  MEN1 MUTATED    3  2
  MEN1 WILD-TYPE 43 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      3    2
  MEN1 WILD-TYPE   43   12
     clus
vv    MEN1 MUTATED MEN1 WILD-TYPE
  NO             3             43
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  MEN1 MUTATED                                       0
  MEN1 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  MEN1 MUTATED                                          0
  MEN1 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  MEN1 MUTATED                                      5
  MEN1 WILD-TYPE                                   53
D52V8, multiclass
                                          clus
vv                                         MEN1 MUTATED MEN1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  MEN1 MUTATED    1  1  1  1
  MEN1 WILD-TYPE 43  3  7  3
D52V9, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  R0            1             43
  R1            1              3
  R2            1              7
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
[1] "Remove cluster labels:" "MEN1 MUTATED"          
clus
  MEN1 MUTATED MEN1 WILD-TYPE 
             1             19 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5L9 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
D52V11, 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(53) Variable = BTBD11 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2               0  1
  BTBD11 MUTATED    4  2
  BTBD11 WILD-TYPE 35 21
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6               56 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               2               21 
$`BTBD11 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J5 TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5KB TCGA-OR-A5KW 
       43.30        12.00        67.59        32.68        24.36        68.25 

$`BTBD11 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        18.15        35.57        16.37        24.62        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-A5L6 
        4.11        58.55        60.89       152.15        31.79        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        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
              12                0 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           68.25           153.63 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           37.99            43.53 
[1] "12.0 - 68.2 (38.0)" "0.0 - 153.6 (43.5)"
[1] "hr=" "1"  
D53V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BTBD11 MUTATED         2        1         3        0
  BTBD11 WILD-TYPE       4       28        11       11
D53V3, multiclass
           clus
vv          BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                2                4
  STAGE II               1               28
  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 31  7 12
D53V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              2                4
  T2              2               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"
D53V5, binary
                  cls
clus                0  1
  BTBD11 MUTATED    5  1
  BTBD11 WILD-TYPE 49  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      5    1
  BTBD11 WILD-TYPE   49    5
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0              5               49
  1              1                5
[1] 2 2
[1] FALSE
D53V6, 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
D53V7, binary
                  cls
clus                0  1
  BTBD11 MUTATED    4  2
  BTBD11 WILD-TYPE 42 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      4    2
  BTBD11 WILD-TYPE   42   12
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO               4               42
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  BTBD11 MUTATED                                       0
  BTBD11 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  BTBD11 MUTATED                                          0
  BTBD11 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  BTBD11 MUTATED                                      6
  BTBD11 WILD-TYPE                                   52
D53V8, multiclass
                                          clus
vv                                         BTBD11 MUTATED BTBD11 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  6               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  BTBD11 MUTATED    5  0  1  0
  BTBD11 WILD-TYPE 39  4  7  4
D53V9, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0              5               39
  R1              0                4
  R2              1                7
  RX              0                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"
D53V10, continuous
D53V11, 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(54) Variable = RNF149 MUTATION ANALYSIS
D54V1, survival
                  sevent
clus2               0  1
  RNF149 MUTATED    4  0
  RNF149 WILD-TYPE 35 23
  RNF149 MUTATED RNF149 WILD-TYPE 
               4               58 
  RNF149 MUTATED RNF149 WILD-TYPE 
               0               23 
$`RNF149 MUTATED`
TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5LP 
       67.59        24.62       153.63        61.05 

$`RNF149 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       76.64        49.22        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        11.31        24.36        46.49        83.80        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
       39.35        36.33        90.08        53.03        79.07        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  RNF149 MUTATED RNF149 WILD-TYPE 
           24.62             0.00 
  RNF149 MUTATED RNF149 WILD-TYPE 
          153.63           152.15 
  RNF149 MUTATED RNF149 WILD-TYPE 
          64.320           41.045 
[1] "24.6 - 153.6 (64.3)" "0.0 - 152.2 (41.0)" 
[1] "hr="     "7.6e+07"
D54V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF149 MUTATED         1        3         0        0
  RNF149 WILD-TYPE       5       26        14       11
D54V3, multiclass
           clus
vv          RNF149 MUTATED RNF149 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               26
  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 30  7 14
D54V4, multiclass
    clus
vv   RNF149 MUTATED RNF149 WILD-TYPE
  T1              1                5
  T2              3               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"
D54V5, binary
                  cls
clus                0  1
  RNF149 MUTATED    4  0
  RNF149 WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      4    0
  RNF149 WILD-TYPE   50    6
   clus
vv  RNF149 MUTATED RNF149 WILD-TYPE
  0              4               50
  1              0                6
[1] 2 2
[1] FALSE
D54V6, 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
D54V7, binary
                  cls
clus                0  1
  RNF149 MUTATED    4  0
  RNF149 WILD-TYPE 42 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      4    0
  RNF149 WILD-TYPE   42   14
     clus
vv    RNF149 MUTATED RNF149 WILD-TYPE
  NO               4               42
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RNF149 MUTATED                                       0
  RNF149 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RNF149 MUTATED                                          0
  RNF149 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RNF149 MUTATED                                      4
  RNF149 WILD-TYPE                                   54
D54V8, multiclass
                                          clus
vv                                         RNF149 MUTATED RNF149 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  4               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  RNF149 MUTATED    4  0  0  0
  RNF149 WILD-TYPE 40  4  8  4
D54V9, multiclass
    clus
vv   RNF149 MUTATED RNF149 WILD-TYPE
  R0              4               40
  R1              0                4
  R2              0                8
  RX              0                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"
D54V10, continuous
[1] "Remove cluster labels:" "RNF149 MUTATED"        
clus
  RNF149 MUTATED RNF149 WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5 
"RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" 
      TCGA-OR-A5KB       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" "RNF149 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO 
"RNF149 WILD-TYPE" "RNF149 WILD-TYPE" 
D54V11, 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(55) Variable = KIAA1984 MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  KIAA1984 MUTATED    3  1
  KIAA1984 WILD-TYPE 36 22
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 4                 58 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 1                 22 
$`KIAA1984 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5K8 TCGA-OR-A5KO 
       42.51        19.04        24.62        46.49 

$`KIAA1984 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
             19.04               0.00 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
             46.49             153.63 
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
            33.565             43.925 
[1] "19.0 - 46.5 (33.6)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.2"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1984 MUTATED         0        1         1        1
  KIAA1984 WILD-TYPE       6       28        13       10
D55V3, multiclass
           clus
vv          KIAA1984 MUTATED KIAA1984 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 1                 28
  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 32  6 13
D55V4, multiclass
    clus
vv   KIAA1984 MUTATED KIAA1984 WILD-TYPE
  T1                0                  6
  T2                1                 32
  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
  KIAA1984 MUTATED    3  0
  KIAA1984 WILD-TYPE 51  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      3    0
  KIAA1984 WILD-TYPE   51    6
   clus
vv  KIAA1984 MUTATED KIAA1984 WILD-TYPE
  0                3                 51
  1                0                  6
[1] 2 2
[1] FALSE
D55V6, 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
D55V7, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    2  2
  KIAA1984 WILD-TYPE 44 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      2    2
  KIAA1984 WILD-TYPE   44   12
     clus
vv    KIAA1984 MUTATED KIAA1984 WILD-TYPE
  NO                 2                 44
  YES                2                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KIAA1984 MUTATED                                       0
  KIAA1984 WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KIAA1984 MUTATED                                          0
  KIAA1984 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KIAA1984 MUTATED                                      4
  KIAA1984 WILD-TYPE                                   54
D55V8, multiclass
                                          clus
vv                                         KIAA1984 MUTATED KIAA1984 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  KIAA1984 MUTATED    3  0  0  0
  KIAA1984 WILD-TYPE 41  4  8  4
D55V9, multiclass
    clus
vv   KIAA1984 MUTATED KIAA1984 WILD-TYPE
  R0                3                 41
  R1                0                  4
  R2                0                  8
  RX                0                  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"
D55V10, continuous
[1] "Remove cluster labels:" "KIAA1984 MUTATED"      
clus
  KIAA1984 MUTATED KIAA1984 WILD-TYPE 
                 1                 19 
        TCGA-OR-A5KP         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J7         TCGA-OR-A5JT 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LL         TCGA-OR-A5LO 
"KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" "KIAA1984 WILD-TYPE" 
        TCGA-OR-A5LP 
"KIAA1984 WILD-TYPE" 
D55V11, 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(56) Variable = CCDC150 MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  CCDC150 MUTATED    1  3
  CCDC150 WILD-TYPE 38 20
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                4                58 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                3                20 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5JB TCGA-OR-A5JC 
       68.75        13.91        12.00        88.87        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
            16.11              0.00 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           127.50            153.63 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           24.675            43.925 
[1] "16.1 - 127.5 (24.7)" "0.0 - 153.6 (43.9)" 
[1] "hr=" "2.7"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC150 MUTATED         0        0         3        1
  CCDC150 WILD-TYPE       6       29        11       10
D56V3, multiclass
           clus
vv          CCDC150 MUTATED CCDC150 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                0                29
  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 32  5 13
D56V4, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  T1               0                 6
  T2               1                32
  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"
D56V5, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    3  1
  CCDC150 WILD-TYPE 51  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      3    1
  CCDC150 WILD-TYPE   51    5
   clus
vv  CCDC150 MUTATED CCDC150 WILD-TYPE
  0               3                51
  1               1                 5
[1] 2 2
[1] FALSE
D56V6, 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
D56V7, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    2  2
  CCDC150 WILD-TYPE 44 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      2    2
  CCDC150 WILD-TYPE   44   12
     clus
vv    CCDC150 MUTATED CCDC150 WILD-TYPE
  NO                2                44
  YES               2                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CCDC150 MUTATED                                       0
  CCDC150 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CCDC150 MUTATED                                          0
  CCDC150 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CCDC150 MUTATED                                      4
  CCDC150 WILD-TYPE                                   54
D56V8, multiclass
                                          clus
vv                                         CCDC150 MUTATED CCDC150 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   4                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  CCDC150 MUTATED    2  2  0  0
  CCDC150 WILD-TYPE 42  2  8  4
D56V9, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  R0               2                42
  R1               2                 2
  R2               0                 8
  RX               0                 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"
D56V10, continuous
D56V11, 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(57) Variable = FAM18B2 MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  FAM18B2 MUTATED    3  1
  FAM18B2 WILD-TYPE 36 22
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                4                58 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                1                22 
$`FAM18B2 MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JF TCGA-OR-A5JW TCGA-OR-A5KV 
       55.13        66.25        72.39       127.50 

$`FAM18B2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
            55.13              0.00 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
           127.50            153.63 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
           69.320            39.465 
[1] "55.1 - 127.5 (69.3)" "0.0 - 153.6 (39.5)" 
[1] "hr=" "2.4"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM18B2 MUTATED         0        2         1        1
  FAM18B2 WILD-TYPE       6       27        13       10
D57V3, multiclass
           clus
vv          FAM18B2 MUTATED FAM18B2 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                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
  FAM18B2 MUTATED    0  3  1  0
  FAM18B2 WILD-TYPE  6 30  6 14
D57V4, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  T1               0                 6
  T2               3                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"
D57V5, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    3  1
  FAM18B2 WILD-TYPE 51  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      3    1
  FAM18B2 WILD-TYPE   51    5
   clus
vv  FAM18B2 MUTATED FAM18B2 WILD-TYPE
  0               3                51
  1               1                 5
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    3  1
  FAM18B2 WILD-TYPE 37 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      3    1
  FAM18B2 WILD-TYPE   37   21
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  FEMALE               3                37
  MALE                 1                21
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    1  3
  FAM18B2 WILD-TYPE 45 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1    3
  FAM18B2 WILD-TYPE   45   11
     clus
vv    FAM18B2 MUTATED FAM18B2 WILD-TYPE
  NO                1                45
  YES               3                11
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  FAM18B2 MUTATED                                       0
  FAM18B2 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  FAM18B2 MUTATED                                          0
  FAM18B2 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  FAM18B2 MUTATED                                      4
  FAM18B2 WILD-TYPE                                   54
D57V8, multiclass
                                          clus
vv                                         FAM18B2 MUTATED FAM18B2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   4                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  FAM18B2 MUTATED    3  0  1  0
  FAM18B2 WILD-TYPE 41  4  7  4
D57V9, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  R0               3                41
  R1               0                 4
  R2               1                 7
  RX               0                 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"
D57V10, continuous
[1] "Remove cluster labels:" "FAM18B2 MUTATED"       
clus
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J7 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5J8        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KW        TCGA-OR-A5L9        TCGA-OR-A5LL 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
D57V11, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    1  1
  FAM18B2 WILD-TYPE  6 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1    1
  FAM18B2 WILD-TYPE    6   26
                        clus
vv                       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(58) Variable = MUC5B MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2              0  1
  MUC5B MUTATED   13  9
  MUC5B WILD-TYPE 26 14
  MUC5B MUTATED MUC5B WILD-TYPE 
             22              40 
  MUC5B MUTATED MUC5B WILD-TYPE 
              9              14 
$`MUC5B MUTATED`
TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JB 
       43.30        42.51        68.75        12.00        19.04        18.12 
TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KB 
       36.26        66.51        72.39        32.68        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5L2 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LJ 
       46.49       153.63        60.89        23.64         5.23        36.33 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-PA-A5YG TCGA-PK-A5H8 
       79.07        61.05        24.85       119.11 

$`MUC5B WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 
       91.30        39.58        44.55        55.13        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       76.64        49.22        67.59        15.25       121.25        29.82 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KS 
       31.23        18.15        35.57        16.37        24.62        83.80 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       127.50        68.25        44.84         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LD TCGA-OR-A5LK 
      152.15        31.79        28.31        28.64        39.35        90.08 
TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        28.04         6.81         0.00 

  MUC5B MUTATED MUC5B WILD-TYPE 
           5.23            0.00 
  MUC5B MUTATED MUC5B WILD-TYPE 
         153.63          152.15 
  MUC5B MUTATED MUC5B WILD-TYPE 
         39.420          44.695 
[1] "5.2 - 153.6 (39.4)" "0.0 - 152.2 (44.7)"
[1] "hr=" "1.2"
D58V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED         1       12         4        4
  MUC5B WILD-TYPE       5       17        10        7
D58V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I               1               5
  STAGE II             12              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 13  2  5
  MUC5B WILD-TYPE  5 20  5  9
D58V4, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  T1             1               5
  T2            13              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"
D58V5, binary
                 cls
clus               0  1
  MUC5B MUTATED   20  1
  MUC5B WILD-TYPE 34  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     20    1
  MUC5B WILD-TYPE   34    5
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0            20              34
  1             1               5
[1] 2 2
[1] FALSE
D58V6, 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
D58V7, binary
                 cls
clus               0  1
  MUC5B MUTATED   17  4
  MUC5B WILD-TYPE 29 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     17    4
  MUC5B WILD-TYPE   29   10
     clus
vv    MUC5B MUTATED MUC5B WILD-TYPE
  NO             17              29
  YES             4              10
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  MUC5B MUTATED                                       1
  MUC5B WILD-TYPE                                     0
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  MUC5B MUTATED                                          0
  MUC5B WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  MUC5B MUTATED                                     21
  MUC5B WILD-TYPE                                   37
D58V8, multiclass
                                          clus
vv                                         MUC5B MUTATED MUC5B WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                1               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                21              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  MUC5B MUTATED   17  1  3  0
  MUC5B WILD-TYPE 27  3  5  4
D58V9, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  R0            17              27
  R1             1               3
  R2             3               5
  RX             0               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"
D58V10, continuous
D58V11, 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(59) Variable = PTPLA MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  PTPLA MUTATED    3  1
  PTPLA WILD-TYPE 36 22
  PTPLA MUTATED PTPLA WILD-TYPE 
              4              58 
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              22 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57        16.37 
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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  PTPLA MUTATED PTPLA WILD-TYPE 
             12               0 
  PTPLA MUTATED PTPLA WILD-TYPE 
         152.15          153.63 
  PTPLA MUTATED PTPLA WILD-TYPE 
         48.375          42.905 
[1] "12.0 - 152.2 (48.4)" "0.0 - 153.6 (42.9)" 
[1] "hr=" "1.5"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTPLA MUTATED         1        2         1        0
  PTPLA WILD-TYPE       5       27        13       11
D59V3, multiclass
           clus
vv          PTPLA MUTATED PTPLA WILD-TYPE
  STAGE I               1               5
  STAGE II              2              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
  PTPLA MUTATED    1  2  0  1
  PTPLA WILD-TYPE  5 31  7 13
D59V4, multiclass
    clus
vv   PTPLA MUTATED PTPLA WILD-TYPE
  T1             1               5
  T2             2              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"
D59V5, binary
                 cls
clus               0  1
  PTPLA MUTATED    4  0
  PTPLA WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      4    0
  PTPLA WILD-TYPE   50    6
   clus
vv  PTPLA MUTATED PTPLA WILD-TYPE
  0             4              50
  1             0               6
[1] 2 2
[1] FALSE
D59V6, 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
D59V7, binary
                 cls
clus               0  1
  PTPLA MUTATED    3  1
  PTPLA WILD-TYPE 43 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      3    1
  PTPLA WILD-TYPE   43   13
     clus
vv    PTPLA MUTATED PTPLA WILD-TYPE
  NO              3              43
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PTPLA MUTATED                                       0
  PTPLA WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PTPLA MUTATED                                          0
  PTPLA WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PTPLA MUTATED                                      4
  PTPLA WILD-TYPE                                   54
D59V8, multiclass
                                          clus
vv                                         PTPLA MUTATED PTPLA WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  PTPLA MUTATED    3  0  1  0
  PTPLA WILD-TYPE 41  4  7  4
D59V9, multiclass
    clus
vv   PTPLA MUTATED PTPLA WILD-TYPE
  R0             3              41
  R1             0               4
  R2             1               7
  RX             0               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"
D59V10, continuous
[1] "Remove cluster labels:" "PTPLA MUTATED"         
clus
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
D59V11, 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(60) Variable = SRPX MUTATION ANALYSIS
D60V1, survival
                sevent
clus2             0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 37 22
  SRPX MUTATED SRPX WILD-TYPE 
             3             59 
  SRPX MUTATED SRPX WILD-TYPE 
             1             22 
$`SRPX MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5KW TCGA-OR-A5L9 
       55.13        68.25        28.64 

$`SRPX WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       16.37        24.62        11.31        24.36        46.49        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-A5LA TCGA-OR-A5LC 
       60.89       152.15        31.79        28.31        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  SRPX MUTATED SRPX WILD-TYPE 
         28.64           0.00 
  SRPX MUTATED SRPX WILD-TYPE 
         68.25         153.63 
  SRPX MUTATED SRPX WILD-TYPE 
         55.13          42.51 
[1] "28.6 - 68.2 (55.1)" "0.0 - 153.6 (42.5)"
[1] "hr=" "1.2"
D60V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SRPX MUTATED         0        1         1        1
  SRPX WILD-TYPE       6       28        13       10
D60V3, multiclass
           clus
vv          SRPX MUTATED SRPX WILD-TYPE
  STAGE I              0              6
  STAGE II             1             28
  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 31  6 14
D60V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            0              6
  T2            2             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"
D60V5, binary
                cls
clus              0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 52  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      2    1
  SRPX WILD-TYPE   52    5
   clus
vv  SRPX MUTATED SRPX WILD-TYPE
  0            2             52
  1            1              5
[1] 2 2
[1] FALSE
D60V6, 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
D60V7, binary
                cls
clus              0  1
  SRPX MUTATED    2  1
  SRPX WILD-TYPE 44 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      2    1
  SRPX WILD-TYPE   44   13
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO             2             44
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SRPX MUTATED                                       0
  SRPX WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SRPX MUTATED                                          0
  SRPX WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SRPX MUTATED                                      3
  SRPX WILD-TYPE                                   55
D60V8, multiclass
                                          clus
vv                                         SRPX MUTATED SRPX WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  SRPX MUTATED    2  0  1  0
  SRPX WILD-TYPE 42  4  7  4
D60V9, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  R0            2             42
  R1            0              4
  R2            1              7
  RX            0              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"
D60V10, continuous
D60V11, 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(61) Variable = GARS MUTATION ANALYSIS
D61V1, survival
                sevent
clus2             0  1
  GARS MUTATED   15  4
  GARS WILD-TYPE 24 19
  GARS MUTATED GARS WILD-TYPE 
            19             43 
  GARS MUTATED GARS WILD-TYPE 
             4             19 
$`GARS MUTATED`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5J6 TCGA-OR-A5JC TCGA-OR-A5JH TCGA-OR-A5JI 
       91.30        43.30        88.87        57.53        69.37        76.64 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K8 TCGA-OR-A5KS 
       67.59        36.26        29.82        66.51        24.62        83.80 
TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
       95.18        44.84         4.11        90.08        79.07        61.05 
TCGA-P6-A5OH 
        0.00 

$`GARS WILD-TYPE`
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       39.58        42.51        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       12.00        16.11        19.04        30.31        18.12        99.88 
TCGA-OR-A5JF TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JW TCGA-OR-A5JX 
       66.25        49.22        15.25       121.25        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        35.57        16.37        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L2 
       46.49       153.63       127.50        68.25        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       39.35        36.33        53.03        28.04         6.81        24.85 
TCGA-PK-A5H8 
      119.11 

  GARS MUTATED GARS WILD-TYPE 
          0.00           5.23 
  GARS MUTATED GARS WILD-TYPE 
         95.18         153.63 
  GARS MUTATED GARS WILD-TYPE 
         66.51          35.57 
[1] "0.0 - 95.2 (66.5)"  "5.2 - 153.6 (35.6)"
[1] "hr=" "2.9"
D61V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GARS MUTATED         4       12         1        1
  GARS WILD-TYPE       2       17        13       10
D61V3, multiclass
           clus
vv          GARS MUTATED GARS WILD-TYPE
  STAGE I              4              2
  STAGE II            12             17
  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 20  7 13
D61V4, multiclass
    clus
vv   GARS MUTATED GARS WILD-TYPE
  T1            4              2
  T2           13             20
  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"
D61V5, binary
                cls
clus              0  1
  GARS MUTATED   17  1
  GARS WILD-TYPE 37  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     17    1
  GARS WILD-TYPE   37    5
   clus
vv  GARS MUTATED GARS WILD-TYPE
  0           17             37
  1            1              5
[1] 2 2
[1] FALSE
D61V6, 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
D61V7, binary
                cls
clus              0  1
  GARS MUTATED   17  1
  GARS WILD-TYPE 29 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED     17    1
  GARS WILD-TYPE   29   13
     clus
vv    GARS MUTATED GARS WILD-TYPE
  NO            17             29
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  GARS MUTATED                                       1
  GARS WILD-TYPE                                     0
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  GARS MUTATED                                          2
  GARS WILD-TYPE                                        1
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  GARS MUTATED                                     16
  GARS WILD-TYPE                                   42
D61V8, multiclass
                                          clus
vv                                         GARS MUTATED GARS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               1              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            2              1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               16             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  GARS MUTATED   16  0  1  1
  GARS WILD-TYPE 28  4  7  3
D61V9, multiclass
    clus
vv   GARS MUTATED GARS WILD-TYPE
  R0           16             28
  R1            0              4
  R2            1              7
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, 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(62) Variable = PRSS27 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2               0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 38 21
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               3               59 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               2               21 
$`PRSS27 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JF 
       12.00        19.04        66.25 

$`PRSS27 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       68.75        13.91        88.87        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       57.53        99.88        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  PRSS27 MUTATED PRSS27 WILD-TYPE 
              12                0 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
           66.25           153.63 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
           19.04            43.30 
[1] "12.0 - 66.2 (19.0)" "0.0 - 153.6 (43.3)"
[1] "hr=" "2.4"
D62V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PRSS27 MUTATED         0        1         2        0
  PRSS27 WILD-TYPE       6       28        12       11
D62V3, multiclass
           clus
vv          PRSS27 MUTATED PRSS27 WILD-TYPE
  STAGE I                0                6
  STAGE II               1               28
  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 32  6 13
D62V4, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  T1              0                6
  T2              1               32
  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
  PRSS27 MUTATED    3  0
  PRSS27 WILD-TYPE 51  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      3    0
  PRSS27 WILD-TYPE   51    6
   clus
vv  PRSS27 MUTATED PRSS27 WILD-TYPE
  0              3               51
  1              0                6
[1] 2 2
[1] FALSE
D62V6, 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
D62V7, binary
                  cls
clus                0  1
  PRSS27 MUTATED    1  2
  PRSS27 WILD-TYPE 45 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      1    2
  PRSS27 WILD-TYPE   45   12
     clus
vv    PRSS27 MUTATED PRSS27 WILD-TYPE
  NO               1               45
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PRSS27 MUTATED                                       0
  PRSS27 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PRSS27 MUTATED                                          0
  PRSS27 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PRSS27 MUTATED                                      3
  PRSS27 WILD-TYPE                                   55
D62V8, multiclass
                                          clus
vv                                         PRSS27 MUTATED PRSS27 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  PRSS27 MUTATED    2  0  1  0
  PRSS27 WILD-TYPE 42  4  7  4
D62V9, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  R0              2               42
  R1              0                4
  R2              1                7
  RX              0                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"
D62V10, continuous
[1] "Remove cluster labels:" "PRSS27 MUTATED"        
clus
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               1               19 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JX 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5       TCGA-OR-A5KB 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
D62V11, 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(63) Variable = SEMA5B MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2               0  1
  SEMA5B MUTATED    5  3
  SEMA5B WILD-TYPE 34 20
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               8               54 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
               3               20 
$`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        90.08 

$`SEMA5B WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25        36.26        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
       11.31        46.49        83.80        95.18       153.63        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84         4.11        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO 
       28.64        23.64         5.23        36.33        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81         0.00        24.85       119.11 

  SEMA5B MUTATED SEMA5B WILD-TYPE 
           18.12             0.00 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
          127.50           153.63 
  SEMA5B MUTATED SEMA5B WILD-TYPE 
          56.840           41.045 
[1] "18.1 - 127.5 (56.8)" "0.0 - 153.6 (41.0)" 
[1] "hr=" "1.2"
D63V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEMA5B MUTATED         1        3         2        2
  SEMA5B WILD-TYPE       5       26        12        9
D63V3, multiclass
           clus
vv          SEMA5B MUTATED SEMA5B WILD-TYPE
  STAGE I                1                5
  STAGE II               3               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
  SEMA5B MUTATED    1  4  1  2
  SEMA5B WILD-TYPE  5 29  6 12
D63V4, multiclass
    clus
vv   SEMA5B MUTATED SEMA5B WILD-TYPE
  T1              1                5
  T2              4               29
  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"
D63V5, binary
                  cls
clus                0  1
  SEMA5B MUTATED    7  1
  SEMA5B WILD-TYPE 47  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      7    1
  SEMA5B WILD-TYPE   47    5
   clus
vv  SEMA5B MUTATED SEMA5B WILD-TYPE
  0              7               47
  1              1                5
[1] 2 2
[1] FALSE
D63V6, 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
D63V7, binary
                  cls
clus                0  1
  SEMA5B MUTATED    6  1
  SEMA5B WILD-TYPE 40 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      6    1
  SEMA5B WILD-TYPE   40   13
     clus
vv    SEMA5B MUTATED SEMA5B WILD-TYPE
  NO               6               40
  YES              1               13
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SEMA5B MUTATED                                       0
  SEMA5B WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SEMA5B MUTATED                                          1
  SEMA5B WILD-TYPE                                        2
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SEMA5B MUTATED                                      7
  SEMA5B WILD-TYPE                                   51
D63V8, multiclass
                                          clus
vv                                         SEMA5B MUTATED SEMA5B WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              1                2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  7               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  SEMA5B MUTATED    5  1  1  1
  SEMA5B WILD-TYPE 39  3  7  3
D63V9, multiclass
    clus
vv   SEMA5B MUTATED SEMA5B WILD-TYPE
  R0              5               39
  R1              1                3
  R2              1                7
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, 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(64) Variable = CD320 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  CD320 MUTATED    2  2
  CD320 WILD-TYPE 37 21
  CD320 MUTATED CD320 WILD-TYPE 
              4              58 
  CD320 MUTATED CD320 WILD-TYPE 
              2              21 
$`CD320 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5K5 TCGA-OR-A5L4 
       12.00        88.87        16.37        31.79 

$`CD320 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       68.75        13.91        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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-A5K8 
       72.39        31.23        18.15        32.68        35.57        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
      152.15        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  CD320 MUTATED CD320 WILD-TYPE 
             12               0 
  CD320 MUTATED CD320 WILD-TYPE 
          88.87          153.63 
  CD320 MUTATED CD320 WILD-TYPE 
         24.080          43.925 
[1] "12.0 - 88.9 (24.1)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.8"
D64V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CD320 MUTATED         0        1         3        0
  CD320 WILD-TYPE       6       28        11       11
D64V3, multiclass
           clus
vv          CD320 MUTATED CD320 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              28
  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 32  6 12
D64V4, multiclass
    clus
vv   CD320 MUTATED CD320 WILD-TYPE
  T1             0               6
  T2             1              32
  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"
D64V5, binary
                 cls
clus               0  1
  CD320 MUTATED    4  0
  CD320 WILD-TYPE 50  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      4    0
  CD320 WILD-TYPE   50    6
   clus
vv  CD320 MUTATED CD320 WILD-TYPE
  0             4              50
  1             0               6
[1] 2 2
[1] FALSE
D64V6, 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
D64V7, binary
                 cls
clus               0  1
  CD320 MUTATED    3  1
  CD320 WILD-TYPE 43 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      3    1
  CD320 WILD-TYPE   43   13
     clus
vv    CD320 MUTATED CD320 WILD-TYPE
  NO              3              43
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CD320 MUTATED                                       0
  CD320 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CD320 MUTATED                                          0
  CD320 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CD320 MUTATED                                      4
  CD320 WILD-TYPE                                   54
D64V8, multiclass
                                          clus
vv                                         CD320 MUTATED CD320 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  CD320 MUTATED    2  0  1  1
  CD320 WILD-TYPE 42  4  7  3
D64V9, multiclass
    clus
vv   CD320 MUTATED CD320 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
[1] "Remove cluster labels:" "CD320 MUTATED"         
clus
  CD320 MUTATED CD320 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5KB 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
D64V11, 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(65) Variable = TAF5 MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  TAF5 MUTATED    2  2
  TAF5 WILD-TYPE 37 21
  TAF5 MUTATED TAF5 WILD-TYPE 
             4             58 
  TAF5 MUTATED TAF5 WILD-TYPE 
             2             21 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57        16.37 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  TAF5 MUTATED TAF5 WILD-TYPE 
         18.15           0.00 
  TAF5 MUTATED TAF5 WILD-TYPE 
         55.13         153.63 
  TAF5 MUTATED TAF5 WILD-TYPE 
        26.330         43.925 
[1] "18.1 - 55.1 (26.3)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1.9"
D65V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TAF5 MUTATED         0        2         0        2
  TAF5 WILD-TYPE       6       27        14        9
D65V3, multiclass
           clus
vv          TAF5 MUTATED TAF5 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             27
  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 31  6 13
D65V4, multiclass
    clus
vv   TAF5 MUTATED TAF5 WILD-TYPE
  T1            0              6
  T2            2             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"
D65V5, binary
                cls
clus              0  1
  TAF5 MUTATED    3  1
  TAF5 WILD-TYPE 51  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      3    1
  TAF5 WILD-TYPE   51    5
   clus
vv  TAF5 MUTATED TAF5 WILD-TYPE
  0            3             51
  1            1              5
[1] 2 2
[1] FALSE
D65V6, 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
D65V7, binary
                cls
clus              0  1
  TAF5 MUTATED    3  1
  TAF5 WILD-TYPE 43 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      3    1
  TAF5 WILD-TYPE   43   13
     clus
vv    TAF5 MUTATED TAF5 WILD-TYPE
  NO             3             43
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TAF5 MUTATED                                       0
  TAF5 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TAF5 MUTATED                                          0
  TAF5 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TAF5 MUTATED                                      4
  TAF5 WILD-TYPE                                   54
D65V8, multiclass
                                          clus
vv                                         TAF5 MUTATED TAF5 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                4             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  TAF5 MUTATED    2  0  2  0
  TAF5 WILD-TYPE 42  4  6  4
D65V9, multiclass
    clus
vv   TAF5 MUTATED TAF5 WILD-TYPE
  R0            2             42
  R1            0              4
  R2            2              6
  RX            0              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"
D65V10, continuous
[1] "Remove cluster labels:" "TAF5 MUTATED"          
clus
  TAF5 MUTATED TAF5 WILD-TYPE 
             2             18 
    TCGA-OR-A5KP     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J7 
"TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JX 
"TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K5     TCGA-OR-A5KB     TCGA-OR-A5KU 
"TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9     TCGA-OR-A5LL 
"TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" "TAF5 WILD-TYPE" 
    TCGA-OR-A5LO     TCGA-OR-A5LP 
"TAF5 WILD-TYPE" "TAF5 WILD-TYPE" 
D65V11, 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(66) Variable = NEFH MUTATION ANALYSIS
D66V1, survival
                sevent
clus2             0  1
  NEFH MUTATED    3  3
  NEFH WILD-TYPE 36 20
  NEFH MUTATED NEFH WILD-TYPE 
             6             56 
  NEFH MUTATED NEFH WILD-TYPE 
             3             20 
$`NEFH MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5JP TCGA-OR-A5K2 TCGA-OR-A5KB 
       91.30        13.91        19.04        15.25        32.68        24.36 

$`NEFH WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       12.00        88.87        16.11        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
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        35.57        16.37        24.62        11.31        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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.64        23.64         5.23        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  NEFH MUTATED NEFH WILD-TYPE 
         13.91           0.00 
  NEFH MUTATED NEFH WILD-TYPE 
         91.30         153.63 
  NEFH MUTATED NEFH WILD-TYPE 
        21.700         44.695 
[1] "13.9 - 91.3 (21.7)" "0.0 - 153.6 (44.7)"
[1] "hr=" "2.1"
D66V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         0        3         2        1
  NEFH WILD-TYPE       6       26        12       10
D66V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              0              6
  STAGE II             3             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
  NEFH MUTATED    0  3  2  1
  NEFH WILD-TYPE  6 30  5 13
D66V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0              6
  T2            3             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"
D66V5, binary
                cls
clus              0  1
  NEFH MUTATED    5  1
  NEFH WILD-TYPE 49  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      5    1
  NEFH WILD-TYPE   49    5
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            5             49
  1            1              5
[1] 2 2
[1] FALSE
D66V6, 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
D66V7, binary
                cls
clus              0  1
  NEFH MUTATED    4  2
  NEFH WILD-TYPE 42 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    2
  NEFH WILD-TYPE   42   12
     clus
vv    NEFH MUTATED NEFH WILD-TYPE
  NO             4             42
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NEFH MUTATED                                       0
  NEFH WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NEFH MUTATED                                          0
  NEFH WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NEFH MUTATED                                      6
  NEFH WILD-TYPE                                   52
D66V8, multiclass
                                          clus
vv                                         NEFH MUTATED NEFH WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                6             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  NEFH MUTATED    5  0  1  0
  NEFH WILD-TYPE 39  4  7  4
D66V9, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  R0            5             39
  R1            0              4
  R2            1              7
  RX            0              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"
D66V10, continuous
D66V11, 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(67) Variable = DMKN MUTATION ANALYSIS
D67V1, survival
                sevent
clus2             0  1
  DMKN MUTATED    3  0
  DMKN WILD-TYPE 36 23
  DMKN MUTATED DMKN WILD-TYPE 
             3             59 
  DMKN MUTATED DMKN WILD-TYPE 
             0             23 
$`DMKN MUTATED`
TCGA-PK-A5HB TCGA-OR-A5KU TCGA-OR-A5L3 
       42.51       153.63       152.15 

$`DMKN WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       16.37        24.62        11.31        24.36        46.49        83.80 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       127.50        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       60.89        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  DMKN MUTATED DMKN WILD-TYPE 
         42.51           0.00 
  DMKN MUTATED DMKN WILD-TYPE 
        153.63         127.50 
  DMKN MUTATED DMKN WILD-TYPE 
        152.15          39.58 
[1] "42.5 - 153.6 (152.2)" "0.0 - 127.5 (39.6)"  
[1] "hr="     "7.5e+07"
D67V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DMKN MUTATED         1        1         0        0
  DMKN WILD-TYPE       5       28        14       11
D67V3, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             58 
    TCGA-OR-A5KP     TCGA-OR-A5L5     TCGA-OR-A5LB     TCGA-OR-A5J1 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF     TCGA-OR-A5JH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KO     TCGA-OR-A5KS     TCGA-OR-A5KT 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L1     TCGA-OR-A5L2     TCGA-OR-A5L4     TCGA-OR-A5L6 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L9     TCGA-OR-A5LA     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     TCGA-PK-A5H8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" 
                vv
clus             T1 T2 T3 T4
  DMKN MUTATED    1  1  0  0
  DMKN WILD-TYPE  5 32  7 14
D67V4, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             58 
    TCGA-OR-A5KP     TCGA-OR-A5L5     TCGA-OR-A5LB     TCGA-OR-A5J1 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF     TCGA-OR-A5JH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KO     TCGA-OR-A5KS     TCGA-OR-A5KT 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L1     TCGA-OR-A5L2     TCGA-OR-A5L4     TCGA-OR-A5L6 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L9     TCGA-OR-A5LA     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     TCGA-PK-A5H8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" 
D67V5, binary
                cls
clus              0  1
  DMKN MUTATED    2  0
  DMKN WILD-TYPE 52  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    0
  DMKN WILD-TYPE   52    6
   clus
vv  DMKN MUTATED DMKN WILD-TYPE
  0            2             52
  1            0              6
[1] 2 2
[1] FALSE
D67V6, 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
D67V7, binary
                cls
clus              0  1
  DMKN MUTATED    2  1
  DMKN WILD-TYPE 44 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      2    1
  DMKN WILD-TYPE   44   13
     clus
vv    DMKN MUTATED DMKN WILD-TYPE
  NO             2             44
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DMKN MUTATED                                       0
  DMKN WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DMKN MUTATED                                          0
  DMKN WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DMKN MUTATED                                      3
  DMKN WILD-TYPE                                   55
D67V8, multiclass
                                          clus
vv                                         DMKN MUTATED DMKN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  DMKN MUTATED    2  0  0  0
  DMKN WILD-TYPE 42  4  8  4
D67V9, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             2             58 
    TCGA-OR-A5KP     TCGA-OR-A5L5     TCGA-OR-A5LB     TCGA-OR-A5J1 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4     TCGA-OR-A5J5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JD     TCGA-OR-A5JF     TCGA-OR-A5JH 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KO     TCGA-OR-A5KS     TCGA-OR-A5KT 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L1     TCGA-OR-A5L2     TCGA-OR-A5L4     TCGA-OR-A5L6 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5L9     TCGA-OR-A5LA     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     TCGA-PK-A5H8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" 
D67V10, continuous
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             1             19 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KB     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
D67V11, 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(68) Variable = NPTX1 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  NPTX1 MUTATED    2  1
  NPTX1 WILD-TYPE 37 22
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              3              59 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              1              22 
$`NPTX1 MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JV TCGA-OR-A5LC 
       76.64        66.51         5.23 

$`NPTX1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
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        35.57        16.37 
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        68.25        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-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           5.23            0.00 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          76.64          153.63 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          66.51           42.51 
[1] "5.2 - 76.6 (66.5)"  "0.0 - 153.6 (42.5)"
[1] "hr=" "1.2"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NPTX1 MUTATED         1        1         0        1
  NPTX1 WILD-TYPE       5       28        14       10
D68V3, multiclass
           clus
vv          NPTX1 MUTATED NPTX1 WILD-TYPE
  STAGE I               1               5
  STAGE II              1              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
  NPTX1 MUTATED    1  1  0  1
  NPTX1 WILD-TYPE  5 32  7 13
D68V4, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  T1             1               5
  T2             1              32
  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"
D68V5, binary
                 cls
clus               0  1
  NPTX1 MUTATED    3  0
  NPTX1 WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      3    0
  NPTX1 WILD-TYPE   51    6
   clus
vv  NPTX1 MUTATED NPTX1 WILD-TYPE
  0             3              51
  1             0               6
[1] 2 2
[1] FALSE
D68V6, 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
D68V7, binary
                 cls
clus               0  1
  NPTX1 MUTATED    3  0
  NPTX1 WILD-TYPE 43 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      3    0
  NPTX1 WILD-TYPE   43   14
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  NO              3              43
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NPTX1 MUTATED                                       0
  NPTX1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NPTX1 MUTATED                                          0
  NPTX1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NPTX1 MUTATED                                      3
  NPTX1 WILD-TYPE                                   55
D68V8, multiclass
                                          clus
vv                                         NPTX1 MUTATED NPTX1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  NPTX1 MUTATED    2  0  1  0
  NPTX1 WILD-TYPE 42  4  7  4
D68V9, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             0               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"
D68V10, continuous
[1] "Remove cluster labels:" "NPTX1 MUTATED"         
clus
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JX 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
D68V11, 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(69) Variable = NOTCH2 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2               0  1
  NOTCH2 MUTATED    4  1
  NOTCH2 WILD-TYPE 35 22
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               5               57 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               1               22 
$`NOTCH2 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5KB TCGA-OR-A5KU TCGA-OR-A5KV 
       42.51        19.04        24.36       153.63       127.50 

$`NOTCH2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KW 
       24.62        11.31        46.49        83.80        95.18        68.25 
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-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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           19.04             0.00 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          153.63           152.15 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           42.51            43.30 
[1] "19.0 - 153.6 (42.5)" "0.0 - 152.2 (43.3)" 
[1] "hr=" "2.2"
D69V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NOTCH2 MUTATED         0        2         2        0
  NOTCH2 WILD-TYPE       6       27        12       11
D69V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               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
  NOTCH2 MUTATED    0  3  1  0
  NOTCH2 WILD-TYPE  6 30  6 14
D69V4, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T1              0                6
  T2              3               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"
D69V5, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    3  1
  NOTCH2 WILD-TYPE 51  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    1
  NOTCH2 WILD-TYPE   51    5
   clus
vv  NOTCH2 MUTATED NOTCH2 WILD-TYPE
  0              3               51
  1              1                5
[1] 2 2
[1] FALSE
D69V6, 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
D69V7, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    2  3
  NOTCH2 WILD-TYPE 44 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      2    3
  NOTCH2 WILD-TYPE   44   11
     clus
vv    NOTCH2 MUTATED NOTCH2 WILD-TYPE
  NO               2               44
  YES              3               11
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NOTCH2 MUTATED                                       0
  NOTCH2 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NOTCH2 MUTATED                                          0
  NOTCH2 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NOTCH2 MUTATED                                      5
  NOTCH2 WILD-TYPE                                   53
D69V8, multiclass
                                          clus
vv                                         NOTCH2 MUTATED NOTCH2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  5               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  NOTCH2 MUTATED    4  0  0  0
  NOTCH2 WILD-TYPE 40  4  8  4
D69V9, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  R0              4               40
  R1              0                4
  R2              0                8
  RX              0                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"
D69V10, continuous
D69V11, 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(70) Variable = RNF39 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2              0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 36 21
  RNF39 MUTATED RNF39 WILD-TYPE 
              5              57 
  RNF39 MUTATED RNF39 WILD-TYPE 
              2              21 
$`RNF39 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5JA TCGA-OR-A5JP TCGA-OR-A5KW 
       42.51        55.13        30.31        15.25        68.25 

$`RNF39 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC 
       12.00        88.87        16.11        19.04        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
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        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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-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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  RNF39 MUTATED RNF39 WILD-TYPE 
          15.25            0.00 
  RNF39 MUTATED RNF39 WILD-TYPE 
          68.25          153.63 
  RNF39 MUTATED RNF39 WILD-TYPE 
          42.51           43.30 
[1] "15.2 - 68.2 (42.5)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.2"
D70V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RNF39 MUTATED         0        1         1        2
  RNF39 WILD-TYPE       6       28        13        9
D70V3, multiclass
           clus
vv          RNF39 MUTATED RNF39 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              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
  RNF39 MUTATED    0  2  1  1
  RNF39 WILD-TYPE  6 31  6 13
D70V4, multiclass
    clus
vv   RNF39 MUTATED RNF39 WILD-TYPE
  T1             0               6
  T2             2              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"
D70V5, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  1
  RNF39 WILD-TYPE 51  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    1
  RNF39 WILD-TYPE   51    5
   clus
vv  RNF39 MUTATED RNF39 WILD-TYPE
  0             3              51
  1             1               5
[1] 2 2
[1] FALSE
D70V6, 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
D70V7, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  2
  RNF39 WILD-TYPE 43 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    2
  RNF39 WILD-TYPE   43   12
     clus
vv    RNF39 MUTATED RNF39 WILD-TYPE
  NO              3              43
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RNF39 MUTATED                                       0
  RNF39 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RNF39 MUTATED                                          0
  RNF39 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RNF39 MUTATED                                      5
  RNF39 WILD-TYPE                                   53
D70V8, multiclass
                                          clus
vv                                         RNF39 MUTATED RNF39 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  RNF39 MUTATED    2  1  1  0
  RNF39 WILD-TYPE 42  3  7  4
D70V9, multiclass
    clus
vv   RNF39 MUTATED RNF39 WILD-TYPE
  R0             2              42
  R1             1               3
  R2             1               7
  RX             0               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"
D70V10, continuous
[1] "Remove cluster labels:" "RNF39 MUTATED"         
clus
  RNF39 MUTATED RNF39 WILD-TYPE 
              2              18 
     TCGA-OR-A5KP      TCGA-OR-A5J3      TCGA-OR-A5J4      TCGA-OR-A5J7 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JX 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5L9      TCGA-OR-A5LL 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-OR-A5LO      TCGA-OR-A5LP 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
D70V11, 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(71) Variable = KBTBD13 MUTATION ANALYSIS
D71V1, survival
                   sevent
clus2                0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 32 21
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                9                53 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
                2                21 
$`KBTBD13 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J2 TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5KT 
       43.30        55.13        67.59        15.25        18.15        95.18 
TCGA-OR-A5KV TCGA-OR-A5L9 TCGA-OR-A5LP 
      127.50        28.64        61.05 

$`KBTBD13 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        39.58        42.51        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        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-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       46.49        83.80       153.63        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA 
       58.55        60.89       152.15        31.79        28.31        23.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
            15.25              0.00 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
           127.50            153.63 
  KBTBD13 MUTATED KBTBD13 WILD-TYPE 
            55.13             39.58 
[1] "15.2 - 127.5 (55.1)" "0.0 - 153.6 (39.6)" 
[1] "hr=" "2"  
D71V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  KBTBD13 MUTATED         3        3         1        2
  KBTBD13 WILD-TYPE       3       26        13        9
D71V3, multiclass
           clus
vv          KBTBD13 MUTATED KBTBD13 WILD-TYPE
  STAGE I                 3                 3
  STAGE II                3                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
  KBTBD13 MUTATED    3  4  1  1
  KBTBD13 WILD-TYPE  3 29  6 13
D71V4, multiclass
    clus
vv   KBTBD13 MUTATED KBTBD13 WILD-TYPE
  T1               3                 3
  T2               4                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"
D71V5, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 47  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      7    2
  KBTBD13 WILD-TYPE   47    4
   clus
vv  KBTBD13 MUTATED KBTBD13 WILD-TYPE
  0               7                47
  1               2                 4
[1] 2 2
[1] FALSE
D71V6, 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
D71V7, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    7  2
  KBTBD13 WILD-TYPE 39 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      7    2
  KBTBD13 WILD-TYPE   39   12
     clus
vv    KBTBD13 MUTATED KBTBD13 WILD-TYPE
  NO                7                39
  YES               2                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KBTBD13 MUTATED                                       0
  KBTBD13 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KBTBD13 MUTATED                                          0
  KBTBD13 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KBTBD13 MUTATED                                      9
  KBTBD13 WILD-TYPE                                   49
D71V8, multiclass
                                          clus
vv                                         KBTBD13 MUTATED KBTBD13 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  KBTBD13 MUTATED    7  0  2  0
  KBTBD13 WILD-TYPE 37  4  6  4
D71V9, multiclass
    clus
vv   KBTBD13 MUTATED KBTBD13 WILD-TYPE
  R0               7                37
  R1               0                 4
  R2               2                 6
  RX               0                 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"
D71V10, continuous
D71V11, 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(72) Variable = IER5 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2             0  1
  IER5 MUTATED    0  3
  IER5 WILD-TYPE 39 20
  IER5 MUTATED IER5 WILD-TYPE 
             3             59 
  IER5 MUTATED IER5 WILD-TYPE 
             3             20 
$`IER5 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-P6-A5OH 
       18.15        32.68         0.00 

$`IER5 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K4 TCGA-OR-A5K5 
       29.82        66.51        72.39        31.23        35.57        16.37 
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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        24.85       119.11 

  IER5 MUTATED IER5 WILD-TYPE 
          0.00           4.11 
  IER5 MUTATED IER5 WILD-TYPE 
         32.68         153.63 
  IER5 MUTATED IER5 WILD-TYPE 
         18.15          44.55 
[1] "0.0 - 32.7 (18.1)"  "4.1 - 153.6 (44.5)"
[1] "hr=" "7.8"
D72V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IER5 MUTATED         0        0         1        2
  IER5 WILD-TYPE       6       29        13        9
D72V3, multiclass
           clus
vv          IER5 MUTATED IER5 WILD-TYPE
  STAGE I              0              6
  STAGE II             0             29
  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 33  7 11
D72V4, multiclass
    clus
vv   IER5 MUTATED IER5 WILD-TYPE
  T1            0              6
  T2            0             33
  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"
D72V5, binary
                cls
clus              0  1
  IER5 MUTATED    2  1
  IER5 WILD-TYPE 52  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      2    1
  IER5 WILD-TYPE   52    5
   clus
vv  IER5 MUTATED IER5 WILD-TYPE
  0            2             52
  1            1              5
[1] 2 2
[1] FALSE
D72V6, 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
D72V7, binary
                cls
clus              0  1
  IER5 MUTATED    1  2
  IER5 WILD-TYPE 45 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      1    2
  IER5 WILD-TYPE   45   12
     clus
vv    IER5 MUTATED IER5 WILD-TYPE
  NO             1             45
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  IER5 MUTATED                                       0
  IER5 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  IER5 MUTATED                                          0
  IER5 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  IER5 MUTATED                                      3
  IER5 WILD-TYPE                                   55
D72V8, multiclass
                                          clus
vv                                         IER5 MUTATED IER5 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  IER5 MUTATED    1  0  2  0
  IER5 WILD-TYPE 43  4  6  4
D72V9, multiclass
    clus
vv   IER5 MUTATED IER5 WILD-TYPE
  R0            1             43
  R1            0              4
  R2            2              6
  RX            0              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"
D72V10, continuous
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             18 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5K5     TCGA-OR-A5KB     TCGA-OR-A5KU 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9     TCGA-OR-A5LL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" 
D72V11, 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(73) Variable = SCRT1 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2              0  1
  SCRT1 MUTATED    1  2
  SCRT1 WILD-TYPE 38 21
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              3              59 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              2              21 
$`SCRT1 MUTATED`
TCGA-OR-A5JY TCGA-OR-A5K9 TCGA-OR-A5L4 
       18.15        11.31        31.79 

$`SCRT1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        24.62        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        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       60.89       152.15        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  SCRT1 MUTATED SCRT1 WILD-TYPE 
          11.31            0.00 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
          31.79          153.63 
  SCRT1 MUTATED SCRT1 WILD-TYPE 
          18.15           44.55 
[1] "11.3 - 31.8 (18.1)" "0.0 - 153.6 (44.5)"
[1] "hr=" "4.4"
D73V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SCRT1 MUTATED         0        1         1        1
  SCRT1 WILD-TYPE       6       28        13       10
D73V3, multiclass
           clus
vv          SCRT1 MUTATED SCRT1 WILD-TYPE
  STAGE I               0               6
  STAGE II              1              28
  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 32  7 12
D73V4, multiclass
    clus
vv   SCRT1 MUTATED SCRT1 WILD-TYPE
  T1             0               6
  T2             1              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"
D73V5, binary
                 cls
clus               0  1
  SCRT1 MUTATED    2  1
  SCRT1 WILD-TYPE 52  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      2    1
  SCRT1 WILD-TYPE   52    5
   clus
vv  SCRT1 MUTATED SCRT1 WILD-TYPE
  0             2              52
  1             1               5
[1] 2 2
[1] FALSE
D73V6, 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
D73V7, binary
                 cls
clus               0  1
  SCRT1 MUTATED    2  1
  SCRT1 WILD-TYPE 44 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      2    1
  SCRT1 WILD-TYPE   44   13
     clus
vv    SCRT1 MUTATED SCRT1 WILD-TYPE
  NO              2              44
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SCRT1 MUTATED                                       0
  SCRT1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SCRT1 MUTATED                                          0
  SCRT1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SCRT1 MUTATED                                      3
  SCRT1 WILD-TYPE                                   55
D73V8, multiclass
                                          clus
vv                                         SCRT1 MUTATED SCRT1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  SCRT1 MUTATED    1  0  1  1
  SCRT1 WILD-TYPE 43  4  7  3
D73V9, multiclass
    clus
vv   SCRT1 MUTATED SCRT1 WILD-TYPE
  R0             1              43
  R1             0               4
  R2             1               7
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
[1] "Remove cluster labels:" "SCRT1 MUTATED"         
clus
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
D73V11, 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(74) Variable = KNDC1 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2              0  1
  KNDC1 MUTATED    7  2
  KNDC1 WILD-TYPE 32 21
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              9              53 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
              2              21 
$`KNDC1 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JT TCGA-OR-A5LA 
       91.30        66.25        76.64        67.59        29.82        23.64 
TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LR 
       36.33        79.07        28.04 

$`KNDC1 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP 
       18.12        57.53        99.88        69.37        49.22        15.25 
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        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL 
       28.31        28.64         5.23        39.35        90.08        53.03 
TCGA-OR-A5LP TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05         6.81         0.00        24.85       119.11 

  KNDC1 MUTATED KNDC1 WILD-TYPE 
          23.64            0.00 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
          91.30          153.63 
  KNDC1 MUTATED KNDC1 WILD-TYPE 
          66.25           42.51 
[1] "23.6 - 91.3 (66.2)" "0.0 - 153.6 (42.5)"
[1] "hr=" "2.1"
D74V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KNDC1 MUTATED         2        6         0        1
  KNDC1 WILD-TYPE       4       23        14       10
D74V3, multiclass
           clus
vv          KNDC1 MUTATED KNDC1 WILD-TYPE
  STAGE I               2               4
  STAGE II              6              23
  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 26  7 14
D74V4, multiclass
    clus
vv   KNDC1 MUTATED KNDC1 WILD-TYPE
  T1             2               4
  T2             7              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"
D74V5, binary
                 cls
clus               0  1
  KNDC1 MUTATED    8  1
  KNDC1 WILD-TYPE 46  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      8    1
  KNDC1 WILD-TYPE   46    5
   clus
vv  KNDC1 MUTATED KNDC1 WILD-TYPE
  0             8              46
  1             1               5
[1] 2 2
[1] FALSE
D74V6, 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
D74V7, binary
                 cls
clus               0  1
  KNDC1 MUTATED    7  2
  KNDC1 WILD-TYPE 39 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      7    2
  KNDC1 WILD-TYPE   39   12
     clus
vv    KNDC1 MUTATED KNDC1 WILD-TYPE
  NO              7              39
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KNDC1 MUTATED                                       0
  KNDC1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KNDC1 MUTATED                                          0
  KNDC1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KNDC1 MUTATED                                      9
  KNDC1 WILD-TYPE                                   49
D74V8, multiclass
                                          clus
vv                                         KNDC1 MUTATED KNDC1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 9              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  KNDC1 MUTATED    8  0  1  0
  KNDC1 WILD-TYPE 36  4  7  4
D74V9, multiclass
    clus
vv   KNDC1 MUTATED KNDC1 WILD-TYPE
  R0             8              36
  R1             0               4
  R2             1               7
  RX             0               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"
D74V10, continuous
D74V11, 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(75) Variable = MAP1S MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2              0  1
  MAP1S MUTATED    3  2
  MAP1S WILD-TYPE 36 21
  MAP1S MUTATED MAP1S WILD-TYPE 
              5              57 
  MAP1S MUTATED MAP1S WILD-TYPE 
              2              21 
$`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        90.08 

$`MAP1S WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       76.64        67.59        15.25        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        35.57        16.37 
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-A5L1 TCGA-OR-A5L2 
      153.63       127.50        68.25        44.84        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       39.35        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  MAP1S MUTATED MAP1S WILD-TYPE 
           4.11            0.00 
  MAP1S MUTATED MAP1S WILD-TYPE 
          90.08          153.63 
  MAP1S MUTATED MAP1S WILD-TYPE 
          36.33           43.30 
[1] "4.1 - 90.1 (36.3)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "1.3"
D75V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MAP1S MUTATED         0        3         0        2
  MAP1S WILD-TYPE       6       26        14        9
D75V3, multiclass
           clus
vv          MAP1S MUTATED MAP1S WILD-TYPE
  STAGE I               0               6
  STAGE II              3              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
  MAP1S MUTATED    0  4  0  1
  MAP1S WILD-TYPE  6 29  7 13
D75V4, multiclass
    clus
vv   MAP1S MUTATED MAP1S WILD-TYPE
  T1             0               6
  T2             4              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"
D75V5, binary
                 cls
clus               0  1
  MAP1S MUTATED    4  1
  MAP1S WILD-TYPE 50  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      4    1
  MAP1S WILD-TYPE   50    5
   clus
vv  MAP1S MUTATED MAP1S WILD-TYPE
  0             4              50
  1             1               5
[1] 2 2
[1] FALSE
D75V6, 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
D75V7, binary
                 cls
clus               0  1
  MAP1S MUTATED    3  2
  MAP1S WILD-TYPE 43 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      3    2
  MAP1S WILD-TYPE   43   12
     clus
vv    MAP1S MUTATED MAP1S WILD-TYPE
  NO              3              43
  YES             2              12
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  MAP1S MUTATED                                       0
  MAP1S WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  MAP1S MUTATED                                          1
  MAP1S WILD-TYPE                                        2
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  MAP1S MUTATED                                      4
  MAP1S WILD-TYPE                                   54
D75V8, multiclass
                                          clus
vv                                         MAP1S MUTATED MAP1S WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             1               2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  MAP1S MUTATED    2  0  2  1
  MAP1S WILD-TYPE 42  4  6  3
D75V9, multiclass
    clus
vv   MAP1S MUTATED MAP1S WILD-TYPE
  R0             2              42
  R1             0               4
  R2             2               6
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
[1] "Remove cluster labels:" "MAP1S MUTATED"         
clus
  MAP1S MUTATED MAP1S WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JV      TCGA-OR-A5JX 
"MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"MAP1S WILD-TYPE" "MAP1S WILD-TYPE" "MAP1S WILD-TYPE" 
D75V11, 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(76) Variable = RGMB MUTATION ANALYSIS
D76V1, survival
                sevent
clus2             0  1
  RGMB MUTATED    4  2
  RGMB WILD-TYPE 35 21
  RGMB MUTATED RGMB WILD-TYPE 
             6             56 
  RGMB MUTATED RGMB WILD-TYPE 
             2             21 
$`RGMB MUTATED`
TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-P6-A5OH 
       24.62        83.80        44.84        58.55        60.89         0.00 

$`RGMB WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       35.57        16.37        11.31        24.36        46.49        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63       127.50        68.25         4.11       152.15        31.79 
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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  RGMB MUTATED RGMB WILD-TYPE 
          0.00           4.11 
  RGMB MUTATED RGMB WILD-TYPE 
         83.80         153.63 
  RGMB MUTATED RGMB WILD-TYPE 
        51.695         41.045 
[1] "0.0 - 83.8 (51.7)"  "4.1 - 153.6 (41.0)"
[1] "hr=" "1.2"
D76V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RGMB MUTATED         0        4         1        1
  RGMB WILD-TYPE       6       25        13       10
D76V3, multiclass
           clus
vv          RGMB MUTATED RGMB WILD-TYPE
  STAGE I              0              6
  STAGE II             4             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
  RGMB MUTATED    0  5  0  1
  RGMB WILD-TYPE  6 28  7 13
D76V4, multiclass
    clus
vv   RGMB MUTATED RGMB WILD-TYPE
  T1            0              6
  T2            5             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"
D76V5, binary
                cls
clus              0  1
  RGMB MUTATED    5  1
  RGMB WILD-TYPE 49  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      5    1
  RGMB WILD-TYPE   49    5
   clus
vv  RGMB MUTATED RGMB WILD-TYPE
  0            5             49
  1            1              5
[1] 2 2
[1] FALSE
D76V6, 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
D76V7, binary
                cls
clus              0  1
  RGMB MUTATED    6  0
  RGMB WILD-TYPE 40 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      6    0
  RGMB WILD-TYPE   40   14
     clus
vv    RGMB MUTATED RGMB WILD-TYPE
  NO             6             40
  YES            0             14
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RGMB MUTATED                                       0
  RGMB WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RGMB MUTATED                                          0
  RGMB WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RGMB MUTATED                                      6
  RGMB WILD-TYPE                                   52
D76V8, multiclass
                                          clus
vv                                         RGMB MUTATED RGMB WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                6             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  RGMB MUTATED    5  0  1  0
  RGMB WILD-TYPE 39  4  7  4
D76V9, multiclass
    clus
vv   RGMB MUTATED RGMB WILD-TYPE
  R0            5             39
  R1            0              4
  R2            1              7
  RX            0              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"
D76V10, continuous
D76V11, 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(77) Variable = LRP11 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2              0  1
  LRP11 MUTATED    4  2
  LRP11 WILD-TYPE 35 21
  LRP11 MUTATED LRP11 WILD-TYPE 
              6              56 
  LRP11 MUTATED LRP11 WILD-TYPE 
              2              21 
$`LRP11 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5L1 TCGA-OR-A5L6 TCGA-P6-A5OF 
       42.51        24.62        11.31        58.55        28.31         6.81 

$`LRP11 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       16.37        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 
      127.50        68.25        44.84         4.11        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        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-A5OH 
       90.08        53.03        79.07        61.05        28.04         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  LRP11 MUTATED LRP11 WILD-TYPE 
           6.81            0.00 
  LRP11 MUTATED LRP11 WILD-TYPE 
          58.55          153.63 
  LRP11 MUTATED LRP11 WILD-TYPE 
         26.465          44.695 
[1] "6.8 - 58.5 (26.5)"  "0.0 - 153.6 (44.7)"
[1] "hr=" "1.4"
D77V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LRP11 MUTATED         0        4         1        0
  LRP11 WILD-TYPE       6       25        13       11
D77V3, multiclass
           clus
vv          LRP11 MUTATED LRP11 WILD-TYPE
  STAGE I               0               6
  STAGE II              4              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
  LRP11 MUTATED    0  4  0  1
  LRP11 WILD-TYPE  6 29  7 13
D77V4, multiclass
    clus
vv   LRP11 MUTATED LRP11 WILD-TYPE
  T1             0               6
  T2             4              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"
D77V5, binary
                 cls
clus               0  1
  LRP11 MUTATED    5  0
  LRP11 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      5    0
  LRP11 WILD-TYPE   49    6
   clus
vv  LRP11 MUTATED LRP11 WILD-TYPE
  0             5              49
  1             0               6
[1] 2 2
[1] FALSE
D77V6, 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
D77V7, binary
                 cls
clus               0  1
  LRP11 MUTATED    5  1
  LRP11 WILD-TYPE 41 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      5    1
  LRP11 WILD-TYPE   41   13
     clus
vv    LRP11 MUTATED LRP11 WILD-TYPE
  NO              5              41
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  LRP11 MUTATED                                       0
  LRP11 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  LRP11 MUTATED                                          0
  LRP11 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  LRP11 MUTATED                                      6
  LRP11 WILD-TYPE                                   52
D77V8, multiclass
                                          clus
vv                                         LRP11 MUTATED LRP11 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 6              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  LRP11 MUTATED    4  0  0  1
  LRP11 WILD-TYPE 40  4  8  3
D77V9, multiclass
    clus
vv   LRP11 MUTATED LRP11 WILD-TYPE
  R0             4              40
  R1             0               4
  R2             0               8
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, continuous
D77V11, 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(78) Variable = AR MUTATION ANALYSIS
D78V1, survival
              sevent
clus2           0  1
  AR MUTATED    1  3
  AR WILD-TYPE 38 20
  AR MUTATED AR WILD-TYPE 
           4           58 
  AR MUTATED AR WILD-TYPE 
           3           20 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        32.68        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  AR MUTATED AR WILD-TYPE 
       18.15         0.00 
  AR MUTATED AR WILD-TYPE 
       69.37       153.63 
  AR MUTATED AR WILD-TYPE 
      34.830       43.925 
[1] "18.1 - 69.4 (34.8)" "0.0 - 153.6 (43.9)"
[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       28        13        9
D78V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            0            6
  STAGE II           1           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
  AR MUTATED    0  1  0  3
  AR WILD-TYPE  6 32  7 11
D78V4, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  T1          0            6
  T2          1           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"
D78V5, binary
              cls
clus            0  1
  AR MUTATED    3  1
  AR WILD-TYPE 51  5
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   51    5
   clus
vv  AR MUTATED AR WILD-TYPE
  0          3           51
  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    3  1
  AR WILD-TYPE 43 13
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    1
  AR WILD-TYPE   43   13
     clus
vv    AR MUTATED AR WILD-TYPE
  NO           3           43
  YES          1           13
[1] 2 2
[1] FALSE
              vv
clus           ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AR MUTATED                                       0
  AR WILD-TYPE                                     1
              vv
clus           ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AR MUTATED                                          1
  AR WILD-TYPE                                        2
              vv
clus           ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AR MUTATED                                      3
  AR WILD-TYPE                                   55
D78V8, multiclass
                                          clus
vv                                         AR MUTATED AR WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE             0            1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE          1            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE              3           55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           R0 R1 R2 RX
  AR MUTATED    1  1  1  1
  AR WILD-TYPE 43  3  7  3
D78V9, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  R0          1           43
  R1          1            3
  R2          1            7
  RX          1            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, continuous
[1] "Remove cluster labels:" "AR MUTATED"            
clus
  AR MUTATED AR WILD-TYPE 
           1           19 
  TCGA-OR-A5KP   TCGA-OR-A5J2   TCGA-OR-A5J3   TCGA-OR-A5J4   TCGA-OR-A5J7 
"AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" 
  TCGA-OR-A5J8   TCGA-OR-A5JT   TCGA-OR-A5JV   TCGA-OR-A5JX   TCGA-OR-A5K2 
"AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" 
  TCGA-OR-A5K5   TCGA-OR-A5KB   TCGA-OR-A5KU   TCGA-OR-A5KV   TCGA-OR-A5KW 
"AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" 
  TCGA-OR-A5L9   TCGA-OR-A5LL   TCGA-OR-A5LO   TCGA-OR-A5LP 
"AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" "AR WILD-TYPE" 
D78V11, 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 = VARS MUTATION ANALYSIS
D79V1, survival
                sevent
clus2             0  1
  VARS MUTATED    4  2
  VARS WILD-TYPE 35 21
  VARS MUTATED VARS WILD-TYPE 
             6             56 
  VARS MUTATED VARS WILD-TYPE 
             2             21 
$`VARS MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JW TCGA-OR-A5L9 
       42.51        68.75        12.00        19.04        72.39        28.64 

$`VARS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 
       91.30        43.30        39.58        44.55        55.13        13.91 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       88.87        16.11        30.31        18.12        57.53        99.88 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       66.25        69.37        76.64        49.22        67.59        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26       121.25        29.82        66.51        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
       28.31        23.64         5.23        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  VARS MUTATED VARS WILD-TYPE 
            12              0 
  VARS MUTATED VARS WILD-TYPE 
         72.39         153.63 
  VARS MUTATED VARS WILD-TYPE 
        35.575         43.925 
[1] "12.0 - 72.4 (35.6)" "0.0 - 153.6 (43.9)"
[1] "hr=" "1"  
D79V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  VARS MUTATED         0        2         3        0
  VARS WILD-TYPE       6       27        11       11
D79V3, multiclass
           clus
vv          VARS MUTATED VARS WILD-TYPE
  STAGE I              0              6
  STAGE II             2             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
  VARS MUTATED    0  2  2  1
  VARS WILD-TYPE  6 31  5 13
D79V4, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  T1            0              6
  T2            2             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"
D79V5, binary
                cls
clus              0  1
  VARS MUTATED    5  0
  VARS WILD-TYPE 49  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      5    0
  VARS WILD-TYPE   49    6
   clus
vv  VARS MUTATED VARS WILD-TYPE
  0            5             49
  1            0              6
[1] 2 2
[1] FALSE
D79V6, 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
D79V7, binary
                cls
clus              0  1
  VARS MUTATED    3  3
  VARS WILD-TYPE 43 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      3    3
  VARS WILD-TYPE   43   11
     clus
vv    VARS MUTATED VARS WILD-TYPE
  NO             3             43
  YES            3             11
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  VARS MUTATED                                       0
  VARS WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  VARS MUTATED                                          0
  VARS WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  VARS MUTATED                                      6
  VARS WILD-TYPE                                   52
D79V8, multiclass
                                          clus
vv                                         VARS MUTATED VARS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                6             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  VARS MUTATED    4  0  1  0
  VARS WILD-TYPE 40  4  7  4
D79V9, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  R0            4             40
  R1            0              4
  R2            1              7
  RX            0              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"
D79V10, continuous
D79V11, 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(80) Variable = SEZ6L2 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2               0  1
  SEZ6L2 MUTATED    6  2
  SEZ6L2 WILD-TYPE 33 21
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               8               54 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
               2               21 
$`SEZ6L2 MUTATED`
TCGA-OR-A5KP TCGA-OR-A5JI TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KW 
       91.30        76.64        32.68        46.49        83.80        68.25 
TCGA-OR-A5LC TCGA-PA-A5YG 
        5.23        24.85 

$`SEZ6L2 WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        99.88        66.25        69.37        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        18.15        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX 
       11.31        24.36        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-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64        39.35        36.33        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PK-A5H8 
       79.07        61.05        28.04         6.81         0.00       119.11 

  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
            5.23             0.00 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
           91.30           153.63 
  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE 
          57.370           41.045 
[1] "5.2 - 91.3 (57.4)"  "0.0 - 153.6 (41.0)"
[1] "hr=" "1.8"
D80V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SEZ6L2 MUTATED         1        3         2        2
  SEZ6L2 WILD-TYPE       5       26        12        9
D80V3, multiclass
           clus
vv          SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  STAGE I                1                5
  STAGE II               3               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
  SEZ6L2 MUTATED    1  4  0  3
  SEZ6L2 WILD-TYPE  5 29  7 11
D80V4, multiclass
    clus
vv   SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  T1              1                5
  T2              4               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"
D80V5, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    7  1
  SEZ6L2 WILD-TYPE 47  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      7    1
  SEZ6L2 WILD-TYPE   47    5
   clus
vv  SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  0              7               47
  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    6  2
  SEZ6L2 WILD-TYPE 40 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      6    2
  SEZ6L2 WILD-TYPE   40   12
     clus
vv    SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  NO               6               40
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SEZ6L2 MUTATED                                       0
  SEZ6L2 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SEZ6L2 MUTATED                                          0
  SEZ6L2 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SEZ6L2 MUTATED                                      8
  SEZ6L2 WILD-TYPE                                   50
D80V8, multiclass
                                          clus
vv                                         SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  8               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  SEZ6L2 MUTATED    7  0  1  0
  SEZ6L2 WILD-TYPE 37  4  7  4
D80V9, multiclass
    clus
vv   SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  R0              7               37
  R1              0                4
  R2              1                7
  RX              0                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"
D80V10, continuous
D80V11, 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 = PABPC1 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    3  1
  PABPC1 WILD-TYPE 36 22
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               4               58 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               22 
$`PABPC1 MUTATED`
TCGA-OR-A5LB TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KX 
       39.58        24.36        83.80        44.84 

$`PABPC1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       16.37        24.62        11.31        46.49        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
      127.50        68.25         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
           24.36             0.00 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           83.80           153.63 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          42.210           42.905 
[1] "24.4 - 83.8 (42.2)" "0.0 - 153.6 (42.9)"
[1] "hr=" "1.6"
D81V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PABPC1 MUTATED         0        2         1        1
  PABPC1 WILD-TYPE       6       27        13       10
D81V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               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
  PABPC1 MUTATED    0  3  0  1
  PABPC1 WILD-TYPE  6 30  7 13
D81V4, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  T1              0                6
  T2              3               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"
D81V5, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  1
  PABPC1 WILD-TYPE 51  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    1
  PABPC1 WILD-TYPE   51    5
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              3               51
  1              1                5
[1] 2 2
[1] FALSE
D81V6, 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
D81V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  1
  PABPC1 WILD-TYPE 43 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    1
  PABPC1 WILD-TYPE   43   13
     clus
vv    PABPC1 MUTATED PABPC1 WILD-TYPE
  NO               3               43
  YES              1               13
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PABPC1 MUTATED                                       0
  PABPC1 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PABPC1 MUTATED                                          0
  PABPC1 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PABPC1 MUTATED                                      4
  PABPC1 WILD-TYPE                                   54
D81V8, multiclass
                                          clus
vv                                         PABPC1 MUTATED PABPC1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  4               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  PABPC1 MUTATED    4  0  0  0
  PABPC1 WILD-TYPE 40  4  8  4
D81V9, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  R0              4               40
  R1              0                4
  R2              0                8
  RX              0                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"
D81V10, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               19 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
D81V11, 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(82) Variable = FANK1 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2              0  1
  FANK1 MUTATED    2  1
  FANK1 WILD-TYPE 37 22
  FANK1 MUTATED FANK1 WILD-TYPE 
              3              59 
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              22 
$`FANK1 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5KT TCGA-OR-A5LJ 
       43.30        95.18        36.33 

$`FANK1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       16.37        24.62        11.31        24.36        46.49        83.80 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  FANK1 MUTATED FANK1 WILD-TYPE 
          36.33            0.00 
  FANK1 MUTATED FANK1 WILD-TYPE 
          95.18          153.63 
  FANK1 MUTATED FANK1 WILD-TYPE 
          43.30           42.51 
[1] "36.3 - 95.2 (43.3)" "0.0 - 153.6 (42.5)"
[1] "hr=" "1.3"
D82V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FANK1 MUTATED         2        0         0        1
  FANK1 WILD-TYPE       4       29        14       10
D82V3, multiclass
           clus
vv          FANK1 MUTATED FANK1 WILD-TYPE
  STAGE I               2               4
  STAGE II              0              29
  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  1  0  0
  FANK1 WILD-TYPE  4 32  7 14
D82V4, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  T1             2               4
  T2             1              32
  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"
D82V5, binary
                 cls
clus               0  1
  FANK1 MUTATED    2  1
  FANK1 WILD-TYPE 52  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      2    1
  FANK1 WILD-TYPE   52    5
   clus
vv  FANK1 MUTATED FANK1 WILD-TYPE
  0             2              52
  1             1               5
[1] 2 2
[1] FALSE
D82V6, binary
                 cls
clus               0  1
  FANK1 MUTATED    3  0
  FANK1 WILD-TYPE 37 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      3    0
  FANK1 WILD-TYPE   37   22
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  FEMALE             3              37
  MALE               0              22
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus               0  1
  FANK1 MUTATED    3  0
  FANK1 WILD-TYPE 43 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      3    0
  FANK1 WILD-TYPE   43   14
     clus
vv    FANK1 MUTATED FANK1 WILD-TYPE
  NO              3              43
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  FANK1 MUTATED                                       0
  FANK1 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  FANK1 MUTATED                                          0
  FANK1 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  FANK1 MUTATED                                      3
  FANK1 WILD-TYPE                                   55
D82V8, multiclass
                                          clus
vv                                         FANK1 MUTATED FANK1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  FANK1 MUTATED    2  0  1  0
  FANK1 WILD-TYPE 42  4  7  4
D82V9, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             0               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"
D82V10, continuous
D82V11, binary
                 cls
clus               0  1
  FANK1 MUTATED    0  3
  FANK1 WILD-TYPE  7 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      0    3
  FANK1 WILD-TYPE    7   24
                        clus
vv                       FANK1 MUTATED FANK1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             3              24
[1] 2 2
[1] FALSE

Clustering(83) Variable = NMU MUTATION ANALYSIS
D83V1, survival
               sevent
clus2            0  1
  NMU MUTATED    3  2
  NMU WILD-TYPE 36 21
  NMU MUTATED NMU WILD-TYPE 
            5            57 
  NMU MUTATED NMU WILD-TYPE 
            2            21 
$`NMU MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JF TCGA-OR-A5JT TCGA-OR-A5KB TCGA-P6-A5OF 
       13.91        66.25        29.82        24.36         6.81 

$`NMU WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25        36.26       121.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       11.31        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  NMU MUTATED NMU WILD-TYPE 
         6.81          0.00 
  NMU MUTATED NMU WILD-TYPE 
        66.25        153.63 
  NMU MUTATED NMU WILD-TYPE 
        24.36         44.55 
[1] "6.8 - 66.2 (24.4)"  "0.0 - 153.6 (44.5)"
[1] "hr=" "1.8"
D83V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NMU MUTATED         0        3         1        1
  NMU WILD-TYPE       6       26        13       10
D83V3, multiclass
           clus
vv          NMU MUTATED NMU WILD-TYPE
  STAGE I             0             6
  STAGE II            3            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
  NMU MUTATED    0  3  1  1
  NMU WILD-TYPE  6 30  6 13
D83V4, multiclass
    clus
vv   NMU MUTATED NMU WILD-TYPE
  T1           0             6
  T2           3            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"
D83V5, binary
               cls
clus             0  1
  NMU MUTATED    4  1
  NMU WILD-TYPE 50  5
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      4    1
  NMU WILD-TYPE   50    5
   clus
vv  NMU MUTATED NMU WILD-TYPE
  0           4            50
  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    3  2
  NMU WILD-TYPE 43 12
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      3    2
  NMU WILD-TYPE   43   12
     clus
vv    NMU MUTATED NMU WILD-TYPE
  NO            3            43
  YES           2            12
[1] 2 2
[1] FALSE
               vv
clus            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NMU MUTATED                                       0
  NMU WILD-TYPE                                     1
               vv
clus            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NMU MUTATED                                          0
  NMU WILD-TYPE                                        3
               vv
clus            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NMU MUTATED                                      5
  NMU WILD-TYPE                                   53
D83V8, multiclass
                                          clus
vv                                         NMU MUTATED NMU WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE              0             1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE           0             3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               5            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            R0 R1 R2 RX
  NMU MUTATED    3  0  1  1
  NMU WILD-TYPE 41  4  7  3
D83V9, multiclass
    clus
vv   NMU MUTATED NMU WILD-TYPE
  R0           3            41
  R1           0             4
  R2           1             7
  RX           1             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, continuous
D83V11, 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 = ADAD2 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2              0  1
  ADAD2 MUTATED    3  1
  ADAD2 WILD-TYPE 36 22
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              4              58 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              1              22 
$`ADAD2 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5JQ TCGA-OR-A5K8 
       42.51        18.12        36.26        24.62 

$`ADAD2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        15.25       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-A5K9 
       31.23        18.15        32.68        35.57        16.37        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  ADAD2 MUTATED ADAD2 WILD-TYPE 
          18.12            0.00 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
          42.51          153.63 
  ADAD2 MUTATED ADAD2 WILD-TYPE 
         30.440          44.695 
[1] "18.1 - 42.5 (30.4)" "0.0 - 153.6 (44.7)"
[1] "hr=" "1"  
D84V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ADAD2 MUTATED         0        2         0        1
  ADAD2 WILD-TYPE       6       27        14       10
D84V3, multiclass
           clus
vv          ADAD2 MUTATED ADAD2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  ADAD2 MUTATED    0  2  0  1
  ADAD2 WILD-TYPE  6 31  7 13
D84V4, multiclass
    clus
vv   ADAD2 MUTATED ADAD2 WILD-TYPE
  T1             0               6
  T2             2              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"
D84V5, binary
                 cls
clus               0  1
  ADAD2 MUTATED    3  0
  ADAD2 WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      3    0
  ADAD2 WILD-TYPE   51    6
   clus
vv  ADAD2 MUTATED ADAD2 WILD-TYPE
  0             3              51
  1             0               6
[1] 2 2
[1] FALSE
D84V6, 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
D84V7, binary
                 cls
clus               0  1
  ADAD2 MUTATED    2  1
  ADAD2 WILD-TYPE 44 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      2    1
  ADAD2 WILD-TYPE   44   13
     clus
vv    ADAD2 MUTATED ADAD2 WILD-TYPE
  NO              2              44
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ADAD2 MUTATED                                       1
  ADAD2 WILD-TYPE                                     0
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ADAD2 MUTATED                                          0
  ADAD2 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ADAD2 MUTATED                                      3
  ADAD2 WILD-TYPE                                   55
D84V8, multiclass
                                          clus
vv                                         ADAD2 MUTATED ADAD2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                1               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  ADAD2 MUTATED    2  1  0  0
  ADAD2 WILD-TYPE 42  3  8  4
D84V9, multiclass
    clus
vv   ADAD2 MUTATED ADAD2 WILD-TYPE
  R0             2              42
  R1             1               3
  R2             0               8
  RX             0               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"
D84V10, continuous
D84V11, 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(85) Variable = CLIC6 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2              0  1
  CLIC6 MUTATED    4  1
  CLIC6 WILD-TYPE 35 22
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              5              57 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              1              22 
$`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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       16.37        24.62        11.31        24.36        46.49        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LJ 
       31.79        28.31        28.64        23.64        39.35        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  CLIC6 MUTATED CLIC6 WILD-TYPE 
           5.23            0.00 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
         153.63          127.50 
  CLIC6 MUTATED CLIC6 WILD-TYPE 
          88.87           39.58 
[1] "5.2 - 153.6 (88.9)" "0.0 - 127.5 (39.6)"
[1] "hr=" "2.9"
D85V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CLIC6 MUTATED         1        3         0        1
  CLIC6 WILD-TYPE       5       26        14       10
D85V3, multiclass
           clus
vv          CLIC6 MUTATED CLIC6 WILD-TYPE
  STAGE I               1               5
  STAGE II              3              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
  CLIC6 MUTATED    1  3  0  1
  CLIC6 WILD-TYPE  5 30  7 13
D85V4, multiclass
    clus
vv   CLIC6 MUTATED CLIC6 WILD-TYPE
  T1             1               5
  T2             3              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
  CLIC6 MUTATED    5  0
  CLIC6 WILD-TYPE 49  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      5    0
  CLIC6 WILD-TYPE   49    6
   clus
vv  CLIC6 MUTATED CLIC6 WILD-TYPE
  0             5              49
  1             0               6
[1] 2 2
[1] FALSE
D85V6, 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
D85V7, binary
                 cls
clus               0  1
  CLIC6 MUTATED    5  0
  CLIC6 WILD-TYPE 41 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      5    0
  CLIC6 WILD-TYPE   41   14
     clus
vv    CLIC6 MUTATED CLIC6 WILD-TYPE
  NO              5              41
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CLIC6 MUTATED                                       0
  CLIC6 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CLIC6 MUTATED                                          0
  CLIC6 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CLIC6 MUTATED                                      5
  CLIC6 WILD-TYPE                                   53
D85V8, multiclass
                                          clus
vv                                         CLIC6 MUTATED CLIC6 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 5              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  CLIC6 MUTATED    4  0  1  0
  CLIC6 WILD-TYPE 40  4  7  4
D85V9, multiclass
    clus
vv   CLIC6 MUTATED CLIC6 WILD-TYPE
  R0             4              40
  R1             0               4
  R2             1               7
  RX             0               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"
D85V10, continuous
[1] "Remove cluster labels:" "CLIC6 MUTATED"         
clus
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5KB      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
D85V11, 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(86) Variable = PCDHB13 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                0  1
  PCDHB13 MUTATED    3  2
  PCDHB13 WILD-TYPE 36 21
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                5                57 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                2                21 
$`PCDHB13 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JI TCGA-OR-A5KB 
       68.75        12.00        30.31        76.64        24.36 

$`PCDHB13 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JC 
       13.91        88.87        16.11        19.04        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP 
       99.88        66.25        69.37        49.22        67.59        15.25 
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        35.57        16.37        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
               12                 0 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            76.64            153.63 
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
            30.31             43.30 
[1] "12.0 - 76.6 (30.3)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.2"
D86V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PCDHB13 MUTATED         1        1         2        1
  PCDHB13 WILD-TYPE       5       28        12       10
D86V3, multiclass
           clus
vv          PCDHB13 MUTATED PCDHB13 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                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
  PCDHB13 MUTATED    1  1  1  2
  PCDHB13 WILD-TYPE  5 32  6 12
D86V4, multiclass
    clus
vv   PCDHB13 MUTATED PCDHB13 WILD-TYPE
  T1               1                 5
  T2               1                32
  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"
D86V5, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    5  0
  PCDHB13 WILD-TYPE 49  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      5    0
  PCDHB13 WILD-TYPE   49    6
   clus
vv  PCDHB13 MUTATED PCDHB13 WILD-TYPE
  0               5                49
  1               0                 6
[1] 2 2
[1] FALSE
D86V6, 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
D86V7, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    5  0
  PCDHB13 WILD-TYPE 41 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      5    0
  PCDHB13 WILD-TYPE   41   14
     clus
vv    PCDHB13 MUTATED PCDHB13 WILD-TYPE
  NO                5                41
  YES               0                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PCDHB13 MUTATED                                       0
  PCDHB13 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PCDHB13 MUTATED                                          0
  PCDHB13 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PCDHB13 MUTATED                                      5
  PCDHB13 WILD-TYPE                                   53
D86V8, multiclass
                                          clus
vv                                         PCDHB13 MUTATED PCDHB13 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  PCDHB13 MUTATED    3  1  1  0
  PCDHB13 WILD-TYPE 41  3  7  4
D86V9, multiclass
    clus
vv   PCDHB13 MUTATED PCDHB13 WILD-TYPE
  R0               3                41
  R1               1                 3
  R2               1                 7
  RX               0                 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"
D86V10, continuous
[1] "Remove cluster labels:" "PCDHB13 MUTATED"       
clus
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J4        TCGA-OR-A5J7 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5J8        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KU 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9        TCGA-OR-A5LL 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
D86V11, 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(87) Variable = PLEC MUTATION ANALYSIS
D87V1, survival
                sevent
clus2             0  1
  PLEC MUTATED   10  3
  PLEC WILD-TYPE 29 20
  PLEC MUTATED PLEC WILD-TYPE 
            13             49 
  PLEC MUTATED PLEC WILD-TYPE 
             3             20 
$`PLEC MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J3 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K4 TCGA-OR-A5K5 
       91.30        68.75        49.22        67.59        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KW TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       24.62        24.36        68.25        28.64        23.64         5.23 
TCGA-P6-A5OH 
        0.00 

$`PLEC WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 
       43.30        39.58        42.51        44.55        55.13        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JP 
       57.53        99.88        66.25        69.37        76.64        15.25 
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-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       18.15        32.68        11.31        46.49        83.80        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-A5L6 TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK 
      152.15        31.79        28.31        39.35        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG 
       53.03        79.07        61.05        28.04         6.81        24.85 
TCGA-PK-A5H8 
      119.11 

  PLEC MUTATED PLEC WILD-TYPE 
          0.00           4.11 
  PLEC MUTATED PLEC WILD-TYPE 
         91.30         153.63 
  PLEC MUTATED PLEC WILD-TYPE 
         28.64          44.55 
[1] "0.0 - 91.3 (28.6)"  "4.1 - 153.6 (44.5)"
[1] "hr=" "1.4"
D87V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PLEC MUTATED         1        5         4        3
  PLEC WILD-TYPE       5       24        10        8
D87V3, multiclass
           clus
vv          PLEC MUTATED PLEC WILD-TYPE
  STAGE I              1              5
  STAGE II             5             24
  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 27  5 10
D87V4, multiclass
    clus
vv   PLEC MUTATED PLEC WILD-TYPE
  T1            1              5
  T2            6             27
  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"
D87V5, binary
                cls
clus              0  1
  PLEC MUTATED   12  1
  PLEC WILD-TYPE 42  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED     12    1
  PLEC WILD-TYPE   42    5
   clus
vv  PLEC MUTATED PLEC WILD-TYPE
  0           12             42
  1            1              5
[1] 2 2
[1] FALSE
D87V6, 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
D87V7, binary
                cls
clus              0  1
  PLEC MUTATED    9  4
  PLEC WILD-TYPE 37 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      9    4
  PLEC WILD-TYPE   37   10
     clus
vv    PLEC MUTATED PLEC WILD-TYPE
  NO             9             37
  YES            4             10
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PLEC MUTATED                                       0
  PLEC WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PLEC MUTATED                                          0
  PLEC WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PLEC MUTATED                                     13
  PLEC WILD-TYPE                                   45
D87V8, multiclass
                                          clus
vv                                         PLEC MUTATED PLEC WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               13             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  PLEC MUTATED    9  1  3  0
  PLEC WILD-TYPE 35  3  5  4
D87V9, multiclass
    clus
vv   PLEC MUTATED PLEC WILD-TYPE
  R0            9             35
  R1            1              3
  R2            3              5
  RX            0              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"
D87V10, continuous
D87V11, 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(88) Variable = AMDHD1 MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2               0  1
  AMDHD1 MUTATED    5  5
  AMDHD1 WILD-TYPE 34 18
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
              10               52 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               5               18 
$`AMDHD1 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JW 
       42.51        19.04        18.12        66.25        67.59        72.39 
TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-OR-A5LO TCGA-P6-A5OH 
       11.31        28.31        79.07         0.00 

$`AMDHD1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        30.31        57.53 
TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       99.88        69.37        76.64        49.22        15.25        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-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       35.57        16.37        24.62        24.36        46.49        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        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LA 
       58.55        60.89       152.15        31.79        28.64        23.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LP 
        5.23        39.35        36.33        90.08        53.03        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81        24.85       119.11 

  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
            0.00             4.11 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
           79.07           153.63 
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
          35.410           43.925 
[1] "0.0 - 79.1 (35.4)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "1.6"
D88V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AMDHD1 MUTATED         1        5         1        2
  AMDHD1 WILD-TYPE       5       24        13        9
D88V3, multiclass
           clus
vv          AMDHD1 MUTATED AMDHD1 WILD-TYPE
  STAGE I                1                5
  STAGE II               5               24
  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 28  6 12
D88V4, multiclass
    clus
vv   AMDHD1 MUTATED AMDHD1 WILD-TYPE
  T1              1                5
  T2              5               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"
D88V5, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    9  0
  AMDHD1 WILD-TYPE 45  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      9    0
  AMDHD1 WILD-TYPE   45    6
   clus
vv  AMDHD1 MUTATED AMDHD1 WILD-TYPE
  0              9               45
  1              0                6
[1] 2 2
[1] FALSE
D88V6, 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
D88V7, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    5  4
  AMDHD1 WILD-TYPE 41 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      5    4
  AMDHD1 WILD-TYPE   41   10
     clus
vv    AMDHD1 MUTATED AMDHD1 WILD-TYPE
  NO               5               41
  YES              4               10
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMDHD1 MUTATED                                       0
  AMDHD1 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMDHD1 MUTATED                                          0
  AMDHD1 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMDHD1 MUTATED                                     10
  AMDHD1 WILD-TYPE                                   48
D88V8, multiclass
                                          clus
vv                                         AMDHD1 MUTATED AMDHD1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 10               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  AMDHD1 MUTATED    7  1  1  0
  AMDHD1 WILD-TYPE 37  3  7  4
D88V9, multiclass
    clus
vv   AMDHD1 MUTATED AMDHD1 WILD-TYPE
  R0              7               37
  R1              1                3
  R2              1                7
  RX              0                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"
D88V10, continuous
[1] "Remove cluster labels:" "AMDHD1 MUTATED"        
clus
  AMDHD1 MUTATED AMDHD1 WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JX 
"AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5       TCGA-OR-A5KB 
"AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LP 
"AMDHD1 WILD-TYPE" "AMDHD1 WILD-TYPE" 
D88V11, 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(89) Variable = DSPP MUTATION ANALYSIS
D89V1, survival
                sevent
clus2             0  1
  DSPP MUTATED    6  3
  DSPP WILD-TYPE 33 20
  DSPP MUTATED DSPP WILD-TYPE 
             9             53 
  DSPP MUTATED DSPP WILD-TYPE 
             3             20 
$`DSPP MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 
       55.13        18.12        68.25        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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       91.30        43.30        39.58        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LA 
      153.63       127.50         4.11        58.55        60.89        23.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        36.33        90.08        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  DSPP MUTATED DSPP WILD-TYPE 
         18.12           0.00 
  DSPP MUTATED DSPP WILD-TYPE 
        152.15         153.63 
  DSPP MUTATED DSPP WILD-TYPE 
         44.84          42.51 
[1] "18.1 - 152.2 (44.8)" "0.0 - 153.6 (42.5)" 
[1] "hr=" "1.1"
D89V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DSPP MUTATED         1        3         3        2
  DSPP WILD-TYPE       5       26        11        9
D89V3, multiclass
           clus
vv          DSPP MUTATED DSPP WILD-TYPE
  STAGE I              1              5
  STAGE II             3             26
  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 28  6 12
D89V4, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  T1            1              5
  T2            5             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"
D89V5, binary
                cls
clus              0  1
  DSPP MUTATED    7  2
  DSPP WILD-TYPE 47  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    2
  DSPP WILD-TYPE   47    4
   clus
vv  DSPP MUTATED DSPP WILD-TYPE
  0            7             47
  1            2              4
[1] 2 2
[1] FALSE
D89V6, 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
D89V7, binary
                cls
clus              0  1
  DSPP MUTATED    7  1
  DSPP WILD-TYPE 39 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      7    1
  DSPP WILD-TYPE   39   13
     clus
vv    DSPP MUTATED DSPP WILD-TYPE
  NO             7             39
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DSPP MUTATED                                       0
  DSPP WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DSPP MUTATED                                          0
  DSPP WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DSPP MUTATED                                      9
  DSPP WILD-TYPE                                   49
D89V8, multiclass
                                          clus
vv                                         DSPP MUTATED DSPP WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                9             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  DSPP MUTATED    6  1  1  1
  DSPP WILD-TYPE 38  3  7  3
D89V9, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  R0            6             38
  R1            1              3
  R2            1              7
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V10, continuous
D89V11, 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(90) Variable = TMEM189 MUTATION ANALYSIS
D90V1, survival
                   sevent
clus2                0  1
  TMEM189 MUTATED    1  2
  TMEM189 WILD-TYPE 38 21
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                3                59 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                21 
$`TMEM189 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-P6-A5OH 
       42.51        55.13         0.00 

$`TMEM189 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        24.85       119.11 

  TMEM189 MUTATED TMEM189 WILD-TYPE 
             0.00              4.11 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
            55.13            153.63 
  TMEM189 MUTATED TMEM189 WILD-TYPE 
            42.51             43.30 
[1] "0.0 - 55.1 (42.5)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "2.6"
D90V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TMEM189 MUTATED         0        0         0        2
  TMEM189 WILD-TYPE       6       29        14        9
D90V3, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                58 
       TCGA-OR-A5KP        TCGA-OR-A5L5        TCGA-OR-A5LB        TCGA-OR-A5J1 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5        TCGA-OR-A5J6 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA        TCGA-OR-A5JB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JD        TCGA-OR-A5JF        TCGA-OR-A5JH        TCGA-OR-A5JI 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP        TCGA-OR-A5JQ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9        TCGA-OR-A5KB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KS        TCGA-OR-A5KT        TCGA-OR-A5KU 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L1        TCGA-OR-A5L2        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA        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        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  TMEM189 MUTATED    0  0  1  1
  TMEM189 WILD-TYPE  6 33  6 13
D90V4, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                58 
       TCGA-OR-A5KP        TCGA-OR-A5L5        TCGA-OR-A5LB        TCGA-OR-A5J1 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5        TCGA-OR-A5J6 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA        TCGA-OR-A5JB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JD        TCGA-OR-A5JF        TCGA-OR-A5JH        TCGA-OR-A5JI 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP        TCGA-OR-A5JQ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9        TCGA-OR-A5KB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KS        TCGA-OR-A5KT        TCGA-OR-A5KU 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L1        TCGA-OR-A5L2        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA        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        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
D90V5, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  0
  TMEM189 WILD-TYPE 52  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    0
  TMEM189 WILD-TYPE   52    6
   clus
vv  TMEM189 MUTATED TMEM189 WILD-TYPE
  0               2                52
  1               0                 6
[1] 2 2
[1] FALSE
D90V6, 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
D90V7, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    2  1
  TMEM189 WILD-TYPE 44 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      2    1
  TMEM189 WILD-TYPE   44   13
     clus
vv    TMEM189 MUTATED TMEM189 WILD-TYPE
  NO                2                44
  YES               1                13
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  TMEM189 MUTATED                                       0
  TMEM189 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  TMEM189 MUTATED                                          0
  TMEM189 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  TMEM189 MUTATED                                      3
  TMEM189 WILD-TYPE                                   55
D90V8, multiclass
                                          clus
vv                                         TMEM189 MUTATED TMEM189 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  TMEM189 MUTATED    0  0  2  0
  TMEM189 WILD-TYPE 44  4  6  4
D90V9, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                58 
       TCGA-OR-A5KP        TCGA-OR-A5L5        TCGA-OR-A5LB        TCGA-OR-A5J1 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5        TCGA-OR-A5J6 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA        TCGA-OR-A5JB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JD        TCGA-OR-A5JF        TCGA-OR-A5JH        TCGA-OR-A5JI 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP        TCGA-OR-A5JQ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9        TCGA-OR-A5KB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KS        TCGA-OR-A5KT        TCGA-OR-A5KU 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L1        TCGA-OR-A5L2        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA        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        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
D90V10, continuous
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                1                19 
       TCGA-OR-A5KP        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J7 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J8        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
D90V11, 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(91) Variable = CRIPAK MUTATION ANALYSIS
D91V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED    8  2
  CRIPAK WILD-TYPE 31 21
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              10               52 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               2               21 
$`CRIPAK MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KZ 
       88.87        67.59        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-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        15.25        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        35.57        16.37 
TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       24.36        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5LA TCGA-OR-A5LC 
       44.84        60.89       152.15        31.79        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            4.11             0.00 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           88.87           153.63 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          28.475           43.925 
[1] "4.1 - 88.9 (28.5)"  "0.0 - 153.6 (43.9)"
[1] "hr=" "1.6"
D91V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CRIPAK MUTATED         1        8         0        1
  CRIPAK WILD-TYPE       5       21        14       10
D91V3, multiclass
           clus
vv          CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                1                5
  STAGE II               8               21
  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 25  7 13
D91V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              1                5
  T2              8               25
  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"
D91V5, binary
                  cls
clus                0  1
  CRIPAK MUTATED   10  0
  CRIPAK WILD-TYPE 44  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     10    0
  CRIPAK WILD-TYPE   44    6
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0             10               44
  1              0                6
[1] 2 2
[1] FALSE
D91V6, 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
D91V7, binary
                  cls
clus                0  1
  CRIPAK MUTATED   10  0
  CRIPAK WILD-TYPE 36 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     10    0
  CRIPAK WILD-TYPE   36   14
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO              10               36
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CRIPAK MUTATED                                       0
  CRIPAK WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CRIPAK MUTATED                                          0
  CRIPAK WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CRIPAK MUTATED                                     10
  CRIPAK WILD-TYPE                                   48
D91V8, multiclass
                                          clus
vv                                         CRIPAK MUTATED CRIPAK WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 10               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  CRIPAK MUTATED    9  0  0  1
  CRIPAK WILD-TYPE 35  4  8  3
D91V9, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  R0              9               35
  R1              0                4
  R2              0                8
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V10, continuous
[1] "Remove cluster labels:" "CRIPAK MUTATED"        
clus
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               1               19 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-OR-A5KB       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
D91V11, 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(92) Variable = PDCD6 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2              0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 37 22
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              3              59 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              1              22 
$`PDCD6 MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JL TCGA-OR-A5JR 
       13.91        67.59       121.25 

$`PDCD6 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       49.22        15.25        36.26        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  PDCD6 MUTATED PDCD6 WILD-TYPE 
          13.91            0.00 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
         121.25          153.63 
  PDCD6 MUTATED PDCD6 WILD-TYPE 
          67.59           42.51 
[1] "13.9 - 121.2 (67.6)" "0.0 - 153.6 (42.5)" 
[1] "hr=" "1.3"
D92V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PDCD6 MUTATED         2        0         0        1
  PDCD6 WILD-TYPE       4       29        14       10
D92V3, multiclass
           clus
vv          PDCD6 MUTATED PDCD6 WILD-TYPE
  STAGE I               2               4
  STAGE II              0              29
  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 33  6 14
D92V4, multiclass
    clus
vv   PDCD6 MUTATED PDCD6 WILD-TYPE
  T1             2               4
  T2             0              33
  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"
D92V5, binary
                 cls
clus               0  1
  PDCD6 MUTATED    2  1
  PDCD6 WILD-TYPE 52  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      2    1
  PDCD6 WILD-TYPE   52    5
   clus
vv  PDCD6 MUTATED PDCD6 WILD-TYPE
  0             2              52
  1             1               5
[1] 2 2
[1] FALSE
D92V6, 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
D92V7, binary
                 cls
clus               0  1
  PDCD6 MUTATED    3  0
  PDCD6 WILD-TYPE 43 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      3    0
  PDCD6 WILD-TYPE   43   14
     clus
vv    PDCD6 MUTATED PDCD6 WILD-TYPE
  NO              3              43
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PDCD6 MUTATED                                       0
  PDCD6 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PDCD6 MUTATED                                          0
  PDCD6 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PDCD6 MUTATED                                      3
  PDCD6 WILD-TYPE                                   55
D92V8, multiclass
                                          clus
vv                                         PDCD6 MUTATED PDCD6 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  PDCD6 MUTATED    2  0  1  0
  PDCD6 WILD-TYPE 42  4  7  4
D92V9, multiclass
    clus
vv   PDCD6 MUTATED PDCD6 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             0               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"
D92V10, continuous
[1] "Remove cluster labels:" "PDCD6 MUTATED"         
clus
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J7 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JX 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
D92V11, 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(93) Variable = MAP7 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 37 22
  MAP7 MUTATED MAP7 WILD-TYPE 
             3             59 
  MAP7 MUTATED MAP7 WILD-TYPE 
             1             22 
$`MAP7 MUTATED`
TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5LA 
       66.51        32.68        23.64 

$`MAP7 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 
       29.82        72.39        31.23        18.15        35.57        16.37 
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        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LC 
       60.89       152.15        31.79        28.31        28.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  MAP7 MUTATED MAP7 WILD-TYPE 
         23.64           0.00 
  MAP7 MUTATED MAP7 WILD-TYPE 
         66.51         153.63 
  MAP7 MUTATED MAP7 WILD-TYPE 
         32.68          43.30 
[1] "23.6 - 66.5 (32.7)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1"  
D93V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MAP7 MUTATED         0        2         1        0
  MAP7 WILD-TYPE       6       27        13       11
D93V3, multiclass
           clus
vv          MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             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
  MAP7 MUTATED    0  2  0  1
  MAP7 WILD-TYPE  6 31  7 13
D93V4, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            0              6
  T2            2             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"
D93V5, binary
                cls
clus              0  1
  MAP7 MUTATED    3  0
  MAP7 WILD-TYPE 51  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      3    0
  MAP7 WILD-TYPE   51    6
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0            3             51
  1            0              6
[1] 2 2
[1] FALSE
D93V6, 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
D93V7, binary
                cls
clus              0  1
  MAP7 MUTATED    2  1
  MAP7 WILD-TYPE 44 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      2    1
  MAP7 WILD-TYPE   44   13
     clus
vv    MAP7 MUTATED MAP7 WILD-TYPE
  NO             2             44
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  MAP7 MUTATED                                       0
  MAP7 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  MAP7 MUTATED                                          0
  MAP7 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  MAP7 MUTATED                                      3
  MAP7 WILD-TYPE                                   55
D93V8, multiclass
                                          clus
vv                                         MAP7 MUTATED MAP7 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  MAP7 MUTATED    3  0  0  0
  MAP7 WILD-TYPE 41  4  8  4
D93V9, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  R0            3             41
  R1            0              4
  R2            0              8
  RX            0              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"
D93V10, continuous
[1] "Remove cluster labels:" "MAP7 MUTATED"          
clus
  MAP7 MUTATED MAP7 WILD-TYPE 
             2             18 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JX 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5JY     TCGA-OR-A5K5     TCGA-OR-A5KB     TCGA-OR-A5KU 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9     TCGA-OR-A5LL 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5LO     TCGA-OR-A5LP 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
D93V11, 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(94) Variable = NOM1 MUTATION ANALYSIS
D94V1, survival
                sevent
clus2             0  1
  NOM1 MUTATED    4  2
  NOM1 WILD-TYPE 35 21
  NOM1 MUTATED NOM1 WILD-TYPE 
             6             56 
  NOM1 MUTATED NOM1 WILD-TYPE 
             2             21 
$`NOM1 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J5 TCGA-OR-A5KB TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LP 
       43.30        12.00        24.36         4.11       152.15        61.05 

$`NOM1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       13.91        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
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-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
      127.50        68.25        44.84        58.55        60.89        31.79 
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-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       90.08        53.03        79.07        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  NOM1 MUTATED NOM1 WILD-TYPE 
          4.11           0.00 
  NOM1 MUTATED NOM1 WILD-TYPE 
        152.15         153.63 
  NOM1 MUTATED NOM1 WILD-TYPE 
         33.83          43.53 
[1] "4.1 - 152.2 (33.8)" "0.0 - 153.6 (43.5)"
[1] "hr=" "1.1"
D94V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NOM1 MUTATED         2        3         1        0
  NOM1 WILD-TYPE       4       26        13       11
D94V3, multiclass
           clus
vv          NOM1 MUTATED NOM1 WILD-TYPE
  STAGE I              2              4
  STAGE II             3             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
  NOM1 MUTATED    2  3  0  1
  NOM1 WILD-TYPE  4 30  7 13
D94V4, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  T1            2              4
  T2            3             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
  NOM1 MUTATED    6  0
  NOM1 WILD-TYPE 48  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      6    0
  NOM1 WILD-TYPE   48    6
   clus
vv  NOM1 MUTATED NOM1 WILD-TYPE
  0            6             48
  1            0              6
[1] 2 2
[1] FALSE
D94V6, 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
D94V7, binary
                cls
clus              0  1
  NOM1 MUTATED    6  0
  NOM1 WILD-TYPE 40 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      6    0
  NOM1 WILD-TYPE   40   14
     clus
vv    NOM1 MUTATED NOM1 WILD-TYPE
  NO             6             40
  YES            0             14
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NOM1 MUTATED                                       0
  NOM1 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NOM1 MUTATED                                          0
  NOM1 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NOM1 MUTATED                                      6
  NOM1 WILD-TYPE                                   52
D94V8, multiclass
                                          clus
vv                                         NOM1 MUTATED NOM1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                6             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  NOM1 MUTATED    4  0  1  1
  NOM1 WILD-TYPE 40  4  7  3
D94V9, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  R0            4             40
  R1            0              4
  R2            1              7
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V10, continuous
[1] "Remove cluster labels:" "NOM1 MUTATED"          
clus
  NOM1 MUTATED NOM1 WILD-TYPE 
             2             18 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2     TCGA-OR-A5K5 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
D94V11, 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(95) Variable = SHOX2 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2              0  1
  SHOX2 MUTATED    3  0
  SHOX2 WILD-TYPE 36 23
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              3              59 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              0              23 
$`SHOX2 MUTATED`
TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5LK 
       24.36       127.50        90.08 

$`SHOX2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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-A5KO TCGA-OR-A5KS 
       35.57        16.37        24.62        11.31        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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        36.33        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  SHOX2 MUTATED SHOX2 WILD-TYPE 
          24.36            0.00 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
         127.50          153.63 
  SHOX2 MUTATED SHOX2 WILD-TYPE 
          90.08           42.51 
[1] "24.4 - 127.5 (90.1)" "0.0 - 153.6 (42.5)" 
[1] "hr="     "7.4e+07"
D95V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SHOX2 MUTATED         0        2         1        0
  SHOX2 WILD-TYPE       6       27        13       11
D95V3, multiclass
           clus
vv          SHOX2 MUTATED SHOX2 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  SHOX2 MUTATED    0  3  0  0
  SHOX2 WILD-TYPE  6 30  7 14
D95V4, multiclass
    clus
vv   SHOX2 MUTATED SHOX2 WILD-TYPE
  T1             0               6
  T2             3              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"
D95V5, binary
                 cls
clus               0  1
  SHOX2 MUTATED    2  1
  SHOX2 WILD-TYPE 52  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      2    1
  SHOX2 WILD-TYPE   52    5
   clus
vv  SHOX2 MUTATED SHOX2 WILD-TYPE
  0             2              52
  1             1               5
[1] 2 2
[1] FALSE
D95V6, 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
D95V7, binary
                 cls
clus               0  1
  SHOX2 MUTATED    2  1
  SHOX2 WILD-TYPE 44 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      2    1
  SHOX2 WILD-TYPE   44   13
     clus
vv    SHOX2 MUTATED SHOX2 WILD-TYPE
  NO              2              44
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SHOX2 MUTATED                                       0
  SHOX2 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SHOX2 MUTATED                                          1
  SHOX2 WILD-TYPE                                        2
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SHOX2 MUTATED                                      2
  SHOX2 WILD-TYPE                                   56
D95V8, multiclass
                                          clus
vv                                         SHOX2 MUTATED SHOX2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             1               2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 2              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  SHOX2 MUTATED    3  0  0  0
  SHOX2 WILD-TYPE 41  4  8  4
D95V9, multiclass
    clus
vv   SHOX2 MUTATED SHOX2 WILD-TYPE
  R0             3              41
  R1             0               4
  R2             0               8
  RX             0               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"
D95V10, continuous
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              18 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5L9      TCGA-OR-A5LL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
D95V11, 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(96) Variable = HSD17B1 MUTATION ANALYSIS
D96V1, survival
                   sevent
clus2                0  1
  HSD17B1 MUTATED    3  1
  HSD17B1 WILD-TYPE 36 22
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                4                58 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                1                22 
$`HSD17B1 MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5K4 TCGA-OR-A5KT TCGA-OR-A5LP 
       19.04        35.57        95.18        61.05 

$`HSD17B1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       68.75        13.91        12.00        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        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 
       66.51        72.39        31.23        18.15        32.68        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
       24.62        11.31        24.36        46.49        83.80       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
       39.35        36.33        90.08        53.03        79.07        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            19.04              0.00 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
            95.18            153.63 
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
           48.310            42.905 
[1] "19.0 - 95.2 (48.3)" "0.0 - 153.6 (42.9)"
[1] "hr=" "1.7"
D96V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  HSD17B1 MUTATED         1        1         2        0
  HSD17B1 WILD-TYPE       5       28        12       11
D96V3, multiclass
           clus
vv          HSD17B1 MUTATED HSD17B1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                1                28
  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 32  6 13
D96V4, multiclass
    clus
vv   HSD17B1 MUTATED HSD17B1 WILD-TYPE
  T1               1                 5
  T2               1                32
  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"
D96V5, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    4  0
  HSD17B1 WILD-TYPE 50  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      4    0
  HSD17B1 WILD-TYPE   50    6
   clus
vv  HSD17B1 MUTATED HSD17B1 WILD-TYPE
  0               4                50
  1               0                 6
[1] 2 2
[1] FALSE
D96V6, 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
D96V7, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    2  2
  HSD17B1 WILD-TYPE 44 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      2    2
  HSD17B1 WILD-TYPE   44   12
     clus
vv    HSD17B1 MUTATED HSD17B1 WILD-TYPE
  NO                2                44
  YES               2                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  HSD17B1 MUTATED                                       0
  HSD17B1 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  HSD17B1 MUTATED                                          0
  HSD17B1 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  HSD17B1 MUTATED                                      4
  HSD17B1 WILD-TYPE                                   54
D96V8, multiclass
                                          clus
vv                                         HSD17B1 MUTATED HSD17B1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   4                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  HSD17B1 MUTATED    3  1  0  0
  HSD17B1 WILD-TYPE 41  3  8  4
D96V9, multiclass
    clus
vv   HSD17B1 MUTATED HSD17B1 WILD-TYPE
  R0               3                41
  R1               1                 3
  R2               0                 8
  RX               0                 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"
D96V10, continuous
[1] "Remove cluster labels:" "HSD17B1 MUTATED"       
clus
  HSD17B1 MUTATED HSD17B1 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J3        TCGA-OR-A5J4 
"HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9 
"HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" 
       TCGA-OR-A5LL        TCGA-OR-A5LO 
"HSD17B1 WILD-TYPE" "HSD17B1 WILD-TYPE" 
D96V11, 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(97) Variable = PRKAR1A MUTATION ANALYSIS
D97V1, survival
                   sevent
clus2                0  1
  PRKAR1A MUTATED    3  3
  PRKAR1A WILD-TYPE 36 20
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                6                56 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
                3                20 
$`PRKAR1A MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JL TCGA-OR-A5JY TCGA-OR-A5KT TCGA-OR-A5LO 
       68.75        30.31        67.59        18.15        95.18        79.07 

$`PRKAR1A WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        19.04        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       24.36        46.49        83.80       153.63       127.50        68.25 
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-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-P6-A5OH 
       90.08        53.03        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            18.15              0.00 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
            95.18            153.63 
  PRKAR1A MUTATED PRKAR1A WILD-TYPE 
           68.170            41.045 
[1] "18.1 - 95.2 (68.2)" "0.0 - 153.6 (41.0)"
[1] "hr=" "1.1"
D97V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  PRKAR1A MUTATED         2        1         1        2
  PRKAR1A WILD-TYPE       4       28        13        9
D97V3, multiclass
           clus
vv          PRKAR1A MUTATED PRKAR1A WILD-TYPE
  STAGE I                 2                 4
  STAGE II                1                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
  PRKAR1A MUTATED    2  1  1  2
  PRKAR1A WILD-TYPE  4 32  6 12
D97V4, multiclass
    clus
vv   PRKAR1A MUTATED PRKAR1A WILD-TYPE
  T1               2                 4
  T2               1                32
  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"
D97V5, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    5  1
  PRKAR1A WILD-TYPE 49  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      5    1
  PRKAR1A WILD-TYPE   49    5
   clus
vv  PRKAR1A MUTATED PRKAR1A WILD-TYPE
  0               5                49
  1               1                 5
[1] 2 2
[1] FALSE
D97V6, 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
D97V7, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    5  1
  PRKAR1A WILD-TYPE 41 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      5    1
  PRKAR1A WILD-TYPE   41   13
     clus
vv    PRKAR1A MUTATED PRKAR1A WILD-TYPE
  NO                5                41
  YES               1                13
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  PRKAR1A MUTATED                                       0
  PRKAR1A WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  PRKAR1A MUTATED                                          0
  PRKAR1A WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  PRKAR1A MUTATED                                      6
  PRKAR1A WILD-TYPE                                   52
D97V8, multiclass
                                          clus
vv                                         PRKAR1A MUTATED PRKAR1A WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  PRKAR1A MUTATED    4  1  1  0
  PRKAR1A WILD-TYPE 40  3  7  4
D97V9, multiclass
    clus
vv   PRKAR1A MUTATED PRKAR1A WILD-TYPE
  R0               4                40
  R1               1                 3
  R2               1                 7
  RX               0                 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"
D97V10, continuous
D97V11, 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(98) Variable = KRTAP5-5 MUTATION ANALYSIS
D98V1, survival
                    sevent
clus2                 0  1
  KRTAP5-5 MUTATED    1  2
  KRTAP5-5 WILD-TYPE 38 21
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 59 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 21 
$`KRTAP5-5 MUTATED`
TCGA-OR-A5LB TCGA-OR-A5K9 TCGA-OR-A5KS 
       39.58        11.31        83.80 

$`KRTAP5-5 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       16.37        24.62        24.36        46.49        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             11.31               0.00 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             83.80             153.63 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             39.58              43.30 
[1] "11.3 - 83.8 (39.6)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.9"
D98V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP5-5 MUTATED         0        2         0        1
  KRTAP5-5 WILD-TYPE       6       27        14       10
D98V3, multiclass
           clus
vv          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  STAGE I                  0                  6
  STAGE II                 2                 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
  KRTAP5-5 MUTATED    0  2  0  1
  KRTAP5-5 WILD-TYPE  6 31  7 13
D98V4, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  T1                0                  6
  T2                2                 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"
D98V5, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    3  0
  KRTAP5-5 WILD-TYPE 51  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      3    0
  KRTAP5-5 WILD-TYPE   51    6
   clus
vv  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  0                3                 51
  1                0                  6
[1] 2 2
[1] FALSE
D98V6, 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
D98V7, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    2  1
  KRTAP5-5 WILD-TYPE 44 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      2    1
  KRTAP5-5 WILD-TYPE   44   13
     clus
vv    KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  NO                 2                 44
  YES                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  KRTAP5-5 MUTATED                                       0
  KRTAP5-5 WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  KRTAP5-5 MUTATED                                          0
  KRTAP5-5 WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  KRTAP5-5 MUTATED                                      3
  KRTAP5-5 WILD-TYPE                                   55
D98V8, multiclass
                                          clus
vv                                         KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  KRTAP5-5 MUTATED    3  0  0  0
  KRTAP5-5 WILD-TYPE 41  4  8  4
D98V9, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  R0                3                 41
  R1                0                  4
  R2                0                  8
  RX                0                  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"
D98V10, continuous
D98V11, 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(99) Variable = DLEU7 MUTATION ANALYSIS
D99V1, survival
                 sevent
clus2              0  1
  DLEU7 MUTATED    2  1
  DLEU7 WILD-TYPE 37 22
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              3              59 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              22 
$`DLEU7 MUTATED`
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-P6-A5OH 
       24.62        24.36         0.00 

$`DLEU7 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT 
       35.57        16.37        11.31        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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        24.85       119.11 

  DLEU7 MUTATED DLEU7 WILD-TYPE 
           0.00            4.11 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
          24.62          153.63 
  DLEU7 MUTATED DLEU7 WILD-TYPE 
          24.36           44.55 
[1] "0.0 - 24.6 (24.4)"  "4.1 - 153.6 (44.5)"
[1] "hr=" "2.4"
D99V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DLEU7 MUTATED         0        2         0        1
  DLEU7 WILD-TYPE       6       27        14       10
D99V3, multiclass
           clus
vv          DLEU7 MUTATED DLEU7 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  DLEU7 MUTATED    0  2  0  1
  DLEU7 WILD-TYPE  6 31  7 13
D99V4, multiclass
    clus
vv   DLEU7 MUTATED DLEU7 WILD-TYPE
  T1             0               6
  T2             2              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"
D99V5, binary
                 cls
clus               0  1
  DLEU7 MUTATED    3  0
  DLEU7 WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      3    0
  DLEU7 WILD-TYPE   51    6
   clus
vv  DLEU7 MUTATED DLEU7 WILD-TYPE
  0             3              51
  1             0               6
[1] 2 2
[1] FALSE
D99V6, 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
D99V7, binary
                 cls
clus               0  1
  DLEU7 MUTATED    3  0
  DLEU7 WILD-TYPE 43 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      3    0
  DLEU7 WILD-TYPE   43   14
     clus
vv    DLEU7 MUTATED DLEU7 WILD-TYPE
  NO              3              43
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DLEU7 MUTATED                                       0
  DLEU7 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DLEU7 MUTATED                                          0
  DLEU7 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DLEU7 MUTATED                                      3
  DLEU7 WILD-TYPE                                   55
D99V8, multiclass
                                          clus
vv                                         DLEU7 MUTATED DLEU7 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  DLEU7 MUTATED    2  0  1  0
  DLEU7 WILD-TYPE 42  4  7  4
D99V9, multiclass
    clus
vv   DLEU7 MUTATED DLEU7 WILD-TYPE
  R0             2              42
  R1             0               4
  R2             1               7
  RX             0               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"
D99V10, continuous
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
D99V11, 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(100) Variable = FEZ2 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2             0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 37 22
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             3             59 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             1             22 
$`FEZ2 MUTATED`
TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LJ 
       28.31        23.64        36.33 

$`FEZ2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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 
       35.57        16.37        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        68.25        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L9 
        4.11        58.55        60.89       152.15        31.79        28.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        39.35        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  FEZ2 MUTATED FEZ2 WILD-TYPE 
         23.64           0.00 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
         36.33         153.63 
  FEZ2 MUTATED FEZ2 WILD-TYPE 
         28.31          44.55 
[1] "23.6 - 36.3 (28.3)" "0.0 - 153.6 (44.5)"
[1] "hr=" "1.4"
D100V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FEZ2 MUTATED         0        2         0        1
  FEZ2 WILD-TYPE       6       27        14       10
D100V3, multiclass
           clus
vv          FEZ2 MUTATED FEZ2 WILD-TYPE
  STAGE I              0              6
  STAGE II             2             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
  FEZ2 MUTATED    0  3  0  0
  FEZ2 WILD-TYPE  6 30  7 14
D100V4, multiclass
    clus
vv   FEZ2 MUTATED FEZ2 WILD-TYPE
  T1            0              6
  T2            3             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"
D100V5, binary
                cls
clus              0  1
  FEZ2 MUTATED    2  1
  FEZ2 WILD-TYPE 52  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      2    1
  FEZ2 WILD-TYPE   52    5
   clus
vv  FEZ2 MUTATED FEZ2 WILD-TYPE
  0            2             52
  1            1              5
[1] 2 2
[1] FALSE
D100V6, 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
D100V7, binary
                cls
clus              0  1
  FEZ2 MUTATED    3  0
  FEZ2 WILD-TYPE 43 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      3    0
  FEZ2 WILD-TYPE   43   14
     clus
vv    FEZ2 MUTATED FEZ2 WILD-TYPE
  NO             3             43
  YES            0             14
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  FEZ2 MUTATED                                       0
  FEZ2 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  FEZ2 MUTATED                                          0
  FEZ2 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  FEZ2 MUTATED                                      3
  FEZ2 WILD-TYPE                                   55
D100V8, multiclass
                                          clus
vv                                         FEZ2 MUTATED FEZ2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  FEZ2 MUTATED    2  0  1  0
  FEZ2 WILD-TYPE 42  4  7  4
D100V9, multiclass
    clus
vv   FEZ2 MUTATED FEZ2 WILD-TYPE
  R0            2             42
  R1            0              4
  R2            1              7
  RX            0              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"
D100V10, continuous
D100V11, 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(101) Variable = RASIP1 MUTATION ANALYSIS
D101V1, survival
                  sevent
clus2               0  1
  RASIP1 MUTATED    2  4
  RASIP1 WILD-TYPE 37 19
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               6               56 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               4               19 
$`RASIP1 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5K2 TCGA-OR-A5KU TCGA-OR-A5LC TCGA-OR-A5LJ 
       12.00        66.25        32.68       153.63         5.23        36.33 

$`RASIP1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        18.15        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       11.31        24.36        46.49        83.80        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LK 
       31.79        28.31        28.64        23.64        39.35        90.08 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH 
       53.03        79.07        61.05        28.04         6.81         0.00 
TCGA-PA-A5YG TCGA-PK-A5H8 
       24.85       119.11 

  RASIP1 MUTATED RASIP1 WILD-TYPE 
            5.23             0.00 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          153.63           152.15 
  RASIP1 MUTATED RASIP1 WILD-TYPE 
          34.505           43.925 
[1] "5.2 - 153.6 (34.5)" "0.0 - 152.2 (43.9)"
[1] "hr=" "2.3"
D101V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RASIP1 MUTATED         0        2         2        2
  RASIP1 WILD-TYPE       6       27        12        9
D101V3, multiclass
           clus
vv          RASIP1 MUTATED RASIP1 WILD-TYPE
  STAGE I                0                6
  STAGE II               2               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
  RASIP1 MUTATED    0  3  0  3
  RASIP1 WILD-TYPE  6 30  7 11
D101V4, multiclass
    clus
vv   RASIP1 MUTATED RASIP1 WILD-TYPE
  T1              0                6
  T2              3               30
  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"
D101V5, binary
                  cls
clus                0  1
  RASIP1 MUTATED    5  1
  RASIP1 WILD-TYPE 49  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      5    1
  RASIP1 WILD-TYPE   49    5
   clus
vv  RASIP1 MUTATED RASIP1 WILD-TYPE
  0              5               49
  1              1                5
[1] 2 2
[1] FALSE
D101V6, 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
D101V7, binary
                  cls
clus                0  1
  RASIP1 MUTATED    4  2
  RASIP1 WILD-TYPE 42 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      4    2
  RASIP1 WILD-TYPE   42   12
     clus
vv    RASIP1 MUTATED RASIP1 WILD-TYPE
  NO               4               42
  YES              2               12
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RASIP1 MUTATED                                       0
  RASIP1 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RASIP1 MUTATED                                          0
  RASIP1 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RASIP1 MUTATED                                      6
  RASIP1 WILD-TYPE                                   52
D101V8, multiclass
                                          clus
vv                                         RASIP1 MUTATED RASIP1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  6               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  RASIP1 MUTATED    3  0  3  0
  RASIP1 WILD-TYPE 41  4  5  4
D101V9, multiclass
    clus
vv   RASIP1 MUTATED RASIP1 WILD-TYPE
  R0              3               41
  R1              0                4
  R2              3                5
  RX              0                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"
D101V10, continuous
[1] "Remove cluster labels:" "RASIP1 MUTATED"        
clus
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K5       TCGA-OR-A5KB 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9       TCGA-OR-A5LL 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5LO       TCGA-OR-A5LP 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
D101V11, 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(102) Variable = JMJD4 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2              0  1
  JMJD4 MUTATED    2  1
  JMJD4 WILD-TYPE 37 22
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              3              59 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              1              22 
$`JMJD4 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JP TCGA-OR-A5KS 
       16.11        15.25        83.80 

$`JMJD4 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        88.87        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       24.62        11.31        24.36        46.49        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  JMJD4 MUTATED JMJD4 WILD-TYPE 
          15.25            0.00 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
          83.80          153.63 
  JMJD4 MUTATED JMJD4 WILD-TYPE 
          16.11           43.30 
[1] "15.2 - 83.8 (16.1)" "0.0 - 153.6 (43.3)"
[1] "hr=" "1.1"
D102V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  JMJD4 MUTATED         0        2         1        0
  JMJD4 WILD-TYPE       6       27        13       11
D102V3, multiclass
           clus
vv          JMJD4 MUTATED JMJD4 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  JMJD4 MUTATED    0  2  1  0
  JMJD4 WILD-TYPE  6 31  6 14
D102V4, multiclass
    clus
vv   JMJD4 MUTATED JMJD4 WILD-TYPE
  T1             0               6
  T2             2              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"
D102V5, binary
                 cls
clus               0  1
  JMJD4 MUTATED    3  0
  JMJD4 WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      3    0
  JMJD4 WILD-TYPE   51    6
   clus
vv  JMJD4 MUTATED JMJD4 WILD-TYPE
  0             3              51
  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    3  0
  JMJD4 WILD-TYPE 43 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      3    0
  JMJD4 WILD-TYPE   43   14
     clus
vv    JMJD4 MUTATED JMJD4 WILD-TYPE
  NO              3              43
  YES             0              14
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  JMJD4 MUTATED                                       0
  JMJD4 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  JMJD4 MUTATED                                          0
  JMJD4 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  JMJD4 MUTATED                                      3
  JMJD4 WILD-TYPE                                   55
D102V8, multiclass
                                          clus
vv                                         JMJD4 MUTATED JMJD4 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  JMJD4 MUTATED    2  1  0  0
  JMJD4 WILD-TYPE 42  3  8  4
D102V9, multiclass
    clus
vv   JMJD4 MUTATED JMJD4 WILD-TYPE
  R0             2              42
  R1             1               3
  R2             0               8
  RX             0               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"
D102V10, continuous
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JX 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
D102V11, 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 = COQ2 MUTATION ANALYSIS
D103V1, survival
                sevent
clus2             0  1
  COQ2 MUTATED    3  2
  COQ2 WILD-TYPE 36 21
  COQ2 MUTATED COQ2 WILD-TYPE 
             5             57 
  COQ2 MUTATED COQ2 WILD-TYPE 
             2             21 
$`COQ2 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5L2 TCGA-OR-A5LK 
       30.31        66.25        67.59        60.89        90.08 

$`COQ2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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-A5L3 
      127.50        68.25        44.84         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        28.64        23.64         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        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  COQ2 MUTATED COQ2 WILD-TYPE 
         30.31           0.00 
  COQ2 MUTATED COQ2 WILD-TYPE 
         90.08         153.63 
  COQ2 MUTATED COQ2 WILD-TYPE 
         66.25          39.58 
[1] "30.3 - 90.1 (66.2)" "0.0 - 153.6 (39.6)"
[1] "hr=" "1.3"
D103V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  COQ2 MUTATED         1        3         0        1
  COQ2 WILD-TYPE       5       26        14       10
D103V3, multiclass
           clus
vv          COQ2 MUTATED COQ2 WILD-TYPE
  STAGE I              1              5
  STAGE II             3             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
  COQ2 MUTATED    1  3  0  1
  COQ2 WILD-TYPE  5 30  7 13
D103V4, multiclass
    clus
vv   COQ2 MUTATED COQ2 WILD-TYPE
  T1            1              5
  T2            3             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"
D103V5, binary
                cls
clus              0  1
  COQ2 MUTATED    5  0
  COQ2 WILD-TYPE 49  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      5    0
  COQ2 WILD-TYPE   49    6
   clus
vv  COQ2 MUTATED COQ2 WILD-TYPE
  0            5             49
  1            0              6
[1] 2 2
[1] FALSE
D103V6, 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
D103V7, binary
                cls
clus              0  1
  COQ2 MUTATED    4  1
  COQ2 WILD-TYPE 42 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      4    1
  COQ2 WILD-TYPE   42   13
     clus
vv    COQ2 MUTATED COQ2 WILD-TYPE
  NO             4             42
  YES            1             13
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  COQ2 MUTATED                                       0
  COQ2 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  COQ2 MUTATED                                          1
  COQ2 WILD-TYPE                                        2
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  COQ2 MUTATED                                      4
  COQ2 WILD-TYPE                                   54
D103V8, multiclass
                                          clus
vv                                         COQ2 MUTATED COQ2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            1              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                4             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  COQ2 MUTATED    4  1  0  0
  COQ2 WILD-TYPE 40  3  8  4
D103V9, multiclass
    clus
vv   COQ2 MUTATED COQ2 WILD-TYPE
  R0            4             40
  R1            1              3
  R2            0              8
  RX            0              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"
D103V10, continuous
D103V11, 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(104) Variable = UQCRFS1 MUTATION ANALYSIS
D104V1, survival
                   sevent
clus2                0  1
  UQCRFS1 MUTATED    2  3
  UQCRFS1 WILD-TYPE 37 20
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                5                57 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                3                20 
$`UQCRFS1 MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5JI TCGA-OR-A5LD TCGA-P6-A5OF 
       68.75        13.91        76.64        39.35         6.81 

$`UQCRFS1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       57.53        99.88        66.25        69.37        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        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        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
             6.81              0.00 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            76.64            153.63 
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
            39.35             43.30 
[1] "6.8 - 76.6 (39.4)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "2"  
D104V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  UQCRFS1 MUTATED         1        0         3        1
  UQCRFS1 WILD-TYPE       5       29        11       10
D104V3, multiclass
           clus
vv          UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                0                29
  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 33  5 12
D104V4, multiclass
    clus
vv   UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  T1               1                 5
  T2               0                33
  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"
D104V5, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    4  1
  UQCRFS1 WILD-TYPE 50  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      4    1
  UQCRFS1 WILD-TYPE   50    5
   clus
vv  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  0               4                50
  1               1                 5
[1] 2 2
[1] FALSE
D104V6, 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
D104V7, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    5  0
  UQCRFS1 WILD-TYPE 41 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      5    0
  UQCRFS1 WILD-TYPE   41   14
     clus
vv    UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  NO                5                41
  YES               0                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  UQCRFS1 MUTATED                                       0
  UQCRFS1 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  UQCRFS1 MUTATED                                          0
  UQCRFS1 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  UQCRFS1 MUTATED                                      5
  UQCRFS1 WILD-TYPE                                   53
D104V8, multiclass
                                          clus
vv                                         UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  UQCRFS1 MUTATED    2  0  1  2
  UQCRFS1 WILD-TYPE 42  4  7  2
D104V9, multiclass
    clus
vv   UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  R0               2                42
  R1               0                 4
  R2               1                 7
  RX               2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V10, continuous
[1] "Remove cluster labels:" "UQCRFS1 MUTATED"       
clus
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J7        TCGA-OR-A5J8 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX        TCGA-OR-A5JY 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB        TCGA-OR-A5KU 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9        TCGA-OR-A5LL 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
D104V11, 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(105) Variable = C9ORF66 MUTATION ANALYSIS
D105V1, survival
                   sevent
clus2                0  1
  C9ORF66 MUTATED    2  3
  C9ORF66 WILD-TYPE 37 20
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                5                57 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                3                20 
$`C9ORF66 MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JF TCGA-OR-A5JR TCGA-OR-A5K9 
       12.00        19.04        66.25       121.25        11.31 

$`C9ORF66 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       68.75        13.91        88.87        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       57.53        99.88        69.37        76.64        49.22        67.59 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       15.25        36.26        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        35.57        16.37        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
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-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 
       90.08        53.03        79.07        61.05        28.04         6.81 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        0.00        24.85       119.11 

  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
            11.31              0.00 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
           121.25            153.63 
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
            19.04             43.30 
[1] "11.3 - 121.2 (19.0)" "0.0 - 153.6 (43.3)" 
[1] "hr=" "2"  
D105V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C9ORF66 MUTATED         1        2         2        0
  C9ORF66 WILD-TYPE       5       27        12       11
D105V3, multiclass
           clus
vv          C9ORF66 MUTATED C9ORF66 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                2                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
  C9ORF66 MUTATED    1  2  1  1
  C9ORF66 WILD-TYPE  5 31  6 13
D105V4, multiclass
    clus
vv   C9ORF66 MUTATED C9ORF66 WILD-TYPE
  T1               1                 5
  T2               2                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"
D105V5, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    5  0
  C9ORF66 WILD-TYPE 49  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      5    0
  C9ORF66 WILD-TYPE   49    6
   clus
vv  C9ORF66 MUTATED C9ORF66 WILD-TYPE
  0               5                49
  1               0                 6
[1] 2 2
[1] FALSE
D105V6, 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
D105V7, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    3  2
  C9ORF66 WILD-TYPE 43 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      3    2
  C9ORF66 WILD-TYPE   43   12
     clus
vv    C9ORF66 MUTATED C9ORF66 WILD-TYPE
  NO                3                43
  YES               2                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  C9ORF66 MUTATED                                       0
  C9ORF66 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  C9ORF66 MUTATED                                          0
  C9ORF66 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  C9ORF66 MUTATED                                      5
  C9ORF66 WILD-TYPE                                   53
D105V8, multiclass
                                          clus
vv                                         C9ORF66 MUTATED C9ORF66 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  C9ORF66 MUTATED    4  0  1  0
  C9ORF66 WILD-TYPE 40  4  7  4
D105V9, multiclass
    clus
vv   C9ORF66 MUTATED C9ORF66 WILD-TYPE
  R0               4                40
  R1               0                 4
  R2               1                 7
  RX               0                 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"
D105V10, continuous
[1] "Remove cluster labels:" "C9ORF66 MUTATED"       
clus
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                1                19 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J3        TCGA-OR-A5J4 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
D105V11, 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(106) Variable = POLRMT MUTATION ANALYSIS
D106V1, survival
                  sevent
clus2               0  1
  POLRMT MUTATED    4  0
  POLRMT WILD-TYPE 35 23
  POLRMT MUTATED POLRMT WILD-TYPE 
               4               58 
  POLRMT MUTATED POLRMT WILD-TYPE 
               0               23 
$`POLRMT MUTATED`
TCGA-OR-A5JL TCGA-OR-A5JV TCGA-OR-A5LK TCGA-OR-A5LP 
       67.59        66.51        90.08        61.05 

$`POLRMT WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       76.64        49.22        15.25        36.26       121.25        29.82 
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        35.57        16.37 
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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LR 
        5.23        39.35        36.33        53.03        79.07        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  POLRMT MUTATED POLRMT WILD-TYPE 
           61.05             0.00 
  POLRMT MUTATED POLRMT WILD-TYPE 
           90.08           153.63 
  POLRMT MUTATED POLRMT WILD-TYPE 
          67.050           39.465 
[1] "61.0 - 90.1 (67.1)" "0.0 - 153.6 (39.5)"
[1] "hr="   "8e+07"
D106V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  POLRMT MUTATED         1        3         0        0
  POLRMT WILD-TYPE       5       26        14       11
D106V3, multiclass
           clus
vv          POLRMT MUTATED POLRMT WILD-TYPE
  STAGE I                1                5
  STAGE II               3               26
  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
  POLRMT MUTATED    1  3  0  0
  POLRMT WILD-TYPE  5 30  7 14
D106V4, multiclass
    clus
vv   POLRMT MUTATED POLRMT WILD-TYPE
  T1              1                5
  T2              3               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"
D106V5, binary
                  cls
clus                0  1
  POLRMT MUTATED    4  0
  POLRMT WILD-TYPE 50  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      4    0
  POLRMT WILD-TYPE   50    6
   clus
vv  POLRMT MUTATED POLRMT WILD-TYPE
  0              4               50
  1              0                6
[1] 2 2
[1] FALSE
D106V6, binary
                  cls
clus                0  1
  POLRMT MUTATED    2  2
  POLRMT WILD-TYPE 38 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      2    2
  POLRMT WILD-TYPE   38   20
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  FEMALE              2               38
  MALE                2               20
[1] 2 2
[1] FALSE
D106V7, binary
                  cls
clus                0  1
  POLRMT MUTATED    4  0
  POLRMT WILD-TYPE 42 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      4    0
  POLRMT WILD-TYPE   42   14
     clus
vv    POLRMT MUTATED POLRMT WILD-TYPE
  NO               4               42
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  POLRMT MUTATED                                       0
  POLRMT WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  POLRMT MUTATED                                          1
  POLRMT WILD-TYPE                                        2
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  POLRMT MUTATED                                      3
  POLRMT WILD-TYPE                                   55
D106V8, multiclass
                                          clus
vv                                         POLRMT MUTATED POLRMT WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              1                2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  POLRMT MUTATED    4  0  0  0
  POLRMT WILD-TYPE 40  4  8  4
D106V9, multiclass
    clus
vv   POLRMT MUTATED POLRMT WILD-TYPE
  R0              4               40
  R1              0                4
  R2              0                8
  RX              0                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"
D106V10, continuous
[1] "Remove cluster labels:" "POLRMT MUTATED"        
clus
  POLRMT MUTATED POLRMT WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JX 
"POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5       TCGA-OR-A5KB 
"POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" "POLRMT WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO 
"POLRMT WILD-TYPE" "POLRMT WILD-TYPE" 
D106V11, binary
                  cls
clus                0  1
  POLRMT MUTATED    0  0
  POLRMT WILD-TYPE  7 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      0    0
  POLRMT WILD-TYPE    7   27

Clustering(107) Variable = ADAMTS7 MUTATION ANALYSIS
D107V1, survival
                   sevent
clus2                0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 35 23
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                4                58 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                0                23 
$`ADAMTS7 MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5JT TCGA-OR-A5KU TCGA-OR-A5LK 
       43.30        29.82       153.63        90.08 

$`ADAMTS7 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       13.91        12.00        88.87        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       49.22        67.59        15.25        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        35.57        16.37 
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-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         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        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
            29.82              0.00 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           153.63            152.15 
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
           66.690            41.045 
[1] "29.8 - 153.6 (66.7)" "0.0 - 152.2 (41.0)" 
[1] "hr="     "7.6e+07"
D107V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ADAMTS7 MUTATED         1        3         0        0
  ADAMTS7 WILD-TYPE       5       26        14       11
D107V3, multiclass
           clus
vv          ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  STAGE I                 1                 5
  STAGE II                3                26
  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 30  7 14
D107V4, multiclass
    clus
vv   ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  T1               1                 5
  T2               3                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"
D107V5, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    4  0
  ADAMTS7 WILD-TYPE 50  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      4    0
  ADAMTS7 WILD-TYPE   50    6
   clus
vv  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  0               4                50
  1               0                 6
[1] 2 2
[1] FALSE
D107V6, 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
D107V7, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    3  1
  ADAMTS7 WILD-TYPE 43 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      3    1
  ADAMTS7 WILD-TYPE   43   13
     clus
vv    ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  NO                3                43
  YES               1                13
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ADAMTS7 MUTATED                                       0
  ADAMTS7 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ADAMTS7 MUTATED                                          1
  ADAMTS7 WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ADAMTS7 MUTATED                                      3
  ADAMTS7 WILD-TYPE                                   55
D107V8, multiclass
                                          clus
vv                                         ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  ADAMTS7 MUTATED    4  0  0  0
  ADAMTS7 WILD-TYPE 40  4  8  4
D107V9, multiclass
    clus
vv   ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  R0               4                40
  R1               0                 4
  R2               0                 8
  RX               0                 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"
D107V10, continuous
[1] "Remove cluster labels:" "ADAMTS7 MUTATED"       
clus
  ADAMTS7 MUTATED ADAMTS7 WILD-TYPE 
                2                18 
       TCGA-OR-A5KP        TCGA-OR-A5J2        TCGA-OR-A5J3        TCGA-OR-A5J4 
"ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" 
       TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JV        TCGA-OR-A5JX 
"ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9        TCGA-OR-A5LL 
"ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP 
"ADAMTS7 WILD-TYPE" "ADAMTS7 WILD-TYPE" 
D107V11, 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(108) Variable = BTNL9 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2              0  1
  BTNL9 MUTATED    3  1
  BTNL9 WILD-TYPE 36 22
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              4              58 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              1              22 
$`BTNL9 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JA TCGA-OR-A5KB TCGA-OR-A5KU 
       42.51        30.31        24.36       153.63 

$`BTNL9 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       13.91        12.00        88.87        16.11        19.04        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       24.62        11.31        46.49        83.80        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  BTNL9 MUTATED BTNL9 WILD-TYPE 
          24.36            0.00 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
         153.63          152.15 
  BTNL9 MUTATED BTNL9 WILD-TYPE 
         36.410          43.925 
[1] "24.4 - 153.6 (36.4)" "0.0 - 152.2 (43.9)" 
[1] "hr=" "1.5"
D108V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  BTNL9 MUTATED         0        2         0        1
  BTNL9 WILD-TYPE       6       27        14       10
D108V3, multiclass
           clus
vv          BTNL9 MUTATED BTNL9 WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  BTNL9 MUTATED    0  2  0  1
  BTNL9 WILD-TYPE  6 31  7 13
D108V4, multiclass
    clus
vv   BTNL9 MUTATED BTNL9 WILD-TYPE
  T1             0               6
  T2             2              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"
D108V5, binary
                 cls
clus               0  1
  BTNL9 MUTATED    3  0
  BTNL9 WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      3    0
  BTNL9 WILD-TYPE   51    6
   clus
vv  BTNL9 MUTATED BTNL9 WILD-TYPE
  0             3              51
  1             0               6
[1] 2 2
[1] FALSE
D108V6, binary
                 cls
clus               0  1
  BTNL9 MUTATED    3  1
  BTNL9 WILD-TYPE 37 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      3    1
  BTNL9 WILD-TYPE   37   21
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  FEMALE             3              37
  MALE               1              21
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus               0  1
  BTNL9 MUTATED    3  1
  BTNL9 WILD-TYPE 43 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      3    1
  BTNL9 WILD-TYPE   43   13
     clus
vv    BTNL9 MUTATED BTNL9 WILD-TYPE
  NO              3              43
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  BTNL9 MUTATED                                       0
  BTNL9 WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  BTNL9 MUTATED                                          0
  BTNL9 WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  BTNL9 MUTATED                                      4
  BTNL9 WILD-TYPE                                   54
D108V8, multiclass
                                          clus
vv                                         BTNL9 MUTATED BTNL9 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  BTNL9 MUTATED    2  1  0  0
  BTNL9 WILD-TYPE 42  3  8  4
D108V9, multiclass
    clus
vv   BTNL9 MUTATED BTNL9 WILD-TYPE
  R0             2              42
  R1             1               3
  R2             0               8
  RX             0               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"
D108V10, continuous
[1] "Remove cluster labels:" "BTNL9 MUTATED"         
clus
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              2              18 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9      TCGA-OR-A5LL 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LO      TCGA-OR-A5LP 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
D108V11, binary
                 cls
clus               0  1
  BTNL9 MUTATED    0  2
  BTNL9 WILD-TYPE  7 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      0    2
  BTNL9 WILD-TYPE    7   25
                        clus
vv                       BTNL9 MUTATED BTNL9 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             2              25
[1] 2 2
[1] FALSE

Clustering(109) Variable = NF1 MUTATION ANALYSIS
D109V1, survival
               sevent
clus2            0  1
  NF1 MUTATED    4  3
  NF1 WILD-TYPE 35 20
  NF1 MUTATED NF1 WILD-TYPE 
            7            55 
  NF1 MUTATED NF1 WILD-TYPE 
            3            20 
$`NF1 MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5KZ 
       42.51        19.04        18.12        15.25        72.39         4.11 
TCGA-OR-A5LA 
       23.64 

$`NF1 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       13.91        12.00        88.87        16.11        30.31        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       99.88        66.25        69.37        76.64        49.22        67.59 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26       121.25        29.82        66.51        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68        35.57        16.37        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64         5.23        39.35        36.33        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04         6.81         0.00        24.85 
TCGA-PK-A5H8 
      119.11 

  NF1 MUTATED NF1 WILD-TYPE 
         4.11          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
        72.39        153.63 
  NF1 MUTATED NF1 WILD-TYPE 
        19.04         44.84 
[1] "4.1 - 72.4 (19.0)"  "0.0 - 153.6 (44.8)"
[1] "hr=" "1.9"
D109V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF1 MUTATED         0        4         1        1
  NF1 WILD-TYPE       6       25        13       10
D109V3, multiclass
           clus
vv          NF1 MUTATED NF1 WILD-TYPE
  STAGE I             0             6
  STAGE II            4            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
  NF1 MUTATED    0  4  1  1
  NF1 WILD-TYPE  6 29  6 13
D109V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           0             6
  T2           4            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"
D109V5, binary
               cls
clus             0  1
  NF1 MUTATED    6  0
  NF1 WILD-TYPE 48  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6    0
  NF1 WILD-TYPE   48    6
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0           6            48
  1           0             6
[1] 2 2
[1] FALSE
D109V6, 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
D109V7, binary
               cls
clus             0  1
  NF1 MUTATED    3  3
  NF1 WILD-TYPE 43 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      3    3
  NF1 WILD-TYPE   43   11
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            3            43
  YES           3            11
[1] 2 2
[1] FALSE
               vv
clus            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  NF1 MUTATED                                       0
  NF1 WILD-TYPE                                     1
               vv
clus            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  NF1 MUTATED                                          0
  NF1 WILD-TYPE                                        3
               vv
clus            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  NF1 MUTATED                                      7
  NF1 WILD-TYPE                                   51
D109V8, multiclass
                                          clus
vv                                         NF1 MUTATED NF1 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE              0             1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE           0             3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE               7            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            R0 R1 R2 RX
  NF1 MUTATED    4  1  0  1
  NF1 WILD-TYPE 40  3  8  3
D109V9, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0           4            40
  R1           1             3
  R2           0             8
  RX           1             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V10, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            19 
   TCGA-OR-A5KP    TCGA-OR-A5J2    TCGA-OR-A5J3    TCGA-OR-A5J4    TCGA-OR-A5J7 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-OR-A5JT    TCGA-OR-A5JV    TCGA-OR-A5JX    TCGA-OR-A5JY    TCGA-OR-A5K2 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-OR-A5K5    TCGA-OR-A5KB    TCGA-OR-A5KU    TCGA-OR-A5KV    TCGA-OR-A5KW 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-OR-A5L9    TCGA-OR-A5LL    TCGA-OR-A5LO    TCGA-OR-A5LP 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
D109V11, 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(110) Variable = ZNF814 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2               0  1
  ZNF814 MUTATED    1  2
  ZNF814 WILD-TYPE 38 21
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               59 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               21 
$`ZNF814 MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JR TCGA-P6-A5OH 
       30.31       121.25         0.00 

$`ZNF814 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        15.25        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        35.57        16.37 
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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
       61.05        28.04         6.81        24.85       119.11 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            0.00             4.11 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          121.25           153.63 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           30.31            43.30 
[1] "0.0 - 121.2 (30.3)" "4.1 - 153.6 (43.3)"
[1] "hr=" "2.4"
D110V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         1        0         0        2
  ZNF814 WILD-TYPE       5       29        14        9
D110V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                1                5
  STAGE II               0               29
  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 33  7 12
D110V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              1                5
  T2              0               33
  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"
D110V5, binary
                  cls
clus                0  1
  ZNF814 MUTATED    3  0
  ZNF814 WILD-TYPE 51  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3    0
  ZNF814 WILD-TYPE   51    6
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              3               51
  1              0                6
[1] 2 2
[1] FALSE
D110V6, 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
D110V7, binary
                  cls
clus                0  1
  ZNF814 MUTATED    3  0
  ZNF814 WILD-TYPE 43 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3    0
  ZNF814 WILD-TYPE   43   14
     clus
vv    ZNF814 MUTATED ZNF814 WILD-TYPE
  NO               3               43
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  ZNF814 MUTATED                                       0
  ZNF814 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  ZNF814 MUTATED                                          0
  ZNF814 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  ZNF814 MUTATED                                      3
  ZNF814 WILD-TYPE                                   55
D110V8, multiclass
                                          clus
vv                                         ZNF814 MUTATED ZNF814 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  ZNF814 MUTATED    1  1  1  0
  ZNF814 WILD-TYPE 43  3  7  4
D110V9, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  R0              1               43
  R1              1                3
  R2              1                7
  RX              0                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"
D110V10, continuous
D110V11, 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(111) Variable = RNF135 MUTATION ANALYSIS
D111V1, survival
                  sevent
clus2               0  1
  RNF135 MUTATED    3  0
  RNF135 WILD-TYPE 36 23
  RNF135 MUTATED RNF135 WILD-TYPE 
               3               59 
  RNF135 MUTATED RNF135 WILD-TYPE 
               0               23 
$`RNF135 MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5KS TCGA-OR-A5L9 
       88.87        83.80        28.64 

$`RNF135 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        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        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       16.37        24.62        11.31        24.36        46.49        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        68.25        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LA TCGA-OR-A5LC 
       60.89       152.15        31.79        28.31        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  RNF135 MUTATED RNF135 WILD-TYPE 
           28.64             0.00 
  RNF135 MUTATED RNF135 WILD-TYPE 
           88.87           153.63 
  RNF135 MUTATED RNF135 WILD-TYPE 
           83.80            42.51 
[1] "28.6 - 88.9 (83.8)" "0.0 - 153.6 (42.5)"
[1] "hr="     "7.4e+07"
D111V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF135 MUTATED         0        3         0        0
  RNF135 WILD-TYPE       6       26        14       11
D111V3, multiclass
           clus
vv          RNF135 MUTATED RNF135 WILD-TYPE
  STAGE I                0                6
  STAGE II               3               26
  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 30  7 14
D111V4, multiclass
    clus
vv   RNF135 MUTATED RNF135 WILD-TYPE
  T1              0                6
  T2              3               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"
D111V5, binary
                  cls
clus                0  1
  RNF135 MUTATED    3  0
  RNF135 WILD-TYPE 51  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      3    0
  RNF135 WILD-TYPE   51    6
   clus
vv  RNF135 MUTATED RNF135 WILD-TYPE
  0              3               51
  1              0                6
[1] 2 2
[1] FALSE
D111V6, 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
D111V7, binary
                  cls
clus                0  1
  RNF135 MUTATED    3  0
  RNF135 WILD-TYPE 43 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      3    0
  RNF135 WILD-TYPE   43   14
     clus
vv    RNF135 MUTATED RNF135 WILD-TYPE
  NO               3               43
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  RNF135 MUTATED                                       0
  RNF135 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  RNF135 MUTATED                                          0
  RNF135 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  RNF135 MUTATED                                      3
  RNF135 WILD-TYPE                                   55
D111V8, multiclass
                                          clus
vv                                         RNF135 MUTATED RNF135 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  RNF135 MUTATED    3  0  0  0
  RNF135 WILD-TYPE 41  4  8  4
D111V9, multiclass
    clus
vv   RNF135 MUTATED RNF135 WILD-TYPE
  R0              3               41
  R1              0                4
  R2              0                8
  RX              0                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"
D111V10, continuous
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               1               19 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KB       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
D111V11, 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(112) Variable = CSGALNACT2 MUTATION ANALYSIS
D112V1, survival
                      sevent
clus2                   0  1
  CSGALNACT2 MUTATED    2  1
  CSGALNACT2 WILD-TYPE 37 22
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                   59 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   22 
$`CSGALNACT2 MUTATED`
TCGA-OR-A5LC TCGA-OR-A5LP TCGA-OR-A5LR 
        5.23        61.05        28.04 

$`CSGALNACT2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        49.22        67.59        15.25        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 
       35.57        16.37        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        68.25        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-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       28.64        23.64        39.35        36.33        90.08        53.03 
TCGA-OR-A5LO TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       79.07         6.81         0.00        24.85       119.11 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                5.23                 0.00 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               61.05               153.63 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               28.04                43.30 
[1] "5.2 - 61.0 (28.0)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "1.2"
D112V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         0        2         0        1
  CSGALNACT2 WILD-TYPE       6       27        14       10
D112V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    0                    6
  STAGE II                   2                   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
  CSGALNACT2 MUTATED    0  2  0  1
  CSGALNACT2 WILD-TYPE  6 31  7 13
D112V4, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                  0                    6
  T2                  2                   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"
D112V5, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 51  6
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   51    6
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  3                   51
  1                  0                    6
[1] 2 2
[1] FALSE
D112V6, 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
D112V7, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 43 14
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   43   14
     clus
vv    CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  NO                   3                   43
  YES                  0                   14
[1] 2 2
[1] FALSE
                      vv
clus                   ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CSGALNACT2 MUTATED                                       0
  CSGALNACT2 WILD-TYPE                                     1
                      vv
clus                   ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CSGALNACT2 MUTATED                                          0
  CSGALNACT2 WILD-TYPE                                        3
                      vv
clus                   ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CSGALNACT2 MUTATED                                      3
  CSGALNACT2 WILD-TYPE                                   55
D112V8, multiclass
                                          clus
vv                                         CSGALNACT2 MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                     0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                  0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                      3
                                          clus
vv                                         CSGALNACT2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                       1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                    3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                       55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   R0 R1 R2 RX
  CSGALNACT2 MUTATED    2  0  1  0
  CSGALNACT2 WILD-TYPE 42  4  7  4
D112V9, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  R0                  2                   42
  R1                  0                    4
  R2                  1                    7
  RX                  0                    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"
D112V10, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   19 
          TCGA-OR-A5KP           TCGA-OR-A5J2           TCGA-OR-A5J3 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5J4           TCGA-OR-A5J7           TCGA-OR-A5J8 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5JT           TCGA-OR-A5JV           TCGA-OR-A5JX 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5JY           TCGA-OR-A5K2           TCGA-OR-A5K5 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5KB           TCGA-OR-A5KU           TCGA-OR-A5KV 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5KW           TCGA-OR-A5L9           TCGA-OR-A5LL 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5LO 
"CSGALNACT2 WILD-TYPE" 
D112V11, 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(113) Variable = SPIRE2 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2               0  1
  SPIRE2 MUTATED    2  1
  SPIRE2 WILD-TYPE 37 22
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               3               59 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               1               22 
$`SPIRE2 MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JL TCGA-OR-A5LP 
       16.11        67.59        61.05 

$`SPIRE2 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        88.87        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        15.25        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        35.57        16.37 
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        68.25        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-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
        5.23        39.35        36.33        90.08        53.03        79.07 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           16.11             0.00 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           67.59           153.63 
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
           61.05            42.51 
[1] "16.1 - 67.6 (61.0)" "0.0 - 153.6 (42.5)"
[1] "hr=" "1.3"
D113V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SPIRE2 MUTATED         1        1         1        0
  SPIRE2 WILD-TYPE       5       28        13       11
D113V3, multiclass
           clus
vv          SPIRE2 MUTATED SPIRE2 WILD-TYPE
  STAGE I                1                5
  STAGE II               1               28
  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 32  6 14
D113V4, multiclass
    clus
vv   SPIRE2 MUTATED SPIRE2 WILD-TYPE
  T1              1                5
  T2              1               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"
D113V5, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 51  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   51    6
   clus
vv  SPIRE2 MUTATED SPIRE2 WILD-TYPE
  0              3               51
  1              0                6
[1] 2 2
[1] FALSE
D113V6, 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
D113V7, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    3  0
  SPIRE2 WILD-TYPE 43 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      3    0
  SPIRE2 WILD-TYPE   43   14
     clus
vv    SPIRE2 MUTATED SPIRE2 WILD-TYPE
  NO               3               43
  YES              0               14
[1] 2 2
[1] FALSE
                  vv
clus               ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  SPIRE2 MUTATED                                       0
  SPIRE2 WILD-TYPE                                     1
                  vv
clus               ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  SPIRE2 MUTATED                                          0
  SPIRE2 WILD-TYPE                                        3
                  vv
clus               ADRENOCORTICAL CARCINOMA- USUAL TYPE
  SPIRE2 MUTATED                                      3
  SPIRE2 WILD-TYPE                                   55
D113V8, multiclass
                                          clus
vv                                         SPIRE2 MUTATED SPIRE2 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                 0                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE              0                3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  SPIRE2 MUTATED    2  1  0  0
  SPIRE2 WILD-TYPE 42  3  8  4
D113V9, multiclass
    clus
vv   SPIRE2 MUTATED SPIRE2 WILD-TYPE
  R0              2               42
  R1              1                3
  R2              0                8
  RX              0                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"
D113V10, continuous
[1] "Remove cluster labels:" "SPIRE2 MUTATED"        
clus
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               2               18 
      TCGA-OR-A5KP       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JX 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K5       TCGA-OR-A5KB 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5L9 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
D113V11, 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(114) Variable = CYP4A22 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                0  1
  CYP4A22 MUTATED    1  3
  CYP4A22 WILD-TYPE 38 20
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                4                58 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                3                20 
$`CYP4A22 MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5K8 TCGA-OR-A5K9 
       39.58        55.13        24.62        11.31 

$`CYP4A22 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        42.51        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       12.00        88.87        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        66.25        69.37        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       67.59        15.25        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        35.57        16.37 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        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 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        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        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81         0.00        24.85       119.11 

  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            11.31              0.00 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            55.13            153.63 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
           32.100            43.925 
[1] "11.3 - 55.1 (32.1)" "0.0 - 153.6 (43.9)"
[1] "hr=" "3"  
D114V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CYP4A22 MUTATED         0        2         0        2
  CYP4A22 WILD-TYPE       6       27        14        9
D114V3, multiclass
           clus
vv          CYP4A22 MUTATED CYP4A22 WILD-TYPE
  STAGE I                 0                 6
  STAGE II                2                27
  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
  CYP4A22 MUTATED    0  2  1  1
  CYP4A22 WILD-TYPE  6 31  6 13
D114V4, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  T1               0                 6
  T2               2                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"
D114V5, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    4  0
  CYP4A22 WILD-TYPE 50  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      4    0
  CYP4A22 WILD-TYPE   50    6
   clus
vv  CYP4A22 MUTATED CYP4A22 WILD-TYPE
  0               4                50
  1               0                 6
[1] 2 2
[1] FALSE
D114V6, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    2  2
  CYP4A22 WILD-TYPE 38 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      2    2
  CYP4A22 WILD-TYPE   38   20
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  FEMALE               2                38
  MALE                 2                20
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    3  1
  CYP4A22 WILD-TYPE 43 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      3    1
  CYP4A22 WILD-TYPE   43   13
     clus
vv    CYP4A22 MUTATED CYP4A22 WILD-TYPE
  NO                3                43
  YES               1                13
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  CYP4A22 MUTATED                                       0
  CYP4A22 WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  CYP4A22 MUTATED                                          0
  CYP4A22 WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  CYP4A22 MUTATED                                      4
  CYP4A22 WILD-TYPE                                   54
D114V8, multiclass
                                          clus
vv                                         CYP4A22 MUTATED CYP4A22 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   4                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  CYP4A22 MUTATED    3  0  1  0
  CYP4A22 WILD-TYPE 41  4  7  4
D114V9, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  R0               3                41
  R1               0                 4
  R2               1                 7
  RX               0                 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"
D114V10, continuous
[1] "Remove cluster labels:" "CYP4A22 MUTATED"       
clus
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                1                19 
       TCGA-OR-A5KP        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J7 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5J8        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5L9 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
D114V11, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    1  2
  CYP4A22 WILD-TYPE  6 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      1    2
  CYP4A22 WILD-TYPE    6   25
                        clus
vv                       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(115) Variable = HLA-A MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2              0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 36 23
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              59 
  HLA-A MUTATED HLA-A WILD-TYPE 
              0              23 
$`HLA-A MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5JP TCGA-OR-A5JX 
       88.87        15.25        31.23 

$`HLA-A WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       68.75        13.91        12.00        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        66.25        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        18.15        32.68        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       39.35        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-P6-A5OF TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H8 
       28.04         6.81         0.00        24.85       119.11 

  HLA-A MUTATED HLA-A WILD-TYPE 
          15.25            0.00 
  HLA-A MUTATED HLA-A WILD-TYPE 
          88.87          153.63 
  HLA-A MUTATED HLA-A WILD-TYPE 
          31.23           43.30 
[1] "15.2 - 88.9 (31.2)" "0.0 - 153.6 (43.3)"
[1] "hr="     "2.6e+07"
D115V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-A MUTATED         0        2         1        0
  HLA-A WILD-TYPE       6       27        13       11
D115V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0               6
  STAGE II              2              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
  HLA-A MUTATED    0  2  1  0
  HLA-A WILD-TYPE  6 31  6 14
D115V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0               6
  T2             2              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"
D115V5, binary
                 cls
clus               0  1
  HLA-A MUTATED    3  0
  HLA-A WILD-TYPE 51  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3    0
  HLA-A WILD-TYPE   51    6
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             3              51
  1             0               6
[1] 2 2
[1] FALSE
D115V6, 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
D115V7, binary
                 cls
clus               0  1
  HLA-A MUTATED    2  1
  HLA-A WILD-TYPE 44 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      2    1
  HLA-A WILD-TYPE   44   13
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              2              44
  YES             1              13
[1] 2 2
[1] FALSE
                 vv
clus              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  HLA-A MUTATED                                       0
  HLA-A WILD-TYPE                                     1
                 vv
clus              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  HLA-A MUTATED                                          0
  HLA-A WILD-TYPE                                        3
                 vv
clus              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  HLA-A MUTATED                                      3
  HLA-A WILD-TYPE                                   55
D115V8, multiclass
                                          clus
vv                                         HLA-A MUTATED HLA-A WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                0               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE             0               3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                 3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              R0 R1 R2 RX
  HLA-A MUTATED    3  0  0  0
  HLA-A WILD-TYPE 41  4  8  4
D115V9, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0             3              41
  R1             0               4
  R2             0               8
  RX             0               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"
D115V10, continuous
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              1              19 
     TCGA-OR-A5KP      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JT      TCGA-OR-A5JV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K5      TCGA-OR-A5KB 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5L9 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
D115V11, 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(116) Variable = GLI3 MUTATION ANALYSIS
D116V1, survival
                sevent
clus2             0  1
  GLI3 MUTATED    2  3
  GLI3 WILD-TYPE 37 20
  GLI3 MUTATED GLI3 WILD-TYPE 
             5             57 
  GLI3 MUTATED GLI3 WILD-TYPE 
             3             20 
$`GLI3 MUTATED`
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5LC TCGA-P6-A5OH 
       49.22        67.59        32.68         5.23         0.00 

$`GLI3 WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        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        99.88        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       76.64        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       72.39        31.23        18.15        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        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        68.25        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        28.31        28.64        23.64        39.35 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OF TCGA-PA-A5YG TCGA-PK-A5H8 
        6.81        24.85       119.11 

  GLI3 MUTATED GLI3 WILD-TYPE 
          0.00           4.11 
  GLI3 MUTATED GLI3 WILD-TYPE 
         67.59         153.63 
  GLI3 MUTATED GLI3 WILD-TYPE 
         32.68          43.30 
[1] "0.0 - 67.6 (32.7)"  "4.1 - 153.6 (43.3)"
[1] "hr=" "2.6"
D116V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GLI3 MUTATED         1        0         1        3
  GLI3 WILD-TYPE       5       29        13        8
D116V3, multiclass
           clus
vv          GLI3 MUTATED GLI3 WILD-TYPE
  STAGE I              1              5
  STAGE II             0             29
  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
  GLI3 MUTATED    1  0  0  4
  GLI3 WILD-TYPE  5 33  7 10
D116V4, multiclass
    clus
vv   GLI3 MUTATED GLI3 WILD-TYPE
  T1            1              5
  T2            0             33
  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"
D116V5, binary
                cls
clus              0  1
  GLI3 MUTATED    5  0
  GLI3 WILD-TYPE 49  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      5    0
  GLI3 WILD-TYPE   49    6
   clus
vv  GLI3 MUTATED GLI3 WILD-TYPE
  0            5             49
  1            0              6
[1] 2 2
[1] FALSE
D116V6, binary
                cls
clus              0  1
  GLI3 MUTATED    4  1
  GLI3 WILD-TYPE 36 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      4    1
  GLI3 WILD-TYPE   36   21
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  FEMALE            4             36
  MALE              1             21
[1] 2 2
[1] FALSE
D116V7, binary
                cls
clus              0  1
  GLI3 MUTATED    3  2
  GLI3 WILD-TYPE 43 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      3    2
  GLI3 WILD-TYPE   43   12
     clus
vv    GLI3 MUTATED GLI3 WILD-TYPE
  NO             3             43
  YES            2             12
[1] 2 2
[1] FALSE
                vv
clus             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  GLI3 MUTATED                                       0
  GLI3 WILD-TYPE                                     1
                vv
clus             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  GLI3 MUTATED                                          0
  GLI3 WILD-TYPE                                        3
                vv
clus             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  GLI3 MUTATED                                      5
  GLI3 WILD-TYPE                                   53
D116V8, multiclass
                                          clus
vv                                         GLI3 MUTATED GLI3 WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE               0              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE            0              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  GLI3 MUTATED    2  0  3  0
  GLI3 WILD-TYPE 42  4  5  4
D116V9, multiclass
    clus
vv   GLI3 MUTATED GLI3 WILD-TYPE
  R0            2             42
  R1            0              4
  R2            3              5
  RX            0              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"
D116V10, continuous
[1] "Remove cluster labels:" "GLI3 MUTATED"          
clus
  GLI3 MUTATED GLI3 WILD-TYPE 
             1             19 
    TCGA-OR-A5KP     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" 
    TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JT     TCGA-OR-A5JV 
"GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" 
    TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K5     TCGA-OR-A5KB 
"GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5L9 
"GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"GLI3 WILD-TYPE" "GLI3 WILD-TYPE" "GLI3 WILD-TYPE" 
D116V11, binary
                cls
clus              0  1
  GLI3 MUTATED    0  2
  GLI3 WILD-TYPE  7 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      0    2
  GLI3 WILD-TYPE    7   25
                        clus
vv                       GLI3 MUTATED GLI3 WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            2             25
[1] 2 2
[1] FALSE
