[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/GDAC_mergedClustering/ACC-TP/20124001/ACC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/19862912/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] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 62 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	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"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 62 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = ZFPM1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZFPM1 MUTATED       10      8      3      3
  ZFPM1 WILD-TYPE     11     12      7      6
D1V1, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1            10              11
  CLUS_2             8              12
  CLUS_3             3               7
  CLUS_4             3               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZFPM1 MUTATED        6      4      4      5      2
  ZFPM1 WILD-TYPE      7      4     10      8      5
D1V2, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             6               7
  CLUS_2             4               4
  CLUS_3             4              10
  CLUS_4             5               8
  CLUS_5             2               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V3, binary
                 cls
clus              0 1
  ZFPM1 MUTATED   5 7
  ZFPM1 WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFPM1 MUTATED      5    7
  ZFPM1 WILD-TYPE    8    8
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             5               8
  CLUS_2             7               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZFPM1 MUTATED        2      4      1      1      1      1      1      1
  ZFPM1 WILD-TYPE      3      2      4      2      2      0      2      1
D1V4, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             4               2
  CLUS_3             1               4
  CLUS_4             1               2
  CLUS_5             1               2
  CLUS_6             1               0
  CLUS_7             1               2
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZFPM1 MUTATED        7      1      7      6
  ZFPM1 WILD-TYPE      9      7      7     10
D1V5, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             7               9
  CLUS_2             1               7
  CLUS_3             7               7
  CLUS_4             6              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              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZFPM1 MUTATED        8      6      1      6
  ZFPM1 WILD-TYPE      8     10      3     12
D1V6, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             8               8
  CLUS_2             6              10
  CLUS_3             1               3
  CLUS_4             6              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZFPM1 MUTATED       10      5      6
  ZFPM1 WILD-TYPE     16      6     12
D1V7, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1            10              16
  CLUS_2             5               6
  CLUS_3             6              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZFPM1 MUTATED        5      8      2      5      1
  ZFPM1 WILD-TYPE      8     10      6      9      1
D1V8, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             5               8
  CLUS_2             8              10
  CLUS_3             2               6
  CLUS_4             5               9
  CLUS_5             1               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZFPM1 MUTATED        9      7      5
  ZFPM1 WILD-TYPE     12      7     14
D1V9, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1             9              12
  CLUS_2             7               7
  CLUS_3             5              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZFPM1 MUTATED       12      7      2
  ZFPM1 WILD-TYPE     18      9      6
D1V10, multiclass
        clus
vv       ZFPM1 MUTATED ZFPM1 WILD-TYPE
  CLUS_1            12              18
  CLUS_2             7               9
  CLUS_3             2               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = LACTB MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LACTB MUTATED        6      5      3      5
  LACTB WILD-TYPE     15     15      7      4
D2V1, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             6              15
  CLUS_2             5              15
  CLUS_3             3               7
  CLUS_4             5               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LACTB MUTATED        2      3      5      4      3
  LACTB WILD-TYPE     11      5      9      9      4
D2V2, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             2              11
  CLUS_2             3               5
  CLUS_3             5               9
  CLUS_4             4               9
  CLUS_5             3               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V3, binary
                 cls
clus               0  1
  LACTB MUTATED    3  5
  LACTB WILD-TYPE 10 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    5
  LACTB WILD-TYPE   10   10
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             3              10
  CLUS_2             5              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LACTB MUTATED        2      1      2      0      2      0      0      1
  LACTB WILD-TYPE      3      5      3      3      1      1      3      1
D2V4, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1               5
  CLUS_3             2               3
  CLUS_4             0               3
  CLUS_5             2               1
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LACTB MUTATED        5      2      5      5
  LACTB WILD-TYPE     11      6      9     11
D2V5, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             5              11
  CLUS_2             2               6
  CLUS_3             5               9
  CLUS_4             5              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              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LACTB MUTATED        4      5      3      5
  LACTB WILD-TYPE     12     11      1     13
D2V6, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             4              12
  CLUS_2             5              11
  CLUS_3             3               1
  CLUS_4             5              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LACTB MUTATED        6      5      6
  LACTB WILD-TYPE     20      6     12
D2V7, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             6              20
  CLUS_2             5               6
  CLUS_3             6              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LACTB MUTATED        4      5      4      4      0
  LACTB WILD-TYPE      9     13      4     10      2
D2V8, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             4               9
  CLUS_2             5              13
  CLUS_3             4               4
  CLUS_4             4              10
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LACTB MUTATED        8      2      7
  LACTB WILD-TYPE     13     12     12
D2V9, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             8              13
  CLUS_2             2              12
  CLUS_3             7              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LACTB MUTATED        8      4      5
  LACTB WILD-TYPE     22     12      3
D2V10, multiclass
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  CLUS_1             8              22
  CLUS_2             4              12
  CLUS_3             5               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CCDC102A MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC102A MUTATED        4      8      0      5
  CCDC102A WILD-TYPE     17     12     10      4
D3V1, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                8                 12
  CLUS_3                0                 10
  CLUS_4                5                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC102A MUTATED        3      2      4      4      3
  CCDC102A WILD-TYPE     10      6     10      9      4
D3V2, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                2                  6
  CLUS_3                4                 10
  CLUS_4                4                  9
  CLUS_5                3                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V3, binary
                    cls
clus                  0  1
  CCDC102A MUTATED    4  3
  CCDC102A WILD-TYPE  9 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC102A MUTATED      4    3
  CCDC102A WILD-TYPE    9   12
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CCDC102A MUTATED        1      1      0      1      1      1      1      1
  CCDC102A WILD-TYPE      4      5      5      2      2      0      2      1
D3V4, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  5
  CLUS_3                0                  5
  CLUS_4                1                  2
  CLUS_5                1                  2
  CLUS_6                1                  0
  CLUS_7                1                  2
  CLUS_8                1                  1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC102A MUTATED        4      3      4      5
  CCDC102A WILD-TYPE     12      5     10     11
D3V5, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                3                  5
  CLUS_3                4                 10
  CLUS_4                5                 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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC102A MUTATED        4      4      1      7
  CCDC102A WILD-TYPE     12     12      3     11
D3V6, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                4                 12
  CLUS_3                1                  3
  CLUS_4                7                 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                 CLUS_1 CLUS_2 CLUS_3
  CCDC102A MUTATED        7      2      7
  CCDC102A WILD-TYPE     19      9     11
D3V7, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                7                 19
  CLUS_2                2                  9
  CLUS_3                7                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC102A MUTATED        2      6      4      4      0
  CCDC102A WILD-TYPE     11     12      4     10      2
D3V8, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                6                 12
  CLUS_3                4                  4
  CLUS_4                4                 10
  CLUS_5                0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  CCDC102A MUTATED        7      3      6
  CCDC102A WILD-TYPE     14     11     13
D3V9, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                7                 14
  CLUS_2                3                 11
  CLUS_3                6                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  CCDC102A MUTATED        7      6      3
  CCDC102A WILD-TYPE     23     10      5
D3V10, multiclass
        clus
vv       CCDC102A MUTATED CCDC102A WILD-TYPE
  CLUS_1                7                 23
  CLUS_2                6                 10
  CLUS_3                3                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = ZNF517 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF517 MUTATED        7      5      0      1
  ZNF517 WILD-TYPE     14     15     10      8
D4V1, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              7               14
  CLUS_2              5               15
  CLUS_3              0               10
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF517 MUTATED        3      1      2      2      1
  ZNF517 WILD-TYPE     10      7     12     11      6
D4V2, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              2               11
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V3, binary
                  cls
clus                0  1
  ZNF517 MUTATED    1  1
  ZNF517 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF517 MUTATED      1    1
  ZNF517 WILD-TYPE   12   14
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF517 MUTATED        0      1      0      0      0      0      1      0
  ZNF517 WILD-TYPE      5      5      5      3      3      1      2      2
D4V4, multiclass
[1] "Remove cluster labels:" "ZNF517 MUTATED"        
clus
  ZNF517 MUTATED ZNF517 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU       TCGA-OR-A5KW 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"ZNF517 WILD-TYPE" "ZNF517 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF517 MUTATED        4      1      2      2
  ZNF517 WILD-TYPE     12      7     12     14
D4V5, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              4               12
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF517 MUTATED        3      2      1      3
  ZNF517 WILD-TYPE     13     14      3     15
D4V6, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              2               14
  CLUS_3              1                3
  CLUS_4              3               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF517 MUTATED        3      4      2
  ZNF517 WILD-TYPE     23      7     16
D4V7, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              3               23
  CLUS_2              4                7
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF517 MUTATED        1      3      1      4      0
  ZNF517 WILD-TYPE     12     15      7     10      2
D4V8, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              3               15
  CLUS_3              1                7
  CLUS_4              4               10
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF517 MUTATED        4      3      2
  ZNF517 WILD-TYPE     17     11     17
D4V9, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              3               11
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF517 MUTATED        5      2      2
  ZNF517 WILD-TYPE     25     14      6
D4V10, multiclass
        clus
vv       ZNF517 MUTATED ZNF517 WILD-TYPE
  CLUS_1              5               25
  CLUS_2              2               14
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MAL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAL2 MUTATED        4      5      2      0
  MAL2 WILD-TYPE     17     15      8      9
D5V1, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            4             17
  CLUS_2            5             15
  CLUS_3            2              8
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAL2 MUTATED        3      2      0      2      1
  MAL2 WILD-TYPE     10      6     14     11      6
D5V2, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            3             10
  CLUS_2            2              6
  CLUS_3            0             14
  CLUS_4            2             11
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V3, binary
                cls
clus              0  1
  MAL2 MUTATED    2  2
  MAL2 WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAL2 MUTATED      2    2
  MAL2 WILD-TYPE   11   13
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MAL2 MUTATED        1      1      1      1      0      0      0      0
  MAL2 WILD-TYPE      4      5      4      2      3      1      3      2
D5V4, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1              5
  CLUS_3            1              4
  CLUS_4            1              2
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAL2 MUTATED        3      2      0      3
  MAL2 WILD-TYPE     13      6     14     13
D5V5, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            3             13
  CLUS_2            2              6
  CLUS_3            0             14
  CLUS_4            3             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAL2 MUTATED        4      1      0      3
  MAL2 WILD-TYPE     12     15      4     15
D5V6, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            1             15
  CLUS_3            0              4
  CLUS_4            3             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAL2 MUTATED        2      3      3
  MAL2 WILD-TYPE     24      8     15
D5V7, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            3              8
  CLUS_3            3             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAL2 MUTATED        0      3      1      4      0
  MAL2 WILD-TYPE     13     15      7     10      2
D5V8, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            3             15
  CLUS_3            1              7
  CLUS_4            4             10
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAL2 MUTATED        3      2      3
  MAL2 WILD-TYPE     18     12     16
D5V9, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            3             18
  CLUS_2            2             12
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAL2 MUTATED        4      3      1
  MAL2 WILD-TYPE     26     13      7
D5V10, multiclass
        clus
vv       MAL2 MUTATED MAL2 WILD-TYPE
  CLUS_1            4             26
  CLUS_2            3             13
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = TOR3A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TOR3A MUTATED        6      3      1      1
  TOR3A WILD-TYPE     15     17      9      8
D6V1, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             6              15
  CLUS_2             3              17
  CLUS_3             1               9
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TOR3A MUTATED        0      0      4      6      1
  TOR3A WILD-TYPE     13      8     10      7      6
D6V2, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0               8
  CLUS_3             4              10
  CLUS_4             6               7
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V3, binary
                 cls
clus               0  1
  TOR3A MUTATED    4  1
  TOR3A WILD-TYPE  9 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOR3A MUTATED      4    1
  TOR3A WILD-TYPE    9   14
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             4               9
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TOR3A MUTATED        0      1      2      0      0      1      1      0
  TOR3A WILD-TYPE      5      5      3      3      3      0      2      2
D6V4, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1               5
  CLUS_3             2               3
  CLUS_4             0               3
  CLUS_5             0               3
  CLUS_6             1               0
  CLUS_7             1               2
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TOR3A MUTATED        2      1      4      4
  TOR3A WILD-TYPE     14      7     10     12
D6V5, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1               7
  CLUS_3             4              10
  CLUS_4             4              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TOR3A MUTATED        0      3      3      5
  TOR3A WILD-TYPE     16     13      1     13
D6V6, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             0              16
  CLUS_2             3              13
  CLUS_3             3               1
  CLUS_4             5              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TOR3A MUTATED        5      2      4
  TOR3A WILD-TYPE     21      9     14
D6V7, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             5              21
  CLUS_2             2               9
  CLUS_3             4              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TOR3A MUTATED        2      5      2      2      0
  TOR3A WILD-TYPE     11     13      6     12      2
D6V8, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             2              11
  CLUS_2             5              13
  CLUS_3             2               6
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TOR3A MUTATED        5      2      4
  TOR3A WILD-TYPE     16     12     15
D6V9, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             5              16
  CLUS_2             2              12
  CLUS_3             4              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TOR3A MUTATED        6      4      1
  TOR3A WILD-TYPE     24     12      7
D6V10, multiclass
        clus
vv       TOR3A MUTATED TOR3A WILD-TYPE
  CLUS_1             6              24
  CLUS_2             4              12
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        6      1      3      3
  TP53 WILD-TYPE     15     19      7      6
D7V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             15
  CLUS_2            1             19
  CLUS_3            3              7
  CLUS_4            3              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        2      3      3      3      1
  TP53 WILD-TYPE     11      5     11     10      6
D7V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            3              5
  CLUS_3            3             11
  CLUS_4            3             10
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V3, binary
                cls
clus              0  1
  TP53 MUTATED    2  6
  TP53 WILD-TYPE 11  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    6
  TP53 WILD-TYPE   11    9
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            6              9
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TP53 MUTATED        3      2      0      1      1      0      1      0
  TP53 WILD-TYPE      2      4      5      2      2      1      2      2
D7V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              2
  CLUS_2            2              4
  CLUS_3            0              5
  CLUS_4            1              2
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            1              2
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        4      2      6      0
  TP53 WILD-TYPE     12      6      8     16
D7V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            2              6
  CLUS_3            6              8
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        4      4      2      2
  TP53 WILD-TYPE     12     12      2     16
D7V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            4             12
  CLUS_3            2              2
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        7      5      0
  TP53 WILD-TYPE     19      6     18
D7V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             19
  CLUS_2            5              6
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        4      2      2      4      0
  TP53 WILD-TYPE      9     16      6     10      2
D7V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4              9
  CLUS_2            2             16
  CLUS_3            2              6
  CLUS_4            4             10
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8      3      1
  TP53 WILD-TYPE     13     11     18
D7V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             13
  CLUS_2            3             11
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        9      1      2
  TP53 WILD-TYPE     21     15      6
D7V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             21
  CLUS_2            1             15
  CLUS_3            2              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = CLDN23 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLDN23 MUTATED        2      5      1      2
  CLDN23 WILD-TYPE     19     15      9      7
D8V1, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              5               15
  CLUS_3              1                9
  CLUS_4              2                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLDN23 MUTATED        1      2      1      3      3
  CLDN23 WILD-TYPE     12      6     13     10      4
D8V2, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2                6
  CLUS_3              1               13
  CLUS_4              3               10
  CLUS_5              3                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V3, binary
                  cls
clus                0  1
  CLDN23 MUTATED    1  2
  CLDN23 WILD-TYPE 12 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN23 MUTATED      1    2
  CLDN23 WILD-TYPE   12   13
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CLDN23 MUTATED        1      0      0      0      1      0      0      1
  CLDN23 WILD-TYPE      4      6      5      3      2      1      3      1
D8V4, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              0                6
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLDN23 MUTATED        1      1      1      7
  CLDN23 WILD-TYPE     15      7     13      9
D8V5, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              7                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLDN23 MUTATED        3      1      0      6
  CLDN23 WILD-TYPE     13     15      4     12
D8V6, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              1               15
  CLUS_3              0                4
  CLUS_4              6               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLDN23 MUTATED        2      2      6
  CLDN23 WILD-TYPE     24      9     12
D8V7, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              2               24
  CLUS_2              2                9
  CLUS_3              6               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLDN23 MUTATED        1      4      3      1      1
  CLDN23 WILD-TYPE     12     14      5     13      1
D8V8, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               14
  CLUS_3              3                5
  CLUS_4              1               13
  CLUS_5              1                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLDN23 MUTATED        4      1      5
  CLDN23 WILD-TYPE     17     13     14
D8V9, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              1               13
  CLUS_3              5               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLDN23 MUTATED        4      4      2
  CLDN23 WILD-TYPE     26     12      6
D8V10, multiclass
        clus
vv       CLDN23 MUTATED CLDN23 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              4               12
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = GDF1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GDF1 MUTATED        2      2      0      1
  GDF1 WILD-TYPE     19     18     10      8
D9V1, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            0             10
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GDF1 MUTATED        0      0      3      1      0
  GDF1 WILD-TYPE     13      8     11     12      7
D9V2, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            0              8
  CLUS_3            3             11
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V3, binary
                cls
clus              0  1
  GDF1 MUTATED    1  1
  GDF1 WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF1 MUTATED      1    1
  GDF1 WILD-TYPE   12   14
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GDF1 MUTATED        0      0      0      0      1      0      0      1
  GDF1 WILD-TYPE      5      6      5      3      2      1      3      1
D9V4, multiclass
[1] "Remove cluster labels:" "GDF1 MUTATED"          
clus
  GDF1 MUTATED GDF1 WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JY     TCGA-OR-A5K4 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KW 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"GDF1 WILD-TYPE" "GDF1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GDF1 MUTATED        0      1      2      1
  GDF1 WILD-TYPE     16      7     12     15
D9V5, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GDF1 MUTATED        0      3      0      1
  GDF1 WILD-TYPE     16     13      4     17
D9V6, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3             13
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GDF1 MUTATED        0      2      2
  GDF1 WILD-TYPE     26      9     16
D9V7, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            2              9
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GDF1 MUTATED        0      3      0      1      0
  GDF1 WILD-TYPE     13     15      8     13      2
D9V8, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            3             15
  CLUS_3            0              8
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GDF1 MUTATED        0      2      2
  GDF1 WILD-TYPE     21     12     17
D9V9, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            0             21
  CLUS_2            2             12
  CLUS_3            2             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GDF1 MUTATED        1      3      0
  GDF1 WILD-TYPE     29     13      8
D9V10, multiclass
        clus
vv       GDF1 MUTATED GDF1 WILD-TYPE
  CLUS_1            1             29
  CLUS_2            3             13
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = LZTR1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        5      0      1      0
  LZTR1 WILD-TYPE     16     20      9      9
D10V1, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             5              16
  CLUS_2             0              20
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LZTR1 MUTATED        2      0      1      1      0
  LZTR1 WILD-TYPE     11      8     13     12      7
D10V2, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V3, binary
                 cls
clus               0  1
  LZTR1 MUTATED    0  1
  LZTR1 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      0    1
  LZTR1 WILD-TYPE   13   14
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LZTR1 MUTATED        0      0      0      0      1      0      0      0
  LZTR1 WILD-TYPE      5      6      5      3      2      1      3      2
D10V4, multiclass
[1] "Remove cluster labels:" "LZTR1 MUTATED"         
clus
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR      TCGA-OR-A5JT 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        3      1      0      0
  LZTR1 WILD-TYPE     13      7     14     16
D10V5, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        2      1      1      0
  LZTR1 WILD-TYPE     14     15      3     18
D10V6, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             1               3
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        3      1      0
  LZTR1 WILD-TYPE     23     10     18
D10V7, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              10
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LZTR1 MUTATED        0      0      0      3      1
  LZTR1 WILD-TYPE     13     18      8     11      1
D10V8, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0              18
  CLUS_3             0               8
  CLUS_4             3              11
  CLUS_5             1               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        2      1      1
  LZTR1 WILD-TYPE     19     13     18
D10V9, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              13
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        3      0      1
  LZTR1 WILD-TYPE     27     16      7
D10V10, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = ANKRD43 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANKRD43 MUTATED        6      6      6      1
  ANKRD43 WILD-TYPE     15     14      4      8
D11V1, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               6                15
  CLUS_2               6                14
  CLUS_3               6                 4
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ANKRD43 MUTATED        5      3      5      2      1
  ANKRD43 WILD-TYPE      8      5      9     11      6
D11V2, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               5                 8
  CLUS_2               3                 5
  CLUS_3               5                 9
  CLUS_4               2                11
  CLUS_5               1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V3, binary
                   cls
clus                 0  1
  ANKRD43 MUTATED    3  5
  ANKRD43 WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD43 MUTATED      3    5
  ANKRD43 WILD-TYPE   10   10
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               5                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ANKRD43 MUTATED        2      2      0      1      1      1      1      0
  ANKRD43 WILD-TYPE      3      4      5      2      2      0      2      2
D11V4, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               2                 3
  CLUS_2               2                 4
  CLUS_3               0                 5
  CLUS_4               1                 2
  CLUS_5               1                 2
  CLUS_6               1                 0
  CLUS_7               1                 2
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANKRD43 MUTATED        4      3      6      2
  ANKRD43 WILD-TYPE     12      5      8     14
D11V5, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               4                12
  CLUS_2               3                 5
  CLUS_3               6                 8
  CLUS_4               2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANKRD43 MUTATED        5      7      0      3
  ANKRD43 WILD-TYPE     11      9      4     15
D11V6, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               5                11
  CLUS_2               7                 9
  CLUS_3               0                 4
  CLUS_4               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ANKRD43 MUTATED        9      4      3
  ANKRD43 WILD-TYPE     17      7     15
D11V7, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               9                17
  CLUS_2               4                 7
  CLUS_3               3                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ANKRD43 MUTATED        6      4      0      6      0
  ANKRD43 WILD-TYPE      7     14      8      8      2
D11V8, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               6                 7
  CLUS_2               4                14
  CLUS_3               0                 8
  CLUS_4               6                 8
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ANKRD43 MUTATED        7      5      4
  ANKRD43 WILD-TYPE     14      9     15
D11V9, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1               7                14
  CLUS_2               5                 9
  CLUS_3               4                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ANKRD43 MUTATED       11      3      2
  ANKRD43 WILD-TYPE     19     13      6
D11V10, multiclass
        clus
vv       ANKRD43 MUTATED ANKRD43 WILD-TYPE
  CLUS_1              11                19
  CLUS_2               3                13
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = KCNK17 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KCNK17 MUTATED        3      1      2      3
  KCNK17 WILD-TYPE     18     19      8      6
D12V1, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              1               19
  CLUS_3              2                8
  CLUS_4              3                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KCNK17 MUTATED        0      2      5      1      0
  KCNK17 WILD-TYPE     13      6      9     12      7
D12V2, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2                6
  CLUS_3              5                9
  CLUS_4              1               12
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V3, binary
                  cls
clus                0  1
  KCNK17 MUTATED    0  6
  KCNK17 WILD-TYPE 13  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK17 MUTATED      0    6
  KCNK17 WILD-TYPE   13    9
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              6                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KCNK17 MUTATED        1      3      0      0      1      0      0      1
  KCNK17 WILD-TYPE      4      3      5      3      2      1      3      1
D12V4, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              3                3
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KCNK17 MUTATED        1      1      5      1
  KCNK17 WILD-TYPE     15      7      9     15
D12V5, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1                7
  CLUS_3              5                9
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KCNK17 MUTATED        0      6      1      1
  KCNK17 WILD-TYPE     16     10      3     17
D12V6, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              6               10
  CLUS_3              1                3
  CLUS_4              1               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  KCNK17 MUTATED        4      2      2
  KCNK17 WILD-TYPE     22      9     16
D12V7, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              2                9
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KCNK17 MUTATED        3      1      2      2      0
  KCNK17 WILD-TYPE     10     17      6     12      2
D12V8, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              1               17
  CLUS_3              2                6
  CLUS_4              2               12
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  KCNK17 MUTATED        4      1      3
  KCNK17 WILD-TYPE     17     13     16
D12V9, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              1               13
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  KCNK17 MUTATED        5      1      2
  KCNK17 WILD-TYPE     25     15      6
D12V10, multiclass
        clus
vv       KCNK17 MUTATED KCNK17 WILD-TYPE
  CLUS_1              5               25
  CLUS_2              1               15
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = RINL MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RINL MUTATED        5      2      0      1
  RINL WILD-TYPE     16     18     10      8
D13V1, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            5             16
  CLUS_2            2             18
  CLUS_3            0             10
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RINL MUTATED        3      1      1      2      0
  RINL WILD-TYPE     10      7     13     11      7
D13V2, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            3             10
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            2             11
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V3, binary
                cls
clus              0  1
  RINL MUTATED    2  2
  RINL WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  RINL MUTATED      2    2
  RINL WILD-TYPE   11   13
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RINL MUTATED        1      0      1      0      1      0      0      1
  RINL WILD-TYPE      4      6      4      3      2      1      3      1
D13V4, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            1              4
  CLUS_2            0              6
  CLUS_3            1              4
  CLUS_4            0              3
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            1              1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RINL MUTATED        4      1      1      1
  RINL WILD-TYPE     12      7     13     15
D13V5, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            4             12
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RINL MUTATED        4      1      1      1
  RINL WILD-TYPE     12     15      3     17
D13V6, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            4             12
  CLUS_2            1             15
  CLUS_3            1              3
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RINL MUTATED        3      2      2
  RINL WILD-TYPE     23      9     16
D13V7, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            3             23
  CLUS_2            2              9
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RINL MUTATED        0      3      0      4      0
  RINL WILD-TYPE     13     15      8     10      2
D13V8, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            0             13
  CLUS_2            3             15
  CLUS_3            0              8
  CLUS_4            4             10
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RINL MUTATED        1      3      3
  RINL WILD-TYPE     20     11     16
D13V9, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            1             20
  CLUS_2            3             11
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RINL MUTATED        3      3      1
  RINL WILD-TYPE     27     13      7
D13V10, multiclass
        clus
vv       RINL MUTATED RINL WILD-TYPE
  CLUS_1            3             27
  CLUS_2            3             13
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = ZAR1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZAR1 MUTATED        4      3      1      3
  ZAR1 WILD-TYPE     17     17      9      6
D14V1, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            4             17
  CLUS_2            3             17
  CLUS_3            1              9
  CLUS_4            3              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZAR1 MUTATED        3      1      1      2      2
  ZAR1 WILD-TYPE     10      7     13     11      5
D14V2, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            3             10
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            2             11
  CLUS_5            2              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V3, binary
                cls
clus              0  1
  ZAR1 MUTATED    2  2
  ZAR1 WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZAR1 MUTATED      2    2
  ZAR1 WILD-TYPE   11   13
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZAR1 MUTATED        0      2      1      0      1      0      0      0
  ZAR1 WILD-TYPE      5      4      4      3      2      1      3      2
D14V4, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            0              5
  CLUS_2            2              4
  CLUS_3            1              4
  CLUS_4            0              3
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZAR1 MUTATED        3      0      2      4
  ZAR1 WILD-TYPE     13      8     12     12
D14V5, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            3             13
  CLUS_2            0              8
  CLUS_3            2             12
  CLUS_4            4             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZAR1 MUTATED        3      2      0      4
  ZAR1 WILD-TYPE     13     14      4     14
D14V6, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            3             13
  CLUS_2            2             14
  CLUS_3            0              4
  CLUS_4            4             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ZAR1 MUTATED        4      1      4
  ZAR1 WILD-TYPE     22     10     14
D14V7, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            4             22
  CLUS_2            1             10
  CLUS_3            4             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZAR1 MUTATED        2      4      1      2      0
  ZAR1 WILD-TYPE     11     14      7     12      2
D14V8, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            4             14
  CLUS_3            1              7
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ZAR1 MUTATED        4      2      3
  ZAR1 WILD-TYPE     17     12     16
D14V9, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            4             17
  CLUS_2            2             12
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ZAR1 MUTATED        4      4      1
  ZAR1 WILD-TYPE     26     12      7
D14V10, multiclass
        clus
vv       ZAR1 MUTATED ZAR1 WILD-TYPE
  CLUS_1            4             26
  CLUS_2            4             12
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        5      2      1      0
  CTNNB1 WILD-TYPE     16     18      9      9
D15V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              5               16
  CLUS_2              2               18
  CLUS_3              1                9
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        3      3      1      0      0
  CTNNB1 WILD-TYPE     10      5     13     13      7
D15V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              3                5
  CLUS_3              1               13
  CLUS_4              0               13
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V3, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    3  2
  CTNNB1 WILD-TYPE 10 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      3    2
  CTNNB1 WILD-TYPE   10   13
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CTNNB1 MUTATED        2      1      0      0      2      0      0      0
  CTNNB1 WILD-TYPE      3      5      5      3      1      1      3      2
D15V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2                3
  CLUS_2              1                5
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              2                1
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        4      3      0      0
  CTNNB1 WILD-TYPE     12      5     14     16
D15V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               12
  CLUS_2              3                5
  CLUS_3              0               14
  CLUS_4              0               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        6      1      0      0
  CTNNB1 WILD-TYPE     10     15      4     18
D15V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              6               10
  CLUS_2              1               15
  CLUS_3              0                4
  CLUS_4              0               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        1      6      0
  CTNNB1 WILD-TYPE     25      5     18
D15V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              6                5
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        0      3      0      4      0
  CTNNB1 WILD-TYPE     13     15      8     10      2
D15V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              3               15
  CLUS_3              0                8
  CLUS_4              4               10
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      4      0
  CTNNB1 WILD-TYPE     18     10     19
D15V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              4               10
  CLUS_3              0               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        4      3      0
  CTNNB1 WILD-TYPE     26     13      8
D15V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              3               13
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = APOE MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOE MUTATED        3      2      1      1
  APOE WILD-TYPE     18     18      9      8
D16V1, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            3             18
  CLUS_2            2             18
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APOE MUTATED        1      0      3      2      0
  APOE WILD-TYPE     12      8     11     11      7
D16V2, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0              8
  CLUS_3            3             11
  CLUS_4            2             11
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V3, binary
                cls
clus              0  1
  APOE MUTATED    1  2
  APOE WILD-TYPE 12 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOE MUTATED      1    2
  APOE WILD-TYPE   12   13
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  APOE MUTATED        0      1      0      0      0      0      1      1
  APOE WILD-TYPE      5      5      5      3      3      1      2      1
D16V4, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            0              5
  CLUS_2            1              5
  CLUS_3            0              5
  CLUS_4            0              3
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            1              2
  CLUS_8            1              1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOE MUTATED        2      0      4      0
  APOE WILD-TYPE     14      8     10     16
D16V5, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0              8
  CLUS_3            4             10
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOE MUTATED        1      3      1      1
  APOE WILD-TYPE     15     13      3     17
D16V6, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            1             15
  CLUS_2            3             13
  CLUS_3            1              3
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOE MUTATED        2      3      1
  APOE WILD-TYPE     24      8     17
D16V7, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            2             24
  CLUS_2            3              8
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APOE MUTATED        1      3      0      2      0
  APOE WILD-TYPE     12     15      8     12      2
D16V8, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            1             12
  CLUS_2            3             15
  CLUS_3            0              8
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOE MUTATED        2      3      1
  APOE WILD-TYPE     19     11     18
D16V9, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            2             19
  CLUS_2            3             11
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOE MUTATED        3      2      1
  APOE WILD-TYPE     27     14      7
D16V10, multiclass
        clus
vv       APOE MUTATED APOE WILD-TYPE
  CLUS_1            3             27
  CLUS_2            2             14
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = GPRIN2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPRIN2 MUTATED        2      3      2      1
  GPRIN2 WILD-TYPE     19     17      8      8
D17V1, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              3               17
  CLUS_3              2                8
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GPRIN2 MUTATED        1      0      4      1      1
  GPRIN2 WILD-TYPE     12      8     10     12      6
D17V2, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0                8
  CLUS_3              4               10
  CLUS_4              1               12
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V3, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    2  2
  GPRIN2 WILD-TYPE 11 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      2    2
  GPRIN2 WILD-TYPE   11   13
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GPRIN2 MUTATED        0      1      1      0      1      0      0      1
  GPRIN2 WILD-TYPE      5      5      4      3      2      1      3      1
D17V4, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              1                5
  CLUS_3              1                4
  CLUS_4              0                3
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPRIN2 MUTATED        1      1      3      2
  GPRIN2 WILD-TYPE     15      7     11     14
D17V5, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1                7
  CLUS_3              3               11
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPRIN2 MUTATED        1      4      0      2
  GPRIN2 WILD-TYPE     15     12      4     16
D17V6, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              4               12
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPRIN2 MUTATED        2      2      3
  GPRIN2 WILD-TYPE     24      9     15
D17V7, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              2               24
  CLUS_2              2                9
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GPRIN2 MUTATED        1      4      1      1      0
  GPRIN2 WILD-TYPE     12     14      7     13      2
D17V8, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               14
  CLUS_3              1                7
  CLUS_4              1               13
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPRIN2 MUTATED        2      3      2
  GPRIN2 WILD-TYPE     19     11     17
D17V9, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              3               11
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPRIN2 MUTATED        2      4      1
  GPRIN2 WILD-TYPE     28     12      7
D17V10, multiclass
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  CLUS_1              2               28
  CLUS_2              4               12
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = ASPDH MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASPDH MUTATED        3      2      3      0
  ASPDH WILD-TYPE     18     18      7      9
D18V1, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             3              18
  CLUS_2             2              18
  CLUS_3             3               7
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ASPDH MUTATED        3      1      3      1      0
  ASPDH WILD-TYPE     10      7     11     12      7
D18V2, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             3              10
  CLUS_2             1               7
  CLUS_3             3              11
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V3, binary
                 cls
clus               0  1
  ASPDH MUTATED    2  3
  ASPDH WILD-TYPE 11 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASPDH MUTATED      2    3
  ASPDH WILD-TYPE   11   12
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             2              11
  CLUS_2             3              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ASPDH MUTATED        0      3      0      1      0      0      1      0
  ASPDH WILD-TYPE      5      3      5      2      3      1      2      2
D18V4, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             0               5
  CLUS_2             3               3
  CLUS_3             0               5
  CLUS_4             1               2
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             1               2
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASPDH MUTATED        3      0      5      0
  ASPDH WILD-TYPE     13      8      9     16
D18V5, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             3              13
  CLUS_2             0               8
  CLUS_3             5               9
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASPDH MUTATED        3      4      0      1
  ASPDH WILD-TYPE     13     12      4     17
D18V6, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             3              13
  CLUS_2             4              12
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASPDH MUTATED        5      2      1
  ASPDH WILD-TYPE     21      9     17
D18V7, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             5              21
  CLUS_2             2               9
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ASPDH MUTATED        4      0      0      4      0
  ASPDH WILD-TYPE      9     18      8     10      2
D18V8, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             4               9
  CLUS_2             0              18
  CLUS_3             0               8
  CLUS_4             4              10
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASPDH MUTATED        3      4      1
  ASPDH WILD-TYPE     18     10     18
D18V9, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             3              18
  CLUS_2             4              10
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASPDH MUTATED        7      0      1
  ASPDH WILD-TYPE     23     16      7
D18V10, multiclass
        clus
vv       ASPDH MUTATED ASPDH WILD-TYPE
  CLUS_1             7              23
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = ERCC2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERCC2 MUTATED        4      3      2      1
  ERCC2 WILD-TYPE     17     17      8      8
D19V1, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4              17
  CLUS_2             3              17
  CLUS_3             2               8
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERCC2 MUTATED        4      3      2      1      0
  ERCC2 WILD-TYPE      9      5     12     12      7
D19V2, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4               9
  CLUS_2             3               5
  CLUS_3             2              12
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V3, binary
                 cls
clus               0  1
  ERCC2 MUTATED    1  7
  ERCC2 WILD-TYPE 12  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      1    7
  ERCC2 WILD-TYPE   12    8
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             7               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ERCC2 MUTATED        2      3      0      1      0      1      0      1
  ERCC2 WILD-TYPE      3      3      5      2      3      0      3      1
D19V4, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             3               3
  CLUS_3             0               5
  CLUS_4             1               2
  CLUS_5             0               3
  CLUS_6             1               0
  CLUS_7             0               3
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERCC2 MUTATED        4      2      3      1
  ERCC2 WILD-TYPE     12      6     11     15
D19V5, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4              12
  CLUS_2             2               6
  CLUS_3             3              11
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERCC2 MUTATED        5      4      0      1
  ERCC2 WILD-TYPE     11     12      4     17
D19V6, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             5              11
  CLUS_2             4              12
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        6      2      2
  ERCC2 WILD-TYPE     20      9     16
D19V7, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             6              20
  CLUS_2             2               9
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERCC2 MUTATED        3      2      0      5      0
  ERCC2 WILD-TYPE     10     16      8      9      2
D19V8, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             3              10
  CLUS_2             2              16
  CLUS_3             0               8
  CLUS_4             5               9
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        6      2      2
  ERCC2 WILD-TYPE     15     12     17
D19V9, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             6              15
  CLUS_2             2              12
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        8      2      0
  ERCC2 WILD-TYPE     22     14      8
D19V10, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             8              22
  CLUS_2             2              14
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = IDUA MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDUA MUTATED        5      1      1      1
  IDUA WILD-TYPE     16     19      9      8
D20V1, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            5             16
  CLUS_2            1             19
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDUA MUTATED        2      1      3      1      0
  IDUA WILD-TYPE     11      7     11     12      7
D20V2, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1              7
  CLUS_3            3             11
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V3, binary
                cls
clus              0  1
  IDUA MUTATED    2  2
  IDUA WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      2    2
  IDUA WILD-TYPE   11   13
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IDUA MUTATED        1      0      1      1      1      0      0      0
  IDUA WILD-TYPE      4      6      4      2      2      1      3      2
D20V4, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            1              4
  CLUS_2            0              6
  CLUS_3            1              4
  CLUS_4            1              2
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDUA MUTATED        3      2      1      1
  IDUA WILD-TYPE     13      6     13     15
D20V5, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            3             13
  CLUS_2            2              6
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDUA MUTATED        3      3      0      1
  IDUA WILD-TYPE     13     13      4     17
D20V6, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            3             13
  CLUS_2            3             13
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDUA MUTATED        3      3      1
  IDUA WILD-TYPE     23      8     17
D20V7, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            3             23
  CLUS_2            3              8
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDUA MUTATED        1      2      0      4      0
  IDUA WILD-TYPE     12     16      8     10      2
D20V8, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             16
  CLUS_3            0              8
  CLUS_4            4             10
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDUA MUTATED        4      2      1
  IDUA WILD-TYPE     17     12     18
D20V9, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            4             17
  CLUS_2            2             12
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDUA MUTATED        5      2      0
  IDUA WILD-TYPE     25     14      8
D20V10, multiclass
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  CLUS_1            5             25
  CLUS_2            2             14
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = C1ORF106 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C1ORF106 MUTATED        4      2      2      1
  C1ORF106 WILD-TYPE     17     18      8      8
D21V1, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                2                 18
  CLUS_3                2                  8
  CLUS_4                1                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C1ORF106 MUTATED        3      0      2      1      2
  C1ORF106 WILD-TYPE     10      8     12     12      5
D21V2, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                0                  8
  CLUS_3                2                 12
  CLUS_4                1                 12
  CLUS_5                2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V3, binary
                    cls
clus                  0  1
  C1ORF106 MUTATED    3  2
  C1ORF106 WILD-TYPE 10 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF106 MUTATED      3    2
  C1ORF106 WILD-TYPE   10   13
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C1ORF106 MUTATED        1      0      0      2      2      0      0      0
  C1ORF106 WILD-TYPE      4      6      5      1      1      1      3      2
D21V4, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                0                  6
  CLUS_3                0                  5
  CLUS_4                2                  1
  CLUS_5                2                  1
  CLUS_6                0                  1
  CLUS_7                0                  3
  CLUS_8                0                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C1ORF106 MUTATED        4      2      1      1
  C1ORF106 WILD-TYPE     12      6     13     15
D21V5, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                2                  6
  CLUS_3                1                 13
  CLUS_4                1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C1ORF106 MUTATED        3      2      1      2
  C1ORF106 WILD-TYPE     13     14      3     16
D21V6, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 14
  CLUS_3                1                  3
  CLUS_4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C1ORF106 MUTATED        5      2      1
  C1ORF106 WILD-TYPE     21      9     17
D21V7, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                5                 21
  CLUS_2                2                  9
  CLUS_3                1                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C1ORF106 MUTATED        1      2      2      3      0
  C1ORF106 WILD-TYPE     12     16      6     11      2
D21V8, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 16
  CLUS_3                2                  6
  CLUS_4                3                 11
  CLUS_5                0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C1ORF106 MUTATED        5      3      0
  C1ORF106 WILD-TYPE     16     11     19
D21V9, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                3                 11
  CLUS_3                0                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C1ORF106 MUTATED        5      2      1
  C1ORF106 WILD-TYPE     25     14      7
D21V10, multiclass
        clus
vv       C1ORF106 MUTATED C1ORF106 WILD-TYPE
  CLUS_1                5                 25
  CLUS_2                2                 14
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = C10ORF95 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C10ORF95 MUTATED        2      0      2      1
  C10ORF95 WILD-TYPE     19     20      8      8
D22V1, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                0                 20
  CLUS_3                2                  8
  CLUS_4                1                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C10ORF95 MUTATED        1      0      3      0      1
  C10ORF95 WILD-TYPE     12      8     11     13      6
D22V2, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                  8
  CLUS_3                3                 11
  CLUS_4                0                 13
  CLUS_5                1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V3, binary
                    cls
clus                  0  1
  C10ORF95 MUTATED    1  1
  C10ORF95 WILD-TYPE 12 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF95 MUTATED      1    1
  C10ORF95 WILD-TYPE   12   14
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C10ORF95 MUTATED        1      0      0      0      0      0      1      0
  C10ORF95 WILD-TYPE      4      6      5      3      3      1      2      2
D22V4, multiclass
[1] "Remove cluster labels:" "C10ORF95 MUTATED"      
clus
  C10ORF95 MUTATED C10ORF95 WILD-TYPE 
                 2                 26 
        TCGA-OR-A5J2         TCGA-OR-A5J3         TCGA-OR-A5J6 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5JP         TCGA-OR-A5JR         TCGA-OR-A5JT 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JW         TCGA-OR-A5JY 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5K4         TCGA-OR-A5K5         TCGA-OR-A5K8 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5KO         TCGA-OR-A5KU         TCGA-OR-A5KW 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5LD 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5LJ         TCGA-OR-A5LK         TCGA-OR-A5LL 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
        TCGA-OR-A5LP         TCGA-PA-A5YG 
"C10ORF95 WILD-TYPE" "C10ORF95 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C10ORF95 MUTATED        1      2      1      1
  C10ORF95 WILD-TYPE     15      6     13     15
D22V5, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                  6
  CLUS_3                1                 13
  CLUS_4                1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C10ORF95 MUTATED        1      2      0      2
  C10ORF95 WILD-TYPE     15     14      4     16
D22V6, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 14
  CLUS_3                0                  4
  CLUS_4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C10ORF95 MUTATED        4      0      1
  C10ORF95 WILD-TYPE     22     11     17
D22V7, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                4                 22
  CLUS_2                0                 11
  CLUS_3                1                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C10ORF95 MUTATED        1      1      1      1      1
  C10ORF95 WILD-TYPE     12     17      7     13      1
D22V8, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 17
  CLUS_3                1                  7
  CLUS_4                1                 13
  CLUS_5                1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C10ORF95 MUTATED        2      1      1
  C10ORF95 WILD-TYPE     19     13     18
D22V9, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                1                 13
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C10ORF95 MUTATED        3      1      0
  C10ORF95 WILD-TYPE     27     15      8
D22V10, multiclass
        clus
vv       C10ORF95 MUTATED C10ORF95 WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                1                 15
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = RGS9BP MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGS9BP MUTATED        3      3      2      0
  RGS9BP WILD-TYPE     18     17      8      9
D23V1, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              3               18
  CLUS_2              3               17
  CLUS_3              2                8
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RGS9BP MUTATED        3      0      3      1      1
  RGS9BP WILD-TYPE     10      8     11     12      6
D23V2, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              3               10
  CLUS_2              0                8
  CLUS_3              3               11
  CLUS_4              1               12
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V3, binary
                  cls
clus                0  1
  RGS9BP MUTATED    1  2
  RGS9BP WILD-TYPE 12 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      1    2
  RGS9BP WILD-TYPE   12   13
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RGS9BP MUTATED        0      2      0      0      0      1      0      0
  RGS9BP WILD-TYPE      5      4      5      3      3      0      3      2
D23V4, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2                4
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              1                0
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGS9BP MUTATED        2      1      2      2
  RGS9BP WILD-TYPE     14      7     12     14
D23V5, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGS9BP MUTATED        2      3      0      2
  RGS9BP WILD-TYPE     14     13      4     16
D23V6, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              2               14
  CLUS_2              3               13
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RGS9BP MUTATED        2      3      3
  RGS9BP WILD-TYPE     24      8     15
D23V7, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              2               24
  CLUS_2              3                8
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RGS9BP MUTATED        2      2      1      3      0
  RGS9BP WILD-TYPE     11     16      7     11      2
D23V8, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2               16
  CLUS_3              1                7
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RGS9BP MUTATED        2      4      2
  RGS9BP WILD-TYPE     19     10     17
D23V9, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              2               19
  CLUS_2              4               10
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RGS9BP MUTATED        4      2      2
  RGS9BP WILD-TYPE     26     14      6
D23V10, multiclass
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  CLUS_1              4               26
  CLUS_2              2               14
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = THEM4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  THEM4 MUTATED        3      0      1      1
  THEM4 WILD-TYPE     18     20      9      8
D24V1, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0              20
  CLUS_3             1               9
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  THEM4 MUTATED        1      1      1      0      1
  THEM4 WILD-TYPE     12      7     13     13      6
D24V2, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1               7
  CLUS_3             1              13
  CLUS_4             0              13
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V3, binary
                 cls
clus               0  1
  THEM4 MUTATED    0  1
  THEM4 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THEM4 MUTATED      0    1
  THEM4 WILD-TYPE   13   14
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  THEM4 MUTATED        1      0      0      0      0      0      0      0
  THEM4 WILD-TYPE      4      6      5      3      3      1      3      2
D24V4, multiclass
[1] "Remove cluster labels:" "THEM4 MUTATED"         
clus
  THEM4 MUTATED THEM4 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5LD      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"THEM4 WILD-TYPE" "THEM4 WILD-TYPE" "THEM4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  THEM4 MUTATED        1      1      2      0
  THEM4 WILD-TYPE     15      7     12     16
D24V5, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  THEM4 MUTATED        2      1      0      1
  THEM4 WILD-TYPE     14     15      4     17
D24V6, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  THEM4 MUTATED        2      2      0
  THEM4 WILD-TYPE     24      9     18
D24V7, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             2               9
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  THEM4 MUTATED        0      0      1      3      0
  THEM4 WILD-TYPE     13     18      7     11      2
D24V8, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0              18
  CLUS_3             1               7
  CLUS_4             3              11
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  THEM4 MUTATED        3      1      0
  THEM4 WILD-TYPE     18     13     19
D24V9, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              13
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  THEM4 MUTATED        4      0      0
  THEM4 WILD-TYPE     26     16      8
D24V10, multiclass
        clus
vv       THEM4 MUTATED THEM4 WILD-TYPE
  CLUS_1             4              26
  CLUS_2             0              16
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = TSC22D2 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TSC22D2 MUTATED        4      2      1      1
  TSC22D2 WILD-TYPE     17     18      9      8
D25V1, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               4                17
  CLUS_2               2                18
  CLUS_3               1                 9
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TSC22D2 MUTATED        2      0      2      1      2
  TSC22D2 WILD-TYPE     11      8     12     12      5
D25V2, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               0                 8
  CLUS_3               2                12
  CLUS_4               1                12
  CLUS_5               2                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V3, binary
                   cls
clus                 0  1
  TSC22D2 MUTATED    1  2
  TSC22D2 WILD-TYPE 12 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D2 MUTATED      1    2
  TSC22D2 WILD-TYPE   12   13
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TSC22D2 MUTATED        0      1      1      0      1      0      0      0
  TSC22D2 WILD-TYPE      5      5      4      3      2      1      3      2
D25V4, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 5
  CLUS_3               1                 4
  CLUS_4               0                 3
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TSC22D2 MUTATED        3      0      2      2
  TSC22D2 WILD-TYPE     13      8     12     14
D25V5, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                 8
  CLUS_3               2                12
  CLUS_4               2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TSC22D2 MUTATED        2      2      1      2
  TSC22D2 WILD-TYPE     14     14      3     16
D25V6, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                14
  CLUS_3               1                 3
  CLUS_4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TSC22D2 MUTATED        3      2      2
  TSC22D2 WILD-TYPE     23      9     16
D25V7, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               3                23
  CLUS_2               2                 9
  CLUS_3               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TSC22D2 MUTATED        1      2      0      4      0
  TSC22D2 WILD-TYPE     12     16      8     10      2
D25V8, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                 8
  CLUS_4               4                10
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TSC22D2 MUTATED        1      3      3
  TSC22D2 WILD-TYPE     20     11     16
D25V9, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               3                11
  CLUS_3               3                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TSC22D2 MUTATED        4      2      1
  TSC22D2 WILD-TYPE     26     14      7
D25V10, multiclass
        clus
vv       TSC22D2 MUTATED TSC22D2 WILD-TYPE
  CLUS_1               4                26
  CLUS_2               2                14
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = SYT8 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SYT8 MUTATED        1      4      2      1
  SYT8 WILD-TYPE     20     16      8      8
D26V1, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            4             16
  CLUS_3            2              8
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SYT8 MUTATED        0      2      2      1      1
  SYT8 WILD-TYPE     13      6     12     12      6
D26V2, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2              6
  CLUS_3            2             12
  CLUS_4            1             12
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V3, binary
                cls
clus              0  1
  SYT8 MUTATED    1  2
  SYT8 WILD-TYPE 12 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT8 MUTATED      1    2
  SYT8 WILD-TYPE   12   13
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SYT8 MUTATED        1      1      1      0      0      0      0      0
  SYT8 WILD-TYPE      4      5      4      3      3      1      3      2
D26V4, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1              5
  CLUS_3            1              4
  CLUS_4            0              3
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SYT8 MUTATED        0      3      1      2
  SYT8 WILD-TYPE     16      5     13     14
D26V5, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3              5
  CLUS_3            1             13
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SYT8 MUTATED        0      4      0      2
  SYT8 WILD-TYPE     16     12      4     16
D26V6, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            4             12
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SYT8 MUTATED        3      1      2
  SYT8 WILD-TYPE     23     10     16
D26V7, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            3             23
  CLUS_2            1             10
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SYT8 MUTATED        1      3      1      0      1
  SYT8 WILD-TYPE     12     15      7     14      1
D26V8, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            3             15
  CLUS_3            1              7
  CLUS_4            0             14
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SYT8 MUTATED        2      1      3
  SYT8 WILD-TYPE     19     13     16
D26V9, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             13
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SYT8 MUTATED        3      3      0
  SYT8 WILD-TYPE     27     13      8
D26V10, multiclass
        clus
vv       SYT8 MUTATED SYT8 WILD-TYPE
  CLUS_1            3             27
  CLUS_2            3             13
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = PLIN5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLIN5 MUTATED        1      3      0      1
  PLIN5 WILD-TYPE     20     17     10      8
D27V1, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             3              17
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLIN5 MUTATED        1      2      1      1      0
  PLIN5 WILD-TYPE     12      6     13     12      7
D27V2, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2               6
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V3, binary
                 cls
clus               0  1
  PLIN5 MUTATED    1  2
  PLIN5 WILD-TYPE 12 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN5 MUTATED      1    2
  PLIN5 WILD-TYPE   12   13
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PLIN5 MUTATED        0      1      0      0      1      0      0      1
  PLIN5 WILD-TYPE      5      5      5      3      2      1      3      1
D27V4, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1               5
  CLUS_3             0               5
  CLUS_4             0               3
  CLUS_5             1               2
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLIN5 MUTATED        1      1      2      1
  PLIN5 WILD-TYPE     15      7     12     15
D27V5, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLIN5 MUTATED        1      3      0      1
  PLIN5 WILD-TYPE     15     13      4     17
D27V6, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             3              13
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLIN5 MUTATED        1      2      2
  PLIN5 WILD-TYPE     25      9     16
D27V7, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             2               9
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLIN5 MUTATED        1      4      0      0      0
  PLIN5 WILD-TYPE     12     14      8     14      2
D27V8, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             4              14
  CLUS_3             0               8
  CLUS_4             0              14
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLIN5 MUTATED        1      1      3
  PLIN5 WILD-TYPE     20     13     16
D27V9, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              13
  CLUS_3             3              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLIN5 MUTATED        1      4      0
  PLIN5 WILD-TYPE     29     12      8
D27V10, multiclass
        clus
vv       PLIN5 MUTATED PLIN5 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             4              12
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = LRIG1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRIG1 MUTATED        5      4      3      4
  LRIG1 WILD-TYPE     16     16      7      5
D28V1, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             5              16
  CLUS_2             4              16
  CLUS_3             3               7
  CLUS_4             4               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LRIG1 MUTATED        3      2      2      3      1
  LRIG1 WILD-TYPE     10      6     12     10      6
D28V2, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             3              10
  CLUS_2             2               6
  CLUS_3             2              12
  CLUS_4             3              10
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V3, binary
                 cls
clus               0  1
  LRIG1 MUTATED    2  2
  LRIG1 WILD-TYPE 11 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      2    2
  LRIG1 WILD-TYPE   11   13
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LRIG1 MUTATED        1      1      1      1      0      0      0      0
  LRIG1 WILD-TYPE      4      5      4      2      3      1      3      2
D28V4, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1               5
  CLUS_3             1               4
  CLUS_4             1               2
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRIG1 MUTATED        2      2      3      3
  LRIG1 WILD-TYPE     14      6     11     13
D28V5, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2               6
  CLUS_3             3              11
  CLUS_4             3              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRIG1 MUTATED        3      2      0      5
  LRIG1 WILD-TYPE     13     14      4     13
D28V6, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             2              14
  CLUS_3             0               4
  CLUS_4             5              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRIG1 MUTATED        4      4      3
  LRIG1 WILD-TYPE     22      7     15
D28V7, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             4               7
  CLUS_3             3              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LRIG1 MUTATED        1      3      3      4      0
  LRIG1 WILD-TYPE     12     15      5     10      2
D28V8, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             3              15
  CLUS_3             3               5
  CLUS_4             4              10
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRIG1 MUTATED        3      4      4
  LRIG1 WILD-TYPE     18     10     15
D28V9, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             4              10
  CLUS_3             4              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRIG1 MUTATED        7      3      1
  LRIG1 WILD-TYPE     23     13      7
D28V10, multiclass
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  CLUS_1             7              23
  CLUS_2             3              13
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = HHIPL1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HHIPL1 MUTATED        3      1      0      2
  HHIPL1 WILD-TYPE     18     19     10      7
D29V1, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              1               19
  CLUS_3              0               10
  CLUS_4              2                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HHIPL1 MUTATED        2      0      0      2      1
  HHIPL1 WILD-TYPE     11      8     14     11      6
D29V2, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              0                8
  CLUS_3              0               14
  CLUS_4              2               11
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V3, binary
                  cls
clus                0  1
  HHIPL1 MUTATED    0  2
  HHIPL1 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL1 MUTATED      0    2
  HHIPL1 WILD-TYPE   13   13
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  HHIPL1 MUTATED        1      0      0      0      1      0      0      0
  HHIPL1 WILD-TYPE      4      6      5      3      2      1      3      2
D29V4, multiclass
[1] "Remove cluster labels:" "HHIPL1 MUTATED"        
clus
  HHIPL1 MUTATED HHIPL1 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"HHIPL1 WILD-TYPE" "HHIPL1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HHIPL1 MUTATED        3      0      1      1
  HHIPL1 WILD-TYPE     13      8     13     15
D29V5, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              0                8
  CLUS_3              1               13
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HHIPL1 MUTATED        2      1      1      1
  HHIPL1 WILD-TYPE     14     15      3     17
D29V6, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               15
  CLUS_3              1                3
  CLUS_4              1               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  HHIPL1 MUTATED        4      1      0
  HHIPL1 WILD-TYPE     22     10     18
D29V7, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              1               10
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HHIPL1 MUTATED        2      0      1      2      0
  HHIPL1 WILD-TYPE     11     18      7     12      2
D29V8, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              0               18
  CLUS_3              1                7
  CLUS_4              2               12
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  HHIPL1 MUTATED        4      0      1
  HHIPL1 WILD-TYPE     17     14     18
D29V9, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              0               14
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  HHIPL1 MUTATED        4      0      1
  HHIPL1 WILD-TYPE     26     16      7
D29V10, multiclass
        clus
vv       HHIPL1 MUTATED HHIPL1 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              0               16
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = CCDC105 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC105 MUTATED        2      2      1      1
  CCDC105 WILD-TYPE     19     18      9      8
D30V1, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               2                18
  CLUS_3               1                 9
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC105 MUTATED        1      3      0      0      2
  CCDC105 WILD-TYPE     12      5     14     13      5
D30V2, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                 5
  CLUS_3               0                14
  CLUS_4               0                13
  CLUS_5               2                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V3, binary
                   cls
clus                 0  1
  CCDC105 MUTATED    0  3
  CCDC105 WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC105 MUTATED      0    3
  CCDC105 WILD-TYPE   13   12
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CCDC105 MUTATED        1      1      0      0      0      0      0      1
  CCDC105 WILD-TYPE      4      5      5      3      3      1      3      1
D30V4, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 5
  CLUS_3               0                 5
  CLUS_4               0                 3
  CLUS_5               0                 3
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               1                 1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC105 MUTATED        1      1      2      2
  CCDC105 WILD-TYPE     15      7     12     14
D30V5, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                 7
  CLUS_3               2                12
  CLUS_4               2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC105 MUTATED        3      1      0      2
  CCDC105 WILD-TYPE     13     15      4     16
D30V6, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                15
  CLUS_3               0                 4
  CLUS_4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC105 MUTATED        3      1      2
  CCDC105 WILD-TYPE     23     10     16
D30V7, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               3                23
  CLUS_2               1                10
  CLUS_3               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC105 MUTATED        1      0      2      2      1
  CCDC105 WILD-TYPE     12     18      6     12      1
D30V8, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                18
  CLUS_3               2                 6
  CLUS_4               2                12
  CLUS_5               1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC105 MUTATED        4      0      2
  CCDC105 WILD-TYPE     17     14     17
D30V9, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               4                17
  CLUS_2               0                14
  CLUS_3               2                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC105 MUTATED        5      0      1
  CCDC105 WILD-TYPE     25     16      7
D30V10, multiclass
        clus
vv       CCDC105 MUTATED CCDC105 WILD-TYPE
  CLUS_1               5                25
  CLUS_2               0                16
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = C19ORF10 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C19ORF10 MUTATED        3      2      0      1
  C19ORF10 WILD-TYPE     18     18     10      8
D31V1, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                2                 18
  CLUS_3                0                 10
  CLUS_4                1                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C19ORF10 MUTATED        2      1      3      0      0
  C19ORF10 WILD-TYPE     11      7     11     13      7
D31V2, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                1                  7
  CLUS_3                3                 11
  CLUS_4                0                 13
  CLUS_5                0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V3, binary
                    cls
clus                  0  1
  C19ORF10 MUTATED    1  3
  C19ORF10 WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF10 MUTATED      1    3
  C19ORF10 WILD-TYPE   12   12
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C19ORF10 MUTATED        0      2      0      0      1      0      0      1
  C19ORF10 WILD-TYPE      5      4      5      3      2      1      3      1
D31V4, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                2                  4
  CLUS_3                0                  5
  CLUS_4                0                  3
  CLUS_5                1                  2
  CLUS_6                0                  1
  CLUS_7                0                  3
  CLUS_8                1                  1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C19ORF10 MUTATED        2      2      2      0
  C19ORF10 WILD-TYPE     14      6     12     16
D31V5, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                  6
  CLUS_3                2                 12
  CLUS_4                0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C19ORF10 MUTATED        2      4      0      0
  C19ORF10 WILD-TYPE     14     12      4     18
D31V6, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                4                 12
  CLUS_3                0                  4
  CLUS_4                0                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C19ORF10 MUTATED        3      2      1
  C19ORF10 WILD-TYPE     23      9     17
D31V7, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                2                  9
  CLUS_3                1                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C19ORF10 MUTATED        2      2      0      2      0
  C19ORF10 WILD-TYPE     11     16      8     12      2
D31V8, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                2                 16
  CLUS_3                0                  8
  CLUS_4                2                 12
  CLUS_5                0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C19ORF10 MUTATED        3      2      1
  C19ORF10 WILD-TYPE     18     12     18
D31V9, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                2                 12
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C19ORF10 MUTATED        4      2      0
  C19ORF10 WILD-TYPE     26     14      8
D31V10, multiclass
        clus
vv       C19ORF10 MUTATED C19ORF10 WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                2                 14
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = OPRD1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OPRD1 MUTATED        5      4      2      1
  OPRD1 WILD-TYPE     16     16      8      8
D32V1, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             5              16
  CLUS_2             4              16
  CLUS_3             2               8
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OPRD1 MUTATED        3      1      3      1      3
  OPRD1 WILD-TYPE     10      7     11     12      4
D32V2, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             3              10
  CLUS_2             1               7
  CLUS_3             3              11
  CLUS_4             1              12
  CLUS_5             3               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V3, binary
                 cls
clus               0  1
  OPRD1 MUTATED    2  4
  OPRD1 WILD-TYPE 11 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRD1 MUTATED      2    4
  OPRD1 WILD-TYPE   11   11
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             4              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OPRD1 MUTATED        0      2      1      1      2      0      0      0
  OPRD1 WILD-TYPE      5      4      4      2      1      1      3      2
D32V4, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2               4
  CLUS_3             1               4
  CLUS_4             1               2
  CLUS_5             2               1
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OPRD1 MUTATED        4      2      3      2
  OPRD1 WILD-TYPE     12      6     11     14
D32V5, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             4              12
  CLUS_2             2               6
  CLUS_3             3              11
  CLUS_4             2              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OPRD1 MUTATED        3      4      1      3
  OPRD1 WILD-TYPE     13     12      3     15
D32V6, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             4              12
  CLUS_3             1               3
  CLUS_4             3              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OPRD1 MUTATED        5      4      2
  OPRD1 WILD-TYPE     21      7     16
D32V7, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             5              21
  CLUS_2             4               7
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OPRD1 MUTATED        1      5      1      4      0
  OPRD1 WILD-TYPE     12     13      7     10      2
D32V8, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             5              13
  CLUS_3             1               7
  CLUS_4             4              10
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OPRD1 MUTATED        4      3      4
  OPRD1 WILD-TYPE     17     11     15
D32V9, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             4              17
  CLUS_2             3              11
  CLUS_3             4              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OPRD1 MUTATED        5      5      1
  OPRD1 WILD-TYPE     25     11      7
D32V10, multiclass
        clus
vv       OPRD1 MUTATED OPRD1 WILD-TYPE
  CLUS_1             5              25
  CLUS_2             5              11
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = ATXN1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATXN1 MUTATED        2      4      3      1
  ATXN1 WILD-TYPE     19     16      7      8
D33V1, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             4              16
  CLUS_3             3               7
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ATXN1 MUTATED        1      4      2      1      1
  ATXN1 WILD-TYPE     12      4     12     12      6
D33V2, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             4               4
  CLUS_3             2              12
  CLUS_4             1              12
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V3, binary
                 cls
clus               0  1
  ATXN1 MUTATED    1  3
  ATXN1 WILD-TYPE 12 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      1    3
  ATXN1 WILD-TYPE   12   12
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             3              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ATXN1 MUTATED        2      1      1      0      0      0      0      0
  ATXN1 WILD-TYPE      3      5      4      3      3      1      3      2
D33V4, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1               5
  CLUS_3             1               4
  CLUS_4             0               3
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATXN1 MUTATED        2      3      3      1
  ATXN1 WILD-TYPE     14      5     11     15
D33V5, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             3               5
  CLUS_3             3              11
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATXN1 MUTATED        3      4      0      2
  ATXN1 WILD-TYPE     13     12      4     16
D33V6, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             4              12
  CLUS_3             0               4
  CLUS_4             2              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ATXN1 MUTATED        5      3      1
  ATXN1 WILD-TYPE     21      8     17
D33V7, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             5              21
  CLUS_2             3               8
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ATXN1 MUTATED        2      2      2      3      0
  ATXN1 WILD-TYPE     11     16      6     11      2
D33V8, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              16
  CLUS_3             2               6
  CLUS_4             3              11
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ATXN1 MUTATED        6      1      2
  ATXN1 WILD-TYPE     15     13     17
D33V9, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             6              15
  CLUS_2             1              13
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ATXN1 MUTATED        7      2      0
  ATXN1 WILD-TYPE     23     14      8
D33V10, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             7              23
  CLUS_2             2              14
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = AATK MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AATK MUTATED        0      4      1      1
  AATK WILD-TYPE     21     16      9      8
D34V1, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0             21
  CLUS_2            4             16
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AATK MUTATED        0      1      2      0      1
  AATK WILD-TYPE     13      7     12     13      6
D34V2, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            0             13
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V3, binary
                cls
clus              0  1
  AATK MUTATED    1  1
  AATK WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    1
  AATK WILD-TYPE   12   14
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AATK MUTATED        0      1      0      0      1      0      0      0
  AATK WILD-TYPE      5      5      5      3      2      1      3      2
D34V4, multiclass
[1] "Remove cluster labels:" "AATK MUTATED"          
clus
  AATK MUTATED AATK WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"AATK WILD-TYPE" "AATK WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AATK MUTATED        0      1      2      1
  AATK WILD-TYPE     16      7     12     15
D34V5, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AATK MUTATED        0      3      0      1
  AATK WILD-TYPE     16     13      4     17
D34V6, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3             13
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  AATK MUTATED        2      1      1
  AATK WILD-TYPE     24     10     17
D34V7, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            2             24
  CLUS_2            1             10
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AATK MUTATED        2      2      0      0      0
  AATK WILD-TYPE     11     16      8     14      2
D34V8, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             16
  CLUS_3            0              8
  CLUS_4            0             14
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  AATK MUTATED        2      1      1
  AATK WILD-TYPE     19     13     18
D34V9, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             13
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  AATK MUTATED        2      2      0
  AATK WILD-TYPE     28     14      8
D34V10, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            2             28
  CLUS_2            2             14
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = ZNF628 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF628 MUTATED        5      1      0      1
  ZNF628 WILD-TYPE     16     19     10      8
D35V1, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              5               16
  CLUS_2              1               19
  CLUS_3              0               10
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF628 MUTATED        2      1      1      1      0
  ZNF628 WILD-TYPE     11      7     13     12      7
D35V2, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              1               12
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V3, binary
                  cls
clus                0  1
  ZNF628 MUTATED    1  2
  ZNF628 WILD-TYPE 12 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF628 MUTATED      1    2
  ZNF628 WILD-TYPE   12   13
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF628 MUTATED        1      1      0      0      0      0      0      1
  ZNF628 WILD-TYPE      4      5      5      3      3      1      3      1
D35V4, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              1                5
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF628 MUTATED        3      1      1      0
  ZNF628 WILD-TYPE     13      7     13     16
D35V5, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              0               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF628 MUTATED        3      1      1      0
  ZNF628 WILD-TYPE     13     15      3     18
D35V6, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              1               15
  CLUS_3              1                3
  CLUS_4              0               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF628 MUTATED        1      3      1
  ZNF628 WILD-TYPE     25      8     17
D35V7, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              3                8
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF628 MUTATED        0      3      0      2      0
  ZNF628 WILD-TYPE     13     15      8     12      2
D35V8, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              3               15
  CLUS_3              0                8
  CLUS_4              2               12
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF628 MUTATED        1      3      1
  ZNF628 WILD-TYPE     20     11     18
D35V9, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              3               11
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF628 MUTATED        2      2      1
  ZNF628 WILD-TYPE     28     14      7
D35V10, multiclass
        clus
vv       ZNF628 MUTATED ZNF628 WILD-TYPE
  CLUS_1              2               28
  CLUS_2              2               14
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = KRTAP4-5 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-5 MUTATED        2      3      0      0
  KRTAP4-5 WILD-TYPE     19     17     10      9
D36V1, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                3                 17
  CLUS_3                0                 10
  CLUS_4                0                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRTAP4-5 MUTATED        1      2      0      1      0
  KRTAP4-5 WILD-TYPE     12      6     14     12      7
D36V2, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                  6
  CLUS_3                0                 14
  CLUS_4                1                 12
  CLUS_5                0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V3, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    0  2
  KRTAP4-5 WILD-TYPE 13 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      0    2
  KRTAP4-5 WILD-TYPE   13   13
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRTAP4-5 MUTATED        0      1      0      1      0      0      0      0
  KRTAP4-5 WILD-TYPE      5      5      5      2      3      1      3      2
D36V4, multiclass
[1] "Remove cluster labels:" "KRTAP4-5 MUTATED"      
clus
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 2                 26 
        TCGA-OR-A5J2         TCGA-OR-A5J6         TCGA-OR-A5J7 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5J8         TCGA-OR-A5JA         TCGA-OR-A5JR 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JW 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5JY         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KU 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5KW         TCGA-OR-A5KX         TCGA-OR-A5KZ 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"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" 
        TCGA-PA-A5YG         TCGA-PK-A5H8 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-5 MUTATED        2      0      1      1
  KRTAP4-5 WILD-TYPE     14      8     13     15
D36V5, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                  8
  CLUS_3                1                 13
  CLUS_4                1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-5 MUTATED        2      1      0      1
  KRTAP4-5 WILD-TYPE     14     15      4     17
D36V6, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 15
  CLUS_3                0                  4
  CLUS_4                1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        2      1      1
  KRTAP4-5 WILD-TYPE     24     10     17
D36V7, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 24
  CLUS_2                1                 10
  CLUS_3                1                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRTAP4-5 MUTATED        1      1      0      2      0
  KRTAP4-5 WILD-TYPE     12     17      8     12      2
D36V8, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 17
  CLUS_3                0                  8
  CLUS_4                2                 12
  CLUS_5                0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        3      0      1
  KRTAP4-5 WILD-TYPE     18     14     18
D36V9, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                0                 14
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        3      1      0
  KRTAP4-5 WILD-TYPE     27     15      8
D36V10, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                1                 15
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = NOXA1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOXA1 MUTATED        3      0      2      0
  NOXA1 WILD-TYPE     18     20      8      9
D37V1, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0              20
  CLUS_3             2               8
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOXA1 MUTATED        2      0      1      0      0
  NOXA1 WILD-TYPE     11      8     13     13      7
D37V2, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V3, binary
                 cls
clus               0  1
  NOXA1 MUTATED    1  1
  NOXA1 WILD-TYPE 12 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOXA1 MUTATED      1    1
  NOXA1 WILD-TYPE   12   14
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NOXA1 MUTATED        1      0      0      1      0      0      0      0
  NOXA1 WILD-TYPE      4      6      5      2      3      1      3      2
D37V4, multiclass
[1] "Remove cluster labels:" "NOXA1 MUTATED"         
clus
  NOXA1 MUTATED NOXA1 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LP 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"NOXA1 WILD-TYPE" "NOXA1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOXA1 MUTATED        2      1      0      0
  NOXA1 WILD-TYPE     14      7     14     16
D37V5, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOXA1 MUTATED        2      1      0      0
  NOXA1 WILD-TYPE     14     15      4     18
D37V6, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             0               4
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NOXA1 MUTATED        3      0      0
  NOXA1 WILD-TYPE     23     11     18
D37V7, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             0              11
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOXA1 MUTATED        1      0      0      2      0
  NOXA1 WILD-TYPE     12     18      8     12      2
D37V8, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              18
  CLUS_3             0               8
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NOXA1 MUTATED        1      2      0
  NOXA1 WILD-TYPE     20     12     19
D37V9, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             2              12
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NOXA1 MUTATED        3      0      0
  NOXA1 WILD-TYPE     27     16      8
D37V10, multiclass
        clus
vv       NOXA1 MUTATED NOXA1 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             0              16
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = TRIOBP MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIOBP MUTATED        4      4      2      0
  TRIOBP WILD-TYPE     17     16      8      9
D38V1, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              4               17
  CLUS_2              4               16
  CLUS_3              2                8
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TRIOBP MUTATED        3      1      0      3      2
  TRIOBP WILD-TYPE     10      7     14     10      5
D38V2, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              3               10
  CLUS_2              1                7
  CLUS_3              0               14
  CLUS_4              3               10
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V3, binary
                  cls
clus                0  1
  TRIOBP MUTATED    2  1
  TRIOBP WILD-TYPE 11 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      2    1
  TRIOBP WILD-TYPE   11   14
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TRIOBP MUTATED        1      0      0      0      0      0      2      0
  TRIOBP WILD-TYPE      4      6      5      3      3      1      1      2
D38V4, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              1                4
  CLUS_2              0                6
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              0                1
  CLUS_7              2                1
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIOBP MUTATED        2      1      2      3
  TRIOBP WILD-TYPE     14      7     12     13
D38V5, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              3               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIOBP MUTATED        3      0      0      5
  TRIOBP WILD-TYPE     13     16      4     13
D38V6, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              3               13
  CLUS_2              0               16
  CLUS_3              0                4
  CLUS_4              5               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIOBP MUTATED        4      1      4
  TRIOBP WILD-TYPE     22     10     14
D38V7, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              4               22
  CLUS_2              1               10
  CLUS_3              4               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TRIOBP MUTATED        2      2      2      3      0
  TRIOBP WILD-TYPE     11     16      6     11      2
D38V8, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2               16
  CLUS_3              2                6
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIOBP MUTATED        4      2      3
  TRIOBP WILD-TYPE     17     12     16
D38V9, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              4               17
  CLUS_2              2               12
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIOBP MUTATED        5      2      2
  TRIOBP WILD-TYPE     25     14      6
D38V10, multiclass
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  CLUS_1              5               25
  CLUS_2              2               14
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = ZNF598 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF598 MUTATED        8      2      1      1
  ZNF598 WILD-TYPE     13     18      9      8
D39V1, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              8               13
  CLUS_2              2               18
  CLUS_3              1                9
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF598 MUTATED        3      0      2      4      0
  ZNF598 WILD-TYPE     10      8     12      9      7
D39V2, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              4                9
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V3, binary
                  cls
clus                0  1
  ZNF598 MUTATED    3  3
  ZNF598 WILD-TYPE 10 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      3    3
  ZNF598 WILD-TYPE   10   12
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              3               10
  CLUS_2              3               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF598 MUTATED        1      0      2      1      1      0      1      0
  ZNF598 WILD-TYPE      4      6      3      2      2      1      2      2
D39V4, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              0                6
  CLUS_3              2                3
  CLUS_4              1                2
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              1                2
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF598 MUTATED        4      0      3      2
  ZNF598 WILD-TYPE     12      8     11     14
D39V5, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              4               12
  CLUS_2              0                8
  CLUS_3              3               11
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF598 MUTATED        3      2      1      3
  ZNF598 WILD-TYPE     13     14      3     15
D39V6, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              2               14
  CLUS_3              1                3
  CLUS_4              3               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF598 MUTATED        4      2      3
  ZNF598 WILD-TYPE     22      9     15
D39V7, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              2                9
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF598 MUTATED        1      3      0      5      0
  ZNF598 WILD-TYPE     12     15      8      9      2
D39V8, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              3               15
  CLUS_3              0                8
  CLUS_4              5                9
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF598 MUTATED        3      2      4
  ZNF598 WILD-TYPE     18     12     15
D39V9, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              2               12
  CLUS_3              4               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF598 MUTATED        5      3      1
  ZNF598 WILD-TYPE     25     13      7
D39V10, multiclass
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  CLUS_1              5               25
  CLUS_2              3               13
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = IRX3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRX3 MUTATED        3      0      2      0
  IRX3 WILD-TYPE     18     20      8      9
D40V1, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            3             18
  CLUS_2            0             20
  CLUS_3            2              8
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IRX3 MUTATED        0      1      2      1      0
  IRX3 WILD-TYPE     13      7     12     12      7
D40V2, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V3, binary
                cls
clus              0  1
  IRX3 MUTATED    0  2
  IRX3 WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX3 MUTATED      0    2
  IRX3 WILD-TYPE   13   13
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IRX3 MUTATED        1      1      0      0      0      0      0      0
  IRX3 WILD-TYPE      4      5      5      3      3      1      3      2
D40V4, multiclass
[1] "Remove cluster labels:" "IRX3 MUTATED"          
clus
  IRX3 MUTATED IRX3 WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JP     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LP 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"IRX3 WILD-TYPE" "IRX3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRX3 MUTATED        2      1      1      0
  IRX3 WILD-TYPE     14      7     13     16
D40V5, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRX3 MUTATED        1      2      1      0
  IRX3 WILD-TYPE     15     14      3     18
D40V6, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            2             14
  CLUS_3            1              3
  CLUS_4            0             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRX3 MUTATED        2      2      0
  IRX3 WILD-TYPE     24      9     18
D40V7, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            2              9
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IRX3 MUTATED        2      1      0      1      0
  IRX3 WILD-TYPE     11     17      8     13      2
D40V8, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1             17
  CLUS_3            0              8
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRX3 MUTATED        3      1      0
  IRX3 WILD-TYPE     18     13     19
D40V9, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            3             18
  CLUS_2            1             13
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRX3 MUTATED        3      0      1
  IRX3 WILD-TYPE     27     16      7
D40V10, multiclass
        clus
vv       IRX3 MUTATED IRX3 WILD-TYPE
  CLUS_1            3             27
  CLUS_2            0             16
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = WDR34 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WDR34 MUTATED        3      1      0      1
  WDR34 WILD-TYPE     18     19     10      8
D41V1, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  WDR34 MUTATED        2      0      1      1      1
  WDR34 WILD-TYPE     11      8     13     12      6
D41V2, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V3, binary
                 cls
clus               0  1
  WDR34 MUTATED    0  2
  WDR34 WILD-TYPE 13 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR34 MUTATED      0    2
  WDR34 WILD-TYPE   13   13
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  WDR34 MUTATED        1      0      0      1      0      0      0      0
  WDR34 WILD-TYPE      4      6      5      2      3      1      3      2
D41V4, multiclass
[1] "Remove cluster labels:" "WDR34 MUTATED"         
clus
  WDR34 MUTATED WDR34 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JR      TCGA-OR-A5JT 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LJ 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"WDR34 WILD-TYPE" "WDR34 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WDR34 MUTATED        2      0      1      2
  WDR34 WILD-TYPE     14      8     13     14
D41V5, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             2              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WDR34 MUTATED        2      2      0      1
  WDR34 WILD-TYPE     14     14      4     17
D41V6, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2              14
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  WDR34 MUTATED        3      1      1
  WDR34 WILD-TYPE     23     10     17
D41V7, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              10
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  WDR34 MUTATED        1      1      0      3      0
  WDR34 WILD-TYPE     12     17      8     11      2
D41V8, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              17
  CLUS_3             0               8
  CLUS_4             3              11
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  WDR34 MUTATED        2      2      1
  WDR34 WILD-TYPE     19     12     18
D41V9, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2              12
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  WDR34 MUTATED        4      0      1
  WDR34 WILD-TYPE     26     16      7
D41V10, multiclass
        clus
vv       WDR34 MUTATED WDR34 WILD-TYPE
  CLUS_1             4              26
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = BHLHE22 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BHLHE22 MUTATED        1      2      2      0
  BHLHE22 WILD-TYPE     20     18      8      9
D42V1, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                18
  CLUS_3               2                 8
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BHLHE22 MUTATED        0      3      1      1      0
  BHLHE22 WILD-TYPE     13      5     13     12      7
D42V2, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                 5
  CLUS_3               1                13
  CLUS_4               1                12
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V3, binary
                   cls
clus                 0  1
  BHLHE22 MUTATED    2  2
  BHLHE22 WILD-TYPE 11 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE22 MUTATED      2    2
  BHLHE22 WILD-TYPE   11   13
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  BHLHE22 MUTATED        2      1      1      0      0      0      0      0
  BHLHE22 WILD-TYPE      3      5      4      3      3      1      3      2
D42V4, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               2                 3
  CLUS_2               1                 5
  CLUS_3               1                 4
  CLUS_4               0                 3
  CLUS_5               0                 3
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BHLHE22 MUTATED        0      2      2      1
  BHLHE22 WILD-TYPE     16      6     12     15
D42V5, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               2                 6
  CLUS_3               2                12
  CLUS_4               1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BHLHE22 MUTATED        2      2      0      1
  BHLHE22 WILD-TYPE     14     14      4     17
D42V6, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                14
  CLUS_3               0                 4
  CLUS_4               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  BHLHE22 MUTATED        2      2      1
  BHLHE22 WILD-TYPE     24      9     17
D42V7, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               2                 9
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BHLHE22 MUTATED        2      2      0      1      0
  BHLHE22 WILD-TYPE     11     16      8     13      2
D42V8, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                16
  CLUS_3               0                 8
  CLUS_4               1                13
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  BHLHE22 MUTATED        3      1      1
  BHLHE22 WILD-TYPE     18     13     18
D42V9, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               3                18
  CLUS_2               1                13
  CLUS_3               1                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  BHLHE22 MUTATED        3      2      0
  BHLHE22 WILD-TYPE     27     14      8
D42V10, multiclass
        clus
vv       BHLHE22 MUTATED BHLHE22 WILD-TYPE
  CLUS_1               3                27
  CLUS_2               2                14
  CLUS_3               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = PANK2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PANK2 MUTATED        3      1      0      1
  PANK2 WILD-TYPE     18     19     10      8
D43V1, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PANK2 MUTATED        2      0      0      1      0
  PANK2 WILD-TYPE     11      8     14     12      7
D43V2, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             0              14
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V3, binary
                 cls
clus               0  1
  PANK2 MUTATED    0  3
  PANK2 WILD-TYPE 13 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      0    3
  PANK2 WILD-TYPE   13   12
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             3              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PANK2 MUTATED        2      0      0      0      1      0      0      0
  PANK2 WILD-TYPE      3      6      5      3      2      1      3      2
D43V4, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             0               6
  CLUS_3             0               5
  CLUS_4             0               3
  CLUS_5             1               2
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PANK2 MUTATED        3      0      0      0
  PANK2 WILD-TYPE     13      8     14     16
D43V5, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             0               8
  CLUS_3             0              14
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PANK2 MUTATED        2      0      1      0
  PANK2 WILD-TYPE     14     16      3     18
D43V6, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0              16
  CLUS_3             1               3
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PANK2 MUTATED        2      1      0
  PANK2 WILD-TYPE     24     10     18
D43V7, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              10
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PANK2 MUTATED        1      0      0      2      0
  PANK2 WILD-TYPE     12     18      8     12      2
D43V8, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              18
  CLUS_3             0               8
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PANK2 MUTATED        1      1      1
  PANK2 WILD-TYPE     20     13     18
D43V9, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              13
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PANK2 MUTATED        2      0      1
  PANK2 WILD-TYPE     28     16      7
D43V10, multiclass
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = FPGS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FPGS MUTATED        2      2      1      0
  FPGS WILD-TYPE     19     18      9      9
D44V1, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            1              9
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FPGS MUTATED        1      1      1      1      0
  FPGS WILD-TYPE     12      7     13     12      7
D44V2, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V3, binary
                cls
clus              0  1
  FPGS MUTATED    1  2
  FPGS WILD-TYPE 12 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPGS MUTATED      1    2
  FPGS WILD-TYPE   12   13
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FPGS MUTATED        1      1      0      0      0      1      0      0
  FPGS WILD-TYPE      4      5      5      3      3      0      3      2
D44V4, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1              5
  CLUS_3            0              5
  CLUS_4            0              3
  CLUS_5            0              3
  CLUS_6            1              0
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FPGS MUTATED        1      1      0      2
  FPGS WILD-TYPE     15      7     14     14
D44V5, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1              7
  CLUS_3            0             14
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FPGS MUTATED        2      0      0      2
  FPGS WILD-TYPE     14     16      4     16
D44V6, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0             16
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FPGS MUTATED        0      2      2
  FPGS WILD-TYPE     26      9     16
D44V7, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            0             26
  CLUS_2            2              9
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FPGS MUTATED        0      2      0      2      0
  FPGS WILD-TYPE     13     16      8     12      2
D44V8, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             16
  CLUS_3            0              8
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FPGS MUTATED        1      1      2
  FPGS WILD-TYPE     20     13     17
D44V9, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             13
  CLUS_3            2             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FPGS MUTATED        2      2      0
  FPGS WILD-TYPE     28     14      8
D44V10, multiclass
        clus
vv       FPGS MUTATED FPGS WILD-TYPE
  CLUS_1            2             28
  CLUS_2            2             14
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = GLTPD2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLTPD2 MUTATED        3      1      1      1
  GLTPD2 WILD-TYPE     18     19      9      8
D45V1, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              1               19
  CLUS_3              1                9
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GLTPD2 MUTATED        1      0      2      2      1
  GLTPD2 WILD-TYPE     12      8     12     11      6
D45V2, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              2               11
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V3, binary
                  cls
clus                0  1
  GLTPD2 MUTATED    0  2
  GLTPD2 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      0    2
  GLTPD2 WILD-TYPE   13   13
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GLTPD2 MUTATED        0      1      0      0      1      0      0      0
  GLTPD2 WILD-TYPE      5      5      5      3      2      1      3      2
D45V4, multiclass
[1] "Remove cluster labels:" "GLTPD2 MUTATED"        
clus
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4       TCGA-OR-A5K5 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU       TCGA-OR-A5KW 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLTPD2 MUTATED        2      0      2      2
  GLTPD2 WILD-TYPE     14      8     12     14
D45V5, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLTPD2 MUTATED        1      3      1      1
  GLTPD2 WILD-TYPE     15     13      3     17
D45V6, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              3               13
  CLUS_3              1                3
  CLUS_4              1               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GLTPD2 MUTATED        3      2      1
  GLTPD2 WILD-TYPE     23      9     17
D45V7, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              3               23
  CLUS_2              2                9
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GLTPD2 MUTATED        2      1      0      3      0
  GLTPD2 WILD-TYPE     11     17      8     11      2
D45V8, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1               17
  CLUS_3              0                8
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GLTPD2 MUTATED        3      1      2
  GLTPD2 WILD-TYPE     18     13     17
D45V9, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              1               13
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GLTPD2 MUTATED        4      0      2
  GLTPD2 WILD-TYPE     26     16      6
D45V10, multiclass
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              0               16
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = TNIP2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNIP2 MUTATED        3      1      0      1
  TNIP2 WILD-TYPE     18     19     10      8
D46V1, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TNIP2 MUTATED        1      1      2      0      0
  TNIP2 WILD-TYPE     12      7     12     13      7
D46V2, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V3, binary
                 cls
clus               0  1
  TNIP2 MUTATED    0  1
  TNIP2 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNIP2 MUTATED      0    1
  TNIP2 WILD-TYPE   13   14
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TNIP2 MUTATED        0      1      0      0      0      0      0      0
  TNIP2 WILD-TYPE      5      5      5      3      3      1      3      2
D46V4, multiclass
[1] "Remove cluster labels:" "TNIP2 MUTATED"         
clus
  TNIP2 MUTATED TNIP2 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" "TNIP2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNIP2 MUTATED        1      0      2      1
  TNIP2 WILD-TYPE     15      8     12     15
D46V5, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNIP2 MUTATED        1      2      0      1
  TNIP2 WILD-TYPE     15     14      4     17
D46V6, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TNIP2 MUTATED        2      1      1
  TNIP2 WILD-TYPE     24     10     17
D46V7, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              10
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TNIP2 MUTATED        1      0      1      2      0
  TNIP2 WILD-TYPE     12     18      7     12      2
D46V8, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              18
  CLUS_3             1               7
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TNIP2 MUTATED        2      1      1
  TNIP2 WILD-TYPE     19     13     18
D46V9, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              13
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TNIP2 MUTATED        3      0      1
  TNIP2 WILD-TYPE     27     16      7
D46V10, multiclass
        clus
vv       TNIP2 MUTATED TNIP2 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = AKAP2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AKAP2 MUTATED        1      1      1      3
  AKAP2 WILD-TYPE     20     19      9      6
D47V1, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             3               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP2 MUTATED        1      0      2      2      1
  AKAP2 WILD-TYPE     12      8     12     11      6
D47V2, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             2              11
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V3, binary
                 cls
clus               0  1
  AKAP2 MUTATED    2  3
  AKAP2 WILD-TYPE 11 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP2 MUTATED      2    3
  AKAP2 WILD-TYPE   11   12
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             3              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AKAP2 MUTATED        1      1      2      0      0      0      0      1
  AKAP2 WILD-TYPE      4      5      3      3      3      1      3      1
D47V4, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1               5
  CLUS_3             2               3
  CLUS_4             0               3
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AKAP2 MUTATED        2      0      2      2
  AKAP2 WILD-TYPE     14      8     12     14
D47V5, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             2              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AKAP2 MUTATED        1      2      1      2
  AKAP2 WILD-TYPE     15     14      3     16
D47V6, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             1               3
  CLUS_4             2              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP2 MUTATED        2      1      3
  AKAP2 WILD-TYPE     24     10     15
D47V7, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              10
  CLUS_3             3              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP2 MUTATED        2      4      0      0      0
  AKAP2 WILD-TYPE     11     14      8     14      2
D47V8, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             4              14
  CLUS_3             0               8
  CLUS_4             0              14
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP2 MUTATED        2      1      3
  AKAP2 WILD-TYPE     19     13     16
D47V9, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              13
  CLUS_3             3              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP2 MUTATED        2      3      1
  AKAP2 WILD-TYPE     28     13      7
D47V10, multiclass
        clus
vv       AKAP2 MUTATED AKAP2 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             3              13
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = RREB1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RREB1 MUTATED        3      1      1      0
  RREB1 WILD-TYPE     18     19      9      9
D48V1, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RREB1 MUTATED        2      0      1      1      0
  RREB1 WILD-TYPE     11      8     13     12      7
D48V2, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V3, binary
                 cls
clus               0  1
  RREB1 MUTATED    2  0
  RREB1 WILD-TYPE 11 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      2    0
  RREB1 WILD-TYPE   11   15
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RREB1 MUTATED        0      0      0      0      1      0      1      0
  RREB1 WILD-TYPE      5      6      5      3      2      1      2      2
D48V4, multiclass
[1] "Remove cluster labels:" "RREB1 MUTATED"         
clus
  RREB1 MUTATED RREB1 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JW      TCGA-OR-A5K4      TCGA-OR-A5K5 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU      TCGA-OR-A5KW 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"RREB1 WILD-TYPE" "RREB1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RREB1 MUTATED        1      1      1      0
  RREB1 WILD-TYPE     15      7     13     16
D48V5, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             1              13
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RREB1 MUTATED        1      1      0      1
  RREB1 WILD-TYPE     15     15      4     17
D48V6, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              15
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RREB1 MUTATED        1      1      2
  RREB1 WILD-TYPE     25     10     16
D48V7, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              10
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RREB1 MUTATED        2      2      0      0      0
  RREB1 WILD-TYPE     11     16      8     14      2
D48V8, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              16
  CLUS_3             0               8
  CLUS_4             0              14
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RREB1 MUTATED        0      2      2
  RREB1 WILD-TYPE     21     12     17
D48V9, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             0              21
  CLUS_2             2              12
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RREB1 MUTATED        1      2      1
  RREB1 WILD-TYPE     29     14      7
D48V10, multiclass
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             2              14
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = TPO MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TPO MUTATED        7      2      1      2
  TPO WILD-TYPE     14     18      9      7
D49V1, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           7            14
  CLUS_2           2            18
  CLUS_3           1             9
  CLUS_4           2             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            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TPO MUTATED        3      3      1      2      0
  TPO WILD-TYPE     10      5     13     11      7
D49V2, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           3            10
  CLUS_2           3             5
  CLUS_3           1            13
  CLUS_4           2            11
  CLUS_5           0             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V3, binary
               cls
clus             0  1
  TPO MUTATED    0  4
  TPO WILD-TYPE 13 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPO MUTATED      0    4
  TPO WILD-TYPE   13   11
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           0            13
  CLUS_2           4            11
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TPO MUTATED        2      1      0      0      1      0      0      0
  TPO WILD-TYPE      3      5      5      3      2      1      3      2
D49V4, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           2             3
  CLUS_2           1             5
  CLUS_3           0             5
  CLUS_4           0             3
  CLUS_5           1             2
  CLUS_6           0             1
  CLUS_7           0             3
  CLUS_8           0             2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TPO MUTATED        5      2      1      1
  TPO WILD-TYPE     11      6     13     15
D49V5, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           5            11
  CLUS_2           2             6
  CLUS_3           1            13
  CLUS_4           1            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TPO MUTATED        4      2      2      1
  TPO WILD-TYPE     12     14      2     17
D49V6, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           4            12
  CLUS_2           2            14
  CLUS_3           2             2
  CLUS_4           1            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TPO MUTATED        4      4      1
  TPO WILD-TYPE     22      7     17
D49V7, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           4            22
  CLUS_2           4             7
  CLUS_3           1            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TPO MUTATED        1      2      1      5      0
  TPO WILD-TYPE     12     16      7      9      2
D49V8, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           1            12
  CLUS_2           2            16
  CLUS_3           1             7
  CLUS_4           5             9
  CLUS_5           0             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TPO MUTATED        4      2      3
  TPO WILD-TYPE     17     12     16
D49V9, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           4            17
  CLUS_2           2            12
  CLUS_3           3            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TPO MUTATED        5      1      3
  TPO WILD-TYPE     25     15      5
D49V10, multiclass
        clus
vv       TPO MUTATED TPO WILD-TYPE
  CLUS_1           5            25
  CLUS_2           1            15
  CLUS_3           3             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = OBSCN MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OBSCN MUTATED        9      6      1      2
  OBSCN WILD-TYPE     12     14      9      7
D50V1, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             9              12
  CLUS_2             6              14
  CLUS_3             1               9
  CLUS_4             2               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OBSCN MUTATED        4      4      2      4      2
  OBSCN WILD-TYPE      9      4     12      9      5
D50V2, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             4               9
  CLUS_2             4               4
  CLUS_3             2              12
  CLUS_4             4               9
  CLUS_5             2               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V3, binary
                 cls
clus               0  1
  OBSCN MUTATED    4  4
  OBSCN WILD-TYPE  9 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      4    4
  OBSCN WILD-TYPE    9   11
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             4               9
  CLUS_2             4              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OBSCN MUTATED        1      2      1      0      2      0      2      0
  OBSCN WILD-TYPE      4      4      4      3      1      1      1      2
D50V4, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             1               4
  CLUS_2             2               4
  CLUS_3             1               4
  CLUS_4             0               3
  CLUS_5             2               1
  CLUS_6             0               1
  CLUS_7             2               1
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OBSCN MUTATED        6      2      5      3
  OBSCN WILD-TYPE     10      6      9     13
D50V5, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             6              10
  CLUS_2             2               6
  CLUS_3             5               9
  CLUS_4             3              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OBSCN MUTATED        5      4      2      5
  OBSCN WILD-TYPE     11     12      2     13
D50V6, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             5              11
  CLUS_2             4              12
  CLUS_3             2               2
  CLUS_4             5              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OBSCN MUTATED        6      6      4
  OBSCN WILD-TYPE     20      5     14
D50V7, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             6              20
  CLUS_2             6               5
  CLUS_3             4              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OBSCN MUTATED        2      5      3      6      0
  OBSCN WILD-TYPE     11     13      5      8      2
D50V8, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             2              11
  CLUS_2             5              13
  CLUS_3             3               5
  CLUS_4             6               8
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OBSCN MUTATED        6      4      6
  OBSCN WILD-TYPE     15     10     13
D50V9, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             6              15
  CLUS_2             4              10
  CLUS_3             6              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OBSCN MUTATED        8      4      4
  OBSCN WILD-TYPE     22     12      4
D50V10, multiclass
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  CLUS_1             8              22
  CLUS_2             4              12
  CLUS_3             4               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = SNED1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SNED1 MUTATED        3      1      0      1
  SNED1 WILD-TYPE     18     19     10      8
D51V1, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SNED1 MUTATED        2      2      1      0      0
  SNED1 WILD-TYPE     11      6     13     13      7
D51V2, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2               6
  CLUS_3             1              13
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V3, binary
                 cls
clus               0  1
  SNED1 MUTATED    1  0
  SNED1 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNED1 MUTATED      1    0
  SNED1 WILD-TYPE   12   15
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SNED1 MUTATED        0      0      0      0      1      0      0      0
  SNED1 WILD-TYPE      5      6      5      3      2      1      3      2
D51V4, multiclass
[1] "Remove cluster labels:" "SNED1 MUTATED"         
clus
  SNED1 MUTATED SNED1 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5K4 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SNED1 WILD-TYPE" "SNED1 WILD-TYPE" "SNED1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SNED1 MUTATED        3      1      0      1
  SNED1 WILD-TYPE     13      7     14     15
D51V5, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SNED1 MUTATED        3      1      0      1
  SNED1 WILD-TYPE     13     15      4     17
D51V6, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             1              15
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SNED1 MUTATED        1      3      1
  SNED1 WILD-TYPE     25      8     17
D51V7, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             3               8
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SNED1 MUTATED        0      2      1      2      0
  SNED1 WILD-TYPE     13     16      7     12      2
D51V8, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              16
  CLUS_3             1               7
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SNED1 MUTATED        2      1      2
  SNED1 WILD-TYPE     19     13     17
D51V9, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              13
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SNED1 MUTATED        2      2      1
  SNED1 WILD-TYPE     28     14      7
D51V10, multiclass
        clus
vv       SNED1 MUTATED SNED1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             2              14
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = MEN1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEN1 MUTATED        1      1      2      0
  MEN1 WILD-TYPE     20     19      8      9
D52V1, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             19
  CLUS_3            2              8
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MEN1 MUTATED        0      1      4      0      0
  MEN1 WILD-TYPE     13      7     10     13      7
D52V2, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            4             10
  CLUS_4            0             13
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V3, binary
                cls
clus              0  1
  MEN1 MUTATED    0  2
  MEN1 WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      0    2
  MEN1 WILD-TYPE   13   13
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MEN1 MUTATED        0      2      0      0      0      0      0      0
  MEN1 WILD-TYPE      5      4      5      3      3      1      3      2
D52V4, multiclass
[1] "Remove cluster labels:" "MEN1 MUTATED"          
clus
  MEN1 MUTATED MEN1 WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JP     TCGA-OR-A5JR     TCGA-OR-A5JT 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"MEN1 WILD-TYPE" "MEN1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEN1 MUTATED        0      1      4      0
  MEN1 WILD-TYPE     16      7     10     16
D52V5, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            4             10
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEN1 MUTATED        0      5      0      0
  MEN1 WILD-TYPE     16     11      4     18
D52V6, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            5             11
  CLUS_3            0              4
  CLUS_4            0             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MEN1 MUTATED        4      1      0
  MEN1 WILD-TYPE     22     10     18
D52V7, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            4             22
  CLUS_2            1             10
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MEN1 MUTATED        4      0      0      1      0
  MEN1 WILD-TYPE      9     18      8     13      2
D52V8, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            4              9
  CLUS_2            0             18
  CLUS_3            0              8
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MEN1 MUTATED        4      1      0
  MEN1 WILD-TYPE     17     13     19
D52V9, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            4             17
  CLUS_2            1             13
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MEN1 MUTATED        5      0      0
  MEN1 WILD-TYPE     25     16      8
D52V10, multiclass
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  CLUS_1            5             25
  CLUS_2            0             16
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = BTBD11 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTBD11 MUTATED        2      2      1      1
  BTBD11 WILD-TYPE     19     18      9      8
D53V1, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              2               18
  CLUS_3              1                9
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BTBD11 MUTATED        1      1      1      0      2
  BTBD11 WILD-TYPE     12      7     13     13      5
D53V2, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              0               13
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V3, binary
                  cls
clus                0  1
  BTBD11 MUTATED    0  1
  BTBD11 WILD-TYPE 13 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      0    1
  BTBD11 WILD-TYPE   13   14
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  BTBD11 MUTATED        0      1      0      0      0      0      0      0
  BTBD11 WILD-TYPE      5      5      5      3      3      1      3      2
D53V4, multiclass
[1] "Remove cluster labels:" "BTBD11 MUTATED"        
clus
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               1               27 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5LJ       TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
      TCGA-OR-A5LP       TCGA-PA-A5YG       TCGA-PK-A5H8 
"BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" "BTBD11 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTBD11 MUTATED        1      0      3      1
  BTBD11 WILD-TYPE     15      8     11     15
D53V5, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              0                8
  CLUS_3              3               11
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTBD11 MUTATED        1      2      0      2
  BTBD11 WILD-TYPE     15     14      4     16
D53V6, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              2               14
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BTBD11 MUTATED        4      0      1
  BTBD11 WILD-TYPE     22     11     17
D53V7, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              0               11
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BTBD11 MUTATED        2      0      2      1      0
  BTBD11 WILD-TYPE     11     18      6     13      2
D53V8, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              0               18
  CLUS_3              2                6
  CLUS_4              1               13
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BTBD11 MUTATED        3      1      1
  BTBD11 WILD-TYPE     18     13     18
D53V9, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              1               13
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BTBD11 MUTATED        4      0      1
  BTBD11 WILD-TYPE     26     16      7
D53V10, multiclass
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              0               16
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = RNF149 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF149 MUTATED        0      2      1      1
  RNF149 WILD-TYPE     21     18      9      8
D54V1, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              2               18
  CLUS_3              1                9
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF149 MUTATED        0      0      2      0      2
  RNF149 WILD-TYPE     13      8     12     13      5
D54V2, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              0               13
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V3, binary
                  cls
clus                0  1
  RNF149 MUTATED    2  1
  RNF149 WILD-TYPE 11 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF149 MUTATED      2    1
  RNF149 WILD-TYPE   11   14
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RNF149 MUTATED        0      1      1      0      1      0      0      0
  RNF149 WILD-TYPE      5      5      4      3      2      1      3      2
D54V4, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              1                5
  CLUS_3              1                4
  CLUS_4              0                3
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF149 MUTATED        0      1      2      1
  RNF149 WILD-TYPE     16      7     12     15
D54V5, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF149 MUTATED        0      2      0      2
  RNF149 WILD-TYPE     16     14      4     16
D54V6, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              2               14
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF149 MUTATED        1      2      1
  RNF149 WILD-TYPE     25      9     17
D54V7, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              2                9
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF149 MUTATED        0      3      1      0      0
  RNF149 WILD-TYPE     13     15      7     14      2
D54V8, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              3               15
  CLUS_3              1                7
  CLUS_4              0               14
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF149 MUTATED        1      2      1
  RNF149 WILD-TYPE     20     12     18
D54V9, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              2               12
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF149 MUTATED        1      3      0
  RNF149 WILD-TYPE     29     13      8
D54V10, multiclass
        clus
vv       RNF149 MUTATED RNF149 WILD-TYPE
  CLUS_1              1               29
  CLUS_2              3               13
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = KIAA1984 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1984 MUTATED        2      0      1      1
  KIAA1984 WILD-TYPE     19     20      9      8
D55V1, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                0                 20
  CLUS_3                1                  9
  CLUS_4                1                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1984 MUTATED        0      1      2      1      0
  KIAA1984 WILD-TYPE     13      7     12     12      7
D55V2, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                  7
  CLUS_3                2                 12
  CLUS_4                1                 12
  CLUS_5                0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V3, binary
                    cls
clus                  0  1
  KIAA1984 MUTATED    0  3
  KIAA1984 WILD-TYPE 13 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1984 MUTATED      0    3
  KIAA1984 WILD-TYPE   13   12
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KIAA1984 MUTATED        0      2      0      0      1      0      0      0
  KIAA1984 WILD-TYPE      5      4      5      3      2      1      3      2
D55V4, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                2                  4
  CLUS_3                0                  5
  CLUS_4                0                  3
  CLUS_5                1                  2
  CLUS_6                0                  1
  CLUS_7                0                  3
  CLUS_8                0                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1984 MUTATED        1      0      3      0
  KIAA1984 WILD-TYPE     15      8     11     16
D55V5, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                0                  8
  CLUS_3                3                 11
  CLUS_4                0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1984 MUTATED        0      3      1      0
  KIAA1984 WILD-TYPE     16     13      3     18
D55V6, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                3                 13
  CLUS_3                1                  3
  CLUS_4                0                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1984 MUTATED        1      3      0
  KIAA1984 WILD-TYPE     25      8     18
D55V7, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                3                  8
  CLUS_3                0                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1984 MUTATED        0      1      1      2      0
  KIAA1984 WILD-TYPE     13     17      7     12      2
D55V8, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                 17
  CLUS_3                1                  7
  CLUS_4                2                 12
  CLUS_5                0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1984 MUTATED        1      2      1
  KIAA1984 WILD-TYPE     20     12     18
D55V9, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                1                 20
  CLUS_2                2                 12
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1984 MUTATED        2      1      1
  KIAA1984 WILD-TYPE     28     15      7
D55V10, multiclass
        clus
vv       KIAA1984 MUTATED KIAA1984 WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                1                 15
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = CCDC150 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC150 MUTATED        2      0      2      0
  CCDC150 WILD-TYPE     19     20      8      9
D56V1, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               0                20
  CLUS_3               2                 8
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC150 MUTATED        2      0      1      1      0
  CCDC150 WILD-TYPE     11      8     13     12      7
D56V2, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               0                 8
  CLUS_3               1                13
  CLUS_4               1                12
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V3, binary
                   cls
clus                 0  1
  CCDC150 MUTATED    0  3
  CCDC150 WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      0    3
  CCDC150 WILD-TYPE   13   12
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CCDC150 MUTATED        0      1      0      1      1      0      0      0
  CCDC150 WILD-TYPE      5      5      5      2      2      1      3      2
D56V4, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 5
  CLUS_3               0                 5
  CLUS_4               1                 2
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC150 MUTATED        3      0      1      0
  CCDC150 WILD-TYPE     13      8     13     16
D56V5, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                 8
  CLUS_3               1                13
  CLUS_4               0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC150 MUTATED        2      1      1      0
  CCDC150 WILD-TYPE     14     15      3     18
D56V6, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                15
  CLUS_3               1                 3
  CLUS_4               0                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC150 MUTATED        3      1      0
  CCDC150 WILD-TYPE     23     10     18
D56V7, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               3                23
  CLUS_2               1                10
  CLUS_3               0                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC150 MUTATED        1      0      0      3      0
  CCDC150 WILD-TYPE     12     18      8     11      2
D56V8, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                18
  CLUS_3               0                 8
  CLUS_4               3                11
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC150 MUTATED        2      1      1
  CCDC150 WILD-TYPE     19     13     18
D56V9, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               1                13
  CLUS_3               1                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC150 MUTATED        3      0      1
  CCDC150 WILD-TYPE     27     16      7
D56V10, multiclass
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  CLUS_1               3                27
  CLUS_2               0                16
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = FAM18B2 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM18B2 MUTATED        2      1      0      1
  FAM18B2 WILD-TYPE     19     19     10      8
D57V1, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               1                19
  CLUS_3               0                10
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM18B2 MUTATED        1      2      1      0      0
  FAM18B2 WILD-TYPE     12      6     13     13      7
D57V2, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                 6
  CLUS_3               1                13
  CLUS_4               0                13
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V3, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    1  1
  FAM18B2 WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1    1
  FAM18B2 WILD-TYPE   12   14
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FAM18B2 MUTATED        1      0      0      0      0      0      0      1
  FAM18B2 WILD-TYPE      4      6      5      3      3      1      3      1
D57V4, multiclass
[1] "Remove cluster labels:" "FAM18B2 MUTATED"       
clus
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                2                26 
       TCGA-OR-A5J3        TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5JA        TCGA-OR-A5JP        TCGA-OR-A5JR        TCGA-OR-A5JT 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5JV        TCGA-OR-A5JY        TCGA-OR-A5K4        TCGA-OR-A5K5 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5K8        TCGA-OR-A5KO        TCGA-OR-A5KU        TCGA-OR-A5KW 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-PA-A5YG        TCGA-PK-A5H8 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM18B2 MUTATED        1      2      1      0
  FAM18B2 WILD-TYPE     15      6     13     16
D57V5, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                 6
  CLUS_3               1                13
  CLUS_4               0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM18B2 MUTATED        2      2      0      0
  FAM18B2 WILD-TYPE     14     14      4     18
D57V6, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                14
  CLUS_3               0                 4
  CLUS_4               0                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM18B2 MUTATED        1      2      1
  FAM18B2 WILD-TYPE     25      9     17
D57V7, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                25
  CLUS_2               2                 9
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM18B2 MUTATED        0      3      0      1      0
  FAM18B2 WILD-TYPE     13     15      8     13      2
D57V8, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               0                 8
  CLUS_4               1                13
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM18B2 MUTATED        1      1      2
  FAM18B2 WILD-TYPE     20     13     17
D57V9, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               1                13
  CLUS_3               2                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM18B2 MUTATED        1      3      0
  FAM18B2 WILD-TYPE     29     13      8
D57V10, multiclass
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  CLUS_1               1                29
  CLUS_2               3                13
  CLUS_3               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = MUC5B MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC5B MUTATED        8      7      3      3
  MUC5B WILD-TYPE     13     13      7      6
D58V1, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             8              13
  CLUS_2             7              13
  CLUS_3             3               7
  CLUS_4             3               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC5B MUTATED        3      3      6      4      4
  MUC5B WILD-TYPE     10      5      8      9      3
D58V2, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             3              10
  CLUS_2             3               5
  CLUS_3             6               8
  CLUS_4             4               9
  CLUS_5             4               3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V3, binary
                 cls
clus              0 1
  MUC5B MUTATED   5 6
  MUC5B WILD-TYPE 8 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      5    6
  MUC5B WILD-TYPE    8    9
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             5               8
  CLUS_2             6               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MUC5B MUTATED        2      2      2      0      2      0      2      1
  MUC5B WILD-TYPE      3      4      3      3      1      1      1      1
D58V4, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             2               3
  CLUS_2             2               4
  CLUS_3             2               3
  CLUS_4             0               3
  CLUS_5             2               1
  CLUS_6             0               1
  CLUS_7             2               1
  CLUS_8             1               1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC5B MUTATED        5      3      7      5
  MUC5B WILD-TYPE     11      5      7     11
D58V5, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             5              11
  CLUS_2             3               5
  CLUS_3             7               7
  CLUS_4             5              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              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC5B MUTATED        4      7      2      7
  MUC5B WILD-TYPE     12      9      2     11
D58V6, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             4              12
  CLUS_2             7               9
  CLUS_3             2               2
  CLUS_4             7              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              CLUS_1 CLUS_2 CLUS_3
  MUC5B MUTATED        8      5      7
  MUC5B WILD-TYPE     18      6     11
D58V7, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             8              18
  CLUS_2             5               6
  CLUS_3             7              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC5B MUTATED        3      7      4      6      0
  MUC5B WILD-TYPE     10     11      4      8      2
D58V8, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             3              10
  CLUS_2             7              11
  CLUS_3             4               4
  CLUS_4             6               8
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC5B MUTATED        7      5      7
  MUC5B WILD-TYPE     14      9     12
D58V9, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             7              14
  CLUS_2             5               9
  CLUS_3             7              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC5B MUTATED        9      6      4
  MUC5B WILD-TYPE     21     10      4
D58V10, multiclass
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  CLUS_1             9              21
  CLUS_2             6              10
  CLUS_3             4               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = PTPLA MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTPLA MUTATED        2      0      1      1
  PTPLA WILD-TYPE     19     20      9      8
D59V1, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              20
  CLUS_3             1               9
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTPLA MUTATED        0      1      2      0      0
  PTPLA WILD-TYPE     13      7     12     13      7
D59V2, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V3, binary
                 cls
clus               0  1
  PTPLA MUTATED    0  1
  PTPLA WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      0    1
  PTPLA WILD-TYPE   13   14
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PTPLA MUTATED        0      0      0      0      0      0      0      1
  PTPLA WILD-TYPE      5      6      5      3      3      1      3      1
D59V4, multiclass
[1] "Remove cluster labels:" "PTPLA MUTATED"         
clus
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JY      TCGA-OR-A5K4 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTPLA MUTATED        1      0      2      0
  PTPLA WILD-TYPE     15      8     12     16
D59V5, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTPLA MUTATED        1      2      0      0
  PTPLA WILD-TYPE     15     14      4     18
D59V6, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             0               4
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTPLA MUTATED        1      1      1
  PTPLA WILD-TYPE     25     10     17
D59V7, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              10
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTPLA MUTATED        1      1      0      1      0
  PTPLA WILD-TYPE     12     17      8     13      2
D59V8, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              17
  CLUS_3             0               8
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTPLA MUTATED        2      0      1
  PTPLA WILD-TYPE     19     14     18
D59V9, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              14
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTPLA MUTATED        2      1      0
  PTPLA WILD-TYPE     28     15      8
D59V10, multiclass
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  CLUS_1             2              28
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = SRPX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRPX MUTATED        1      2      0      0
  SRPX WILD-TYPE     20     18     10      9
D60V1, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             20
  CLUS_2            2             18
  CLUS_3            0             10
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SRPX MUTATED        0      2      0      1      0
  SRPX WILD-TYPE     13      6     14     12      7
D60V2, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2              6
  CLUS_3            0             14
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V3, binary
                cls
clus              0  1
  SRPX MUTATED    1  1
  SRPX WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    1
  SRPX WILD-TYPE   12   14
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SRPX MUTATED        1      1      0      0      0      0      0      0
  SRPX WILD-TYPE      4      5      5      3      3      1      3      2
D60V4, multiclass
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             2             26 
    TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR     TCGA-OR-A5JT 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRPX MUTATED        0      1      1      1
  SRPX WILD-TYPE     16      7     13     15
D60V5, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRPX MUTATED        1      1      0      1
  SRPX WILD-TYPE     15     15      4     17
D60V6, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1             15
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SRPX MUTATED        1      1      1
  SRPX WILD-TYPE     25     10     17
D60V7, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             10
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SRPX MUTATED        1      2      0      0      0
  SRPX WILD-TYPE     12     16      8     14      2
D60V8, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             16
  CLUS_3            0              8
  CLUS_4            0             14
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SRPX MUTATED        1      1      1
  SRPX WILD-TYPE     20     13     18
D60V9, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             13
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SRPX MUTATED        1      2      0
  SRPX WILD-TYPE     29     14      8
D60V10, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             29
  CLUS_2            2             14
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = GARS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GARS MUTATED        5      4      4      6
  GARS WILD-TYPE     16     16      6      3
D61V1, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            5             16
  CLUS_2            4             16
  CLUS_3            4              6
  CLUS_4            6              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GARS MUTATED        2      0      4      5      4
  GARS WILD-TYPE     11      8     10      8      3
D61V2, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            2             11
  CLUS_2            0              8
  CLUS_3            4             10
  CLUS_4            5              8
  CLUS_5            4              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V3, binary
                cls
clus              0  1
  GARS MUTATED    6  3
  GARS WILD-TYPE  7 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  GARS MUTATED      6    3
  GARS WILD-TYPE    7   12
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            6              7
  CLUS_2            3             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GARS MUTATED        2      1      4      1      0      0      1      0
  GARS WILD-TYPE      3      5      1      2      3      1      2      2
D61V4, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            2              3
  CLUS_2            1              5
  CLUS_3            4              1
  CLUS_4            1              2
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            1              2
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GARS MUTATED        3      1      4      7
  GARS WILD-TYPE     13      7     10      9
D61V5, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            3             13
  CLUS_2            1              7
  CLUS_3            4             10
  CLUS_4            7              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GARS MUTATED        2      3      2      8
  GARS WILD-TYPE     14     13      2     10
D61V6, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            2             14
  CLUS_2            3             13
  CLUS_3            2              2
  CLUS_4            8             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GARS MUTATED        6      1      8
  GARS WILD-TYPE     20     10     10
D61V7, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            6             20
  CLUS_2            1             10
  CLUS_3            8             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GARS MUTATED        3      6      4      2      0
  GARS WILD-TYPE     10     12      4     12      2
D61V8, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            3             10
  CLUS_2            6             12
  CLUS_3            4              4
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GARS MUTATED        5      2      8
  GARS WILD-TYPE     16     12     11
D61V9, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            5             16
  CLUS_2            2             12
  CLUS_3            8             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GARS MUTATED        6      6      3
  GARS WILD-TYPE     24     10      5
D61V10, multiclass
        clus
vv       GARS MUTATED GARS WILD-TYPE
  CLUS_1            6             24
  CLUS_2            6             10
  CLUS_3            3              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = PRSS27 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRSS27 MUTATED        1      1      1      0
  PRSS27 WILD-TYPE     20     19      9      9
D62V1, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              1               19
  CLUS_3              1                9
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRSS27 MUTATED        0      1      1      1      0
  PRSS27 WILD-TYPE     13      7     13     12      7
D62V2, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              1               12
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V3, binary
                  cls
clus                0  1
  PRSS27 MUTATED    0  1
  PRSS27 WILD-TYPE 13 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      0    1
  PRSS27 WILD-TYPE   13   14
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PRSS27 MUTATED        0      0      0      0      1      0      0      0
  PRSS27 WILD-TYPE      5      6      5      3      2      1      3      2
D62V4, multiclass
[1] "Remove cluster labels:" "PRSS27 MUTATED"        
clus
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               1               27 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5LJ       TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-OR-A5LP       TCGA-PA-A5YG       TCGA-PK-A5H8 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRSS27 MUTATED        1      1      1      0
  PRSS27 WILD-TYPE     15      7     13     16
D62V5, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              0               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRSS27 MUTATED        0      2      1      0
  PRSS27 WILD-TYPE     16     14      3     18
D62V6, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              2               14
  CLUS_3              1                3
  CLUS_4              0               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PRSS27 MUTATED        1      2      0
  PRSS27 WILD-TYPE     25      9     18
D62V7, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              2                9
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRSS27 MUTATED        1      1      0      1      0
  PRSS27 WILD-TYPE     12     17      8     13      2
D62V8, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               17
  CLUS_3              0                8
  CLUS_4              1               13
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PRSS27 MUTATED        1      0      2
  PRSS27 WILD-TYPE     20     14     17
D62V9, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              0               14
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PRSS27 MUTATED        1      1      1
  PRSS27 WILD-TYPE     29     15      7
D62V10, multiclass
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  CLUS_1              1               29
  CLUS_2              1               15
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = SEMA5B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA5B MUTATED        5      2      0      1
  SEMA5B WILD-TYPE     16     18     10      8
D63V1, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              5               16
  CLUS_2              2               18
  CLUS_3              0               10
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SEMA5B MUTATED        2      1      0      3      0
  SEMA5B WILD-TYPE     11      7     14     10      7
D63V2, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1                7
  CLUS_3              0               14
  CLUS_4              3               10
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V3, binary
                  cls
clus                0  1
  SEMA5B MUTATED    3  1
  SEMA5B WILD-TYPE 10 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA5B MUTATED      3    1
  SEMA5B WILD-TYPE   10   14
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              3               10
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SEMA5B MUTATED        2      0      1      0      0      1      0      0
  SEMA5B WILD-TYPE      3      6      4      3      3      0      3      2
D63V4, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              2                3
  CLUS_2              0                6
  CLUS_3              1                4
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              1                0
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA5B MUTATED        3      1      0      2
  SEMA5B WILD-TYPE     13      7     14     14
D63V5, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              3               13
  CLUS_2              1                7
  CLUS_3              0               14
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA5B MUTATED        3      0      1      2
  SEMA5B WILD-TYPE     13     16      3     16
D63V6, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              3               13
  CLUS_2              0               16
  CLUS_3              1                3
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA5B MUTATED        2      2      2
  SEMA5B WILD-TYPE     24      9     16
D63V7, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              2               24
  CLUS_2              2                9
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SEMA5B MUTATED        0      4      0      2      0
  SEMA5B WILD-TYPE     13     14      8     12      2
D63V8, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              0               13
  CLUS_2              4               14
  CLUS_3              0                8
  CLUS_4              2               12
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA5B MUTATED        1      3      2
  SEMA5B WILD-TYPE     20     11     17
D63V9, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              1               20
  CLUS_2              3               11
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA5B MUTATED        2      3      1
  SEMA5B WILD-TYPE     28     13      7
D63V10, multiclass
        clus
vv       SEMA5B MUTATED SEMA5B WILD-TYPE
  CLUS_1              2               28
  CLUS_2              3               13
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = CD320 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD320 MUTATED        2      1      1      0
  CD320 WILD-TYPE     19     19      9      9
D64V1, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CD320 MUTATED        1      0      1      2      0
  CD320 WILD-TYPE     12      8     13     11      7
D64V2, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             2              11
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V3, binary
                 cls
clus               0  1
  CD320 MUTATED    1  1
  CD320 WILD-TYPE 12 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD320 MUTATED      1    1
  CD320 WILD-TYPE   12   14
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CD320 MUTATED        0      1      1      0      0      0      0      0
  CD320 WILD-TYPE      5      5      4      3      3      1      3      2
D64V4, multiclass
[1] "Remove cluster labels:" "CD320 MUTATED"         
clus
  CD320 MUTATED CD320 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J7      TCGA-OR-A5J8 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR      TCGA-OR-A5JT 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU      TCGA-OR-A5KW 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" "CD320 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"CD320 WILD-TYPE" "CD320 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD320 MUTATED        1      0      2      1
  CD320 WILD-TYPE     15      8     12     15
D64V5, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD320 MUTATED        1      1      1      1
  CD320 WILD-TYPE     15     15      3     17
D64V6, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              15
  CLUS_3             1               3
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD320 MUTATED        3      1      0
  CD320 WILD-TYPE     23     10     18
D64V7, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              10
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CD320 MUTATED        1      0      2      1      0
  CD320 WILD-TYPE     12     18      6     13      2
D64V8, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              18
  CLUS_3             2               6
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD320 MUTATED        3      1      0
  CD320 WILD-TYPE     18     13     19
D64V9, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              13
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD320 MUTATED        4      0      0
  CD320 WILD-TYPE     26     16      8
D64V10, multiclass
        clus
vv       CD320 MUTATED CD320 WILD-TYPE
  CLUS_1             4              26
  CLUS_2             0              16
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = TAF5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TAF5 MUTATED        2      1      1      0
  TAF5 WILD-TYPE     19     19      9      9
D65V1, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             19
  CLUS_3            1              9
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TAF5 MUTATED        1      1      1      0      1
  TAF5 WILD-TYPE     12      7     13     13      6
D65V2, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            0             13
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V3, binary
                cls
clus              0  1
  TAF5 MUTATED    2  1
  TAF5 WILD-TYPE 11 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF5 MUTATED      2    1
  TAF5 WILD-TYPE   11   14
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TAF5 MUTATED        1      1      0      0      1      0      0      0
  TAF5 WILD-TYPE      4      5      5      3      2      1      3      2
D65V4, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1              5
  CLUS_3            0              5
  CLUS_4            0              3
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TAF5 MUTATED        1      1      1      1
  TAF5 WILD-TYPE     15      7     13     15
D65V5, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TAF5 MUTATED        2      1      0      1
  TAF5 WILD-TYPE     14     15      4     17
D65V6, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             15
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TAF5 MUTATED        0      3      1
  TAF5 WILD-TYPE     26      8     17
D65V7, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            3              8
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TAF5 MUTATED        0      4      0      0      0
  TAF5 WILD-TYPE     13     14      8     14      2
D65V8, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            4             14
  CLUS_3            0              8
  CLUS_4            0             14
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TAF5 MUTATED        0      3      1
  TAF5 WILD-TYPE     21     11     18
D65V9, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            0             21
  CLUS_2            3             11
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TAF5 MUTATED        0      4      0
  TAF5 WILD-TYPE     30     12      8
D65V10, multiclass
        clus
vv       TAF5 MUTATED TAF5 WILD-TYPE
  CLUS_1            0             30
  CLUS_2            4             12
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = NEFH MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        5      0      1      0
  NEFH WILD-TYPE     16     20      9      9
D66V1, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            5             16
  CLUS_2            0             20
  CLUS_3            1              9
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NEFH MUTATED        3      0      0      1      0
  NEFH WILD-TYPE     10      8     14     12      7
D66V2, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             10
  CLUS_2            0              8
  CLUS_3            0             14
  CLUS_4            1             12
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V3, binary
                cls
clus              0  1
  NEFH MUTATED    0  2
  NEFH WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    2
  NEFH WILD-TYPE   13   13
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NEFH MUTATED        0      0      0      1      1      0      0      0
  NEFH WILD-TYPE      5      6      5      2      2      1      3      2
D66V4, multiclass
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4     TCGA-OR-A5K5 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU     TCGA-OR-A5KW 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        3      0      0      0
  NEFH WILD-TYPE     13      8     14     16
D66V5, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             13
  CLUS_2            0              8
  CLUS_3            0             14
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        2      0      1      0
  NEFH WILD-TYPE     14     16      3     18
D66V6, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0             16
  CLUS_3            1              3
  CLUS_4            0             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      1      0
  NEFH WILD-TYPE     23     10     18
D66V7, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             23
  CLUS_2            1             10
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NEFH MUTATED        1      0      0      3      0
  NEFH WILD-TYPE     12     18      8     11      2
D66V8, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0             18
  CLUS_3            0              8
  CLUS_4            3             11
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        1      2      1
  NEFH WILD-TYPE     20     12     18
D66V9, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            1             20
  CLUS_2            2             12
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      0      1
  NEFH WILD-TYPE     27     16      7
D66V10, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             27
  CLUS_2            0             16
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DMKN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DMKN MUTATED        2      1      0      0
  DMKN WILD-TYPE     19     19     10      9
D67V1, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             19
  CLUS_3            0             10
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DMKN MUTATED        0      1      2      0      0
  DMKN WILD-TYPE     13      7     12     13      7
D67V2, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            0             13
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V3, binary
                cls
clus              0  1
  DMKN MUTATED    1  0
  DMKN WILD-TYPE 12 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMKN MUTATED      1    0
  DMKN WILD-TYPE   12   15
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0             15
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  DMKN MUTATED        0      0      0      0      1      0      0      0
  DMKN WILD-TYPE      5      6      5      3      2      1      3      2
D67V4, multiclass
[1] "Remove cluster labels:" "DMKN MUTATED"          
clus
  DMKN MUTATED DMKN WILD-TYPE 
             1             27 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ     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-PA-A5YG     TCGA-PK-A5H8 
"DMKN WILD-TYPE" "DMKN WILD-TYPE" "DMKN WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DMKN MUTATED        1      1      1      0
  DMKN WILD-TYPE     15      7     13     16
D67V5, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DMKN MUTATED        1      2      0      0
  DMKN WILD-TYPE     15     14      4     18
D67V6, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            1             15
  CLUS_2            2             14
  CLUS_3            0              4
  CLUS_4            0             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DMKN MUTATED        0      3      0
  DMKN WILD-TYPE     26      8     18
D67V7, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            0             26
  CLUS_2            3              8
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DMKN MUTATED        0      1      0      2      0
  DMKN WILD-TYPE     13     17      8     12      2
D67V8, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1             17
  CLUS_3            0              8
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DMKN MUTATED        1      2      0
  DMKN WILD-TYPE     20     12     19
D67V9, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            1             20
  CLUS_2            2             12
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DMKN MUTATED        2      1      0
  DMKN WILD-TYPE     28     15      8
D67V10, multiclass
        clus
vv       DMKN MUTATED DMKN WILD-TYPE
  CLUS_1            2             28
  CLUS_2            1             15
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = NPTX1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPTX1 MUTATED        1      1      0      1
  NPTX1 WILD-TYPE     20     19     10      8
D68V1, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NPTX1 MUTATED        1      0      1      1      0
  NPTX1 WILD-TYPE     12      8     13     12      7
D68V2, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V3, binary
                 cls
clus               0  1
  NPTX1 MUTATED    1  0
  NPTX1 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      1    0
  NPTX1 WILD-TYPE   12   15
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NPTX1 MUTATED        0      0      0      0      0      0      1      0
  NPTX1 WILD-TYPE      5      6      5      3      3      1      2      2
D68V4, multiclass
[1] "Remove cluster labels:" "NPTX1 MUTATED"         
clus
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" "NPTX1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPTX1 MUTATED        1      0      1      1
  NPTX1 WILD-TYPE     15      8     13     15
D68V5, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPTX1 MUTATED        1      0      0      2
  NPTX1 WILD-TYPE     15     16      4     16
D68V6, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0              16
  CLUS_3             0               4
  CLUS_4             2              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NPTX1 MUTATED        1      0      2
  NPTX1 WILD-TYPE     25     11     16
D68V7, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              11
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NPTX1 MUTATED        0      1      1      1      0
  NPTX1 WILD-TYPE     13     17      7     13      2
D68V8, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              17
  CLUS_3             1               7
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NPTX1 MUTATED        0      1      2
  NPTX1 WILD-TYPE     21     13     17
D68V9, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             0              21
  CLUS_2             1              13
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NPTX1 MUTATED        1      1      1
  NPTX1 WILD-TYPE     29     15      7
D68V10, multiclass
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             1              15
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = NOTCH2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH2 MUTATED        4      1      0      0
  NOTCH2 WILD-TYPE     17     19     10      9
D69V1, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              1               19
  CLUS_3              0               10
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOTCH2 MUTATED        1      0      2      1      0
  NOTCH2 WILD-TYPE     12      8     12     12      7
D69V2, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              1               12
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V3, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    1  1
  NOTCH2 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      1    1
  NOTCH2 WILD-TYPE   12   14
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NOTCH2 MUTATED        0      0      0      0      2      0      0      0
  NOTCH2 WILD-TYPE      5      6      5      3      1      1      3      2
D69V4, multiclass
[1] "Remove cluster labels:" "NOTCH2 MUTATED"        
clus
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KW 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"NOTCH2 WILD-TYPE" "NOTCH2 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH2 MUTATED        2      1      1      0
  NOTCH2 WILD-TYPE     14      7     13     16
D69V5, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1                7
  CLUS_3              1               13
  CLUS_4              0               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH2 MUTATED        1      2      1      0
  NOTCH2 WILD-TYPE     15     14      3     18
D69V6, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              2               14
  CLUS_3              1                3
  CLUS_4              0               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH2 MUTATED        1      3      0
  NOTCH2 WILD-TYPE     25      8     18
D69V7, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              3                8
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOTCH2 MUTATED        0      1      0      3      0
  NOTCH2 WILD-TYPE     13     17      8     11      2
D69V8, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1               17
  CLUS_3              0                8
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH2 MUTATED        1      2      1
  NOTCH2 WILD-TYPE     20     12     18
D69V9, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              2               12
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH2 MUTATED        2      1      1
  NOTCH2 WILD-TYPE     28     15      7
D69V10, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              2               28
  CLUS_2              1               15
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = RNF39 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF39 MUTATED        3      1      1      0
  RNF39 WILD-TYPE     18     19      9      9
D70V1, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF39 MUTATED        1      2      2      0      0
  RNF39 WILD-TYPE     12      6     12     13      7
D70V2, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2               6
  CLUS_3             2              12
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V3, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  3
  RNF39 WILD-TYPE 12 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    3
  RNF39 WILD-TYPE   12   12
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             3              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RNF39 MUTATED        1      2      0      1      0      0      0      0
  RNF39 WILD-TYPE      4      4      5      2      3      1      3      2
D70V4, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             2               4
  CLUS_3             0               5
  CLUS_4             1               2
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF39 MUTATED        1      1      3      0
  RNF39 WILD-TYPE     15      7     11     16
D70V5, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             3              11
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF39 MUTATED        2      3      0      0
  RNF39 WILD-TYPE     14     13      4     18
D70V6, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             3              13
  CLUS_3             0               4
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF39 MUTATED        3      2      0
  RNF39 WILD-TYPE     23      9     18
D70V7, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             2               9
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF39 MUTATED        2      1      0      2      0
  RNF39 WILD-TYPE     11     17      8     12      2
D70V8, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             1              17
  CLUS_3             0               8
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF39 MUTATED        3      2      0
  RNF39 WILD-TYPE     18     12     19
D70V9, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             2              12
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF39 MUTATED        4      1      0
  RNF39 WILD-TYPE     26     15      8
D70V10, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             4              26
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = KBTBD13 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KBTBD13 MUTATED        5      3      0      1
  KBTBD13 WILD-TYPE     16     17     10      8
D71V1, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               5                16
  CLUS_2               3                17
  CLUS_3               0                10
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KBTBD13 MUTATED        3      1      0      2      3
  KBTBD13 WILD-TYPE     10      7     14     11      4
D71V2, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                 7
  CLUS_3               0                14
  CLUS_4               2                11
  CLUS_5               3                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V3, binary
                   cls
clus                 0  1
  KBTBD13 MUTATED    3  1
  KBTBD13 WILD-TYPE 10 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD13 MUTATED      3    1
  KBTBD13 WILD-TYPE   10   14
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KBTBD13 MUTATED        1      0      1      1      1      0      0      0
  KBTBD13 WILD-TYPE      4      6      4      2      2      1      3      2
D71V4, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               0                 6
  CLUS_3               1                 4
  CLUS_4               1                 2
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KBTBD13 MUTATED        4      1      1      3
  KBTBD13 WILD-TYPE     12      7     13     13
D71V5, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               4                12
  CLUS_2               1                 7
  CLUS_3               1                13
  CLUS_4               3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KBTBD13 MUTATED        4      0      1      4
  KBTBD13 WILD-TYPE     12     16      3     14
D71V6, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                16
  CLUS_3               1                 3
  CLUS_4               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  KBTBD13 MUTATED        4      2      3
  KBTBD13 WILD-TYPE     22      9     15
D71V7, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               4                22
  CLUS_2               2                 9
  CLUS_3               3                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KBTBD13 MUTATED        0      4      2      3      0
  KBTBD13 WILD-TYPE     13     14      6     11      2
D71V8, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               4                14
  CLUS_3               2                 6
  CLUS_4               3                11
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  KBTBD13 MUTATED        4      2      3
  KBTBD13 WILD-TYPE     17     12     16
D71V9, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               4                17
  CLUS_2               2                12
  CLUS_3               3                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  KBTBD13 MUTATED        4      4      1
  KBTBD13 WILD-TYPE     26     12      7
D71V10, multiclass
        clus
vv       KBTBD13 MUTATED KBTBD13 WILD-TYPE
  CLUS_1               4                26
  CLUS_2               4                12
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = IER5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IER5 MUTATED        3      0      0      0
  IER5 WILD-TYPE     18     20     10      9
D72V1, multiclass
        clus
vv       IER5 MUTATED IER5 WILD-TYPE
  CLUS_1            3             18
  CLUS_2            0             20
  CLUS_3            0             10
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IER5 MUTATED        2      0      0      0      0
  IER5 WILD-TYPE     11      8     14     13      7
D72V2, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-PK-A5HB 
"IER5 WILD-TYPE" 
D72V3, binary
                cls
clus              0  1
  IER5 MUTATED    1  0
  IER5 WILD-TYPE 12 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  IER5 MUTATED      1    0
  IER5 WILD-TYPE   12   15
        clus
vv       IER5 MUTATED IER5 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0             15
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IER5 MUTATED        0      0      0      0      1      0      0      0
  IER5 WILD-TYPE      5      6      5      3      2      1      3      2
D72V4, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             1             27 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LP     TCGA-PA-A5YG     TCGA-PK-A5H8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IER5 MUTATED        2      0      0      0
  IER5 WILD-TYPE     14      8     14     16
D72V5, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD     TCGA-OR-A5JF 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4     TCGA-OR-A5K5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO     TCGA-OR-A5KT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5KX 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4     TCGA-OR-A5L5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8     TCGA-PK-A5HB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IER5 MUTATED        2      0      0      0
  IER5 WILD-TYPE     14     16      4     18
D72V6, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD     TCGA-OR-A5JF 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4     TCGA-OR-A5K5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO     TCGA-OR-A5KT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW     TCGA-OR-A5KX 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4     TCGA-OR-A5L5 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8     TCGA-PK-A5HB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IER5 MUTATED        1      1      0
  IER5 WILD-TYPE     25     10     18
D72V7, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-PK-A5HB 
"IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IER5 MUTATED        0      1      0      1      0
  IER5 WILD-TYPE     13     17      8     13      2
D72V8, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-PK-A5HB 
"IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IER5 MUTATED        0      2      0
  IER5 WILD-TYPE     21     12     19
D72V9, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5HB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IER5 MUTATED        1      1      0
  IER5 WILD-TYPE     29     15      8
D72V10, multiclass
[1] "Remove cluster labels:" "IER5 MUTATED"          
clus
  IER5 MUTATED IER5 WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5K4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5K9     TCGA-OR-A5KO 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5HB 
"IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" "IER5 WILD-TYPE" 

Clustering(73) Variable = SCRT1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCRT1 MUTATED        2      1      0      0
  SCRT1 WILD-TYPE     19     19     10      9
D73V1, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SCRT1 MUTATED        2      0      0      1      0
  SCRT1 WILD-TYPE     11      8     14     12      7
D73V2, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               8
  CLUS_3             0              14
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V3, binary
                 cls
clus               0  1
  SCRT1 MUTATED    1  0
  SCRT1 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRT1 MUTATED      1    0
  SCRT1 WILD-TYPE   12   15
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SCRT1 MUTATED        0      0      0      0      1      0      0      0
  SCRT1 WILD-TYPE      5      6      5      3      2      1      3      2
D73V4, multiclass
[1] "Remove cluster labels:" "SCRT1 MUTATED"         
clus
  SCRT1 MUTATED SCRT1 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5K4 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" "SCRT1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCRT1 MUTATED        2      0      1      0
  SCRT1 WILD-TYPE     14      8     13     16
D73V5, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCRT1 MUTATED        2      0      0      1
  SCRT1 WILD-TYPE     14     16      4     17
D73V6, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0              16
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SCRT1 MUTATED        2      1      0
  SCRT1 WILD-TYPE     24     10     18
D73V7, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              10
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SCRT1 MUTATED        0      1      1      1      0
  SCRT1 WILD-TYPE     13     17      7     13      2
D73V8, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              17
  CLUS_3             1               7
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SCRT1 MUTATED        2      1      0
  SCRT1 WILD-TYPE     19     13     19
D73V9, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              13
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SCRT1 MUTATED        2      1      0
  SCRT1 WILD-TYPE     28     15      8
D73V10, multiclass
        clus
vv       SCRT1 MUTATED SCRT1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = KNDC1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KNDC1 MUTATED        1      4      2      2
  KNDC1 WILD-TYPE     20     16      8      7
D74V1, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             4              16
  CLUS_3             2               8
  CLUS_4             2               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KNDC1 MUTATED        0      2      2      1      3
  KNDC1 WILD-TYPE     13      6     12     12      4
D74V2, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2               6
  CLUS_3             2              12
  CLUS_4             1              12
  CLUS_5             3               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V3, binary
                 cls
clus               0  1
  KNDC1 MUTATED    1  2
  KNDC1 WILD-TYPE 12 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNDC1 MUTATED      1    2
  KNDC1 WILD-TYPE   12   13
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KNDC1 MUTATED        2      0      1      0      0      0      0      0
  KNDC1 WILD-TYPE      3      6      4      3      3      1      3      2
D74V4, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             0               6
  CLUS_3             1               4
  CLUS_4             0               3
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KNDC1 MUTATED        0      3      1      4
  KNDC1 WILD-TYPE     16      5     13     12
D74V5, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             3               5
  CLUS_3             1              13
  CLUS_4             4              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KNDC1 MUTATED        1      2      0      5
  KNDC1 WILD-TYPE     15     14      4     13
D74V6, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             0               4
  CLUS_4             5              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KNDC1 MUTATED        2      2      4
  KNDC1 WILD-TYPE     24      9     14
D74V7, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             2               9
  CLUS_3             4              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KNDC1 MUTATED        1      3      3      1      0
  KNDC1 WILD-TYPE     12     15      5     13      2
D74V8, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             3              15
  CLUS_3             3               5
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KNDC1 MUTATED        4      0      4
  KNDC1 WILD-TYPE     17     14     15
D74V9, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             4              17
  CLUS_2             0              14
  CLUS_3             4              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KNDC1 MUTATED        3      3      2
  KNDC1 WILD-TYPE     27     13      6
D74V10, multiclass
        clus
vv       KNDC1 MUTATED KNDC1 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             3              13
  CLUS_3             2               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = MAP1S MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP1S MUTATED        0      2      1      2
  MAP1S WILD-TYPE     21     18      9      7
D75V1, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             0              21
  CLUS_2             2              18
  CLUS_3             1               9
  CLUS_4             2               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAP1S MUTATED        1      1      0      3      0
  MAP1S WILD-TYPE     12      7     14     10      7
D75V2, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             3              10
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V3, binary
                 cls
clus               0  1
  MAP1S MUTATED    2  2
  MAP1S WILD-TYPE 11 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1S MUTATED      2    2
  MAP1S WILD-TYPE   11   13
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MAP1S MUTATED        2      0      2      0      0      0      0      0
  MAP1S WILD-TYPE      3      6      3      3      3      1      3      2
D75V4, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             2               3
  CLUS_2             0               6
  CLUS_3             2               3
  CLUS_4             0               3
  CLUS_5             0               3
  CLUS_6             0               1
  CLUS_7             0               3
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP1S MUTATED        1      1      0      3
  MAP1S WILD-TYPE     15      7     14     13
D75V5, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             3              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP1S MUTATED        2      1      0      2
  MAP1S WILD-TYPE     14     15      4     16
D75V6, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             0               4
  CLUS_4             2              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAP1S MUTATED        2      1      2
  MAP1S WILD-TYPE     24     10     16
D75V7, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              10
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAP1S MUTATED        2      2      0      1      0
  MAP1S WILD-TYPE     11     16      8     13      2
D75V8, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              16
  CLUS_3             0               8
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAP1S MUTATED        3      0      2
  MAP1S WILD-TYPE     18     14     17
D75V9, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0              14
  CLUS_3             2              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAP1S MUTATED        3      2      0
  MAP1S WILD-TYPE     27     14      8
D75V10, multiclass
        clus
vv       MAP1S MUTATED MAP1S WILD-TYPE
  CLUS_1             3              27
  CLUS_2             2              14
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = RGMB MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGMB MUTATED        2      2      2      0
  RGMB WILD-TYPE     19     18      8      9
D76V1, multiclass
        clus
vv       RGMB MUTATED RGMB WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            2              8
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RGMB MUTATED        1      0      1      0      0
  RGMB WILD-TYPE     12      8     13     13      7
D76V2, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-PK-A5HB 
"RGMB WILD-TYPE" 
D76V3, binary
                cls
clus              0  1
  RGMB MUTATED    1  1
  RGMB WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGMB MUTATED      1    1
  RGMB WILD-TYPE   12   14
        clus
vv       RGMB MUTATED RGMB WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RGMB MUTATED        0      1      0      1      0      0      0      0
  RGMB WILD-TYPE      5      5      5      2      3      1      3      2
D76V4, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5KO     TCGA-OR-A5KU 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGMB MUTATED        1      0      1      0
  RGMB WILD-TYPE     15      8     13     16
D76V5, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J5 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD     TCGA-OR-A5JF 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9     TCGA-OR-A5KO 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4     TCGA-OR-A5L5 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8     TCGA-PK-A5HB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGMB MUTATED        1      1      0      0
  RGMB WILD-TYPE     15     15      4     18
D76V6, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J5 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8     TCGA-OR-A5JA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD     TCGA-OR-A5JF 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL     TCGA-OR-A5JP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT     TCGA-OR-A5JV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY     TCGA-OR-A5K2 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9     TCGA-OR-A5KO 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV     TCGA-OR-A5KW 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4     TCGA-OR-A5L5 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA     TCGA-OR-A5LB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ     TCGA-OR-A5LK 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP     TCGA-OR-A5LR 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8     TCGA-PK-A5HB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RGMB MUTATED        1      1      0
  RGMB WILD-TYPE     25     10     18
D76V7, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-PK-A5HB 
"RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RGMB MUTATED        0      1      0      1      0
  RGMB WILD-TYPE     13     17      8     13      2
D76V8, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             53 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5H8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-PK-A5HB 
"RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RGMB MUTATED        0      2      0
  RGMB WILD-TYPE     21     12     19
D76V9, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5HB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RGMB MUTATED        1      1      0
  RGMB WILD-TYPE     29     15      8
D76V10, multiclass
[1] "Remove cluster labels:" "RGMB MUTATED"          
clus
  RGMB MUTATED RGMB WILD-TYPE 
             2             52 
    TCGA-OR-A5J1     TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5J5     TCGA-OR-A5J6     TCGA-OR-A5J7     TCGA-OR-A5J8 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JA     TCGA-OR-A5JB     TCGA-OR-A5JC     TCGA-OR-A5JD 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JF     TCGA-OR-A5JI     TCGA-OR-A5JK     TCGA-OR-A5JL 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JP     TCGA-OR-A5JQ     TCGA-OR-A5JR     TCGA-OR-A5JT 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JX     TCGA-OR-A5JY 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5K2     TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K9 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KO     TCGA-OR-A5KT     TCGA-OR-A5KU     TCGA-OR-A5KV 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KZ     TCGA-OR-A5L3     TCGA-OR-A5L4 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5L5     TCGA-OR-A5L6     TCGA-OR-A5L9     TCGA-OR-A5LA 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LB     TCGA-OR-A5LC     TCGA-OR-A5LD     TCGA-OR-A5LJ 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 
    TCGA-OR-A5LR     TCGA-P6-A5OF     TCGA-PA-A5YG     TCGA-PK-A5HB 
"RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" "RGMB WILD-TYPE" 

Clustering(77) Variable = LRP11 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRP11 MUTATED        2      2      1      0
  LRP11 WILD-TYPE     19     18      9      9
D77V1, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2              18
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LRP11 MUTATED        1      0      4      0      0
  LRP11 WILD-TYPE     12      8     10     13      7
D77V2, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             4              10
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V3, binary
                 cls
clus               0  1
  LRP11 MUTATED    0  1
  LRP11 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP11 MUTATED      0    1
  LRP11 WILD-TYPE   13   14
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LRP11 MUTATED        0      1      0      0      0      0      0      0
  LRP11 WILD-TYPE      5      5      5      3      3      1      3      2
D77V4, multiclass
[1] "Remove cluster labels:" "LRP11 MUTATED"         
clus
  LRP11 MUTATED LRP11 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5KO      TCGA-OR-A5KU 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"LRP11 WILD-TYPE" "LRP11 WILD-TYPE" "LRP11 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRP11 MUTATED        1      1      2      1
  LRP11 WILD-TYPE     15      7     12     15
D77V5, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRP11 MUTATED        1      3      0      1
  LRP11 WILD-TYPE     15     13      4     17
D77V6, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             3              13
  CLUS_3             0               4
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRP11 MUTATED        2      2      1
  LRP11 WILD-TYPE     24      9     17
D77V7, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             2               9
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LRP11 MUTATED        1      2      0      2      0
  LRP11 WILD-TYPE     12     16      8     12      2
D77V8, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2              16
  CLUS_3             0               8
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRP11 MUTATED        2      2      1
  LRP11 WILD-TYPE     19     12     18
D77V9, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2              12
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LRP11 MUTATED        3      2      0
  LRP11 WILD-TYPE     27     14      8
D77V10, multiclass
        clus
vv       LRP11 MUTATED LRP11 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             2              14
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = AR MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AR MUTATED        2      0      1      1
  AR WILD-TYPE     19     20      9      8
D78V1, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           19
  CLUS_2          0           20
  CLUS_3          1            9
  CLUS_4          1            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           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AR MUTATED        2      0      1      0      0
  AR WILD-TYPE     11      8     13     13      7
D78V2, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           11
  CLUS_2          0            8
  CLUS_3          1           13
  CLUS_4          0           13
  CLUS_5          0            7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V3, binary
              cls
clus            0  1
  AR MUTATED    1  2
  AR WILD-TYPE 12 13
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      1    2
  AR WILD-TYPE   12   13
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           12
  CLUS_2          2           13
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AR MUTATED        1      1      0      0      1      0      0      0
  AR WILD-TYPE      4      5      5      3      2      1      3      2
D78V4, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1            4
  CLUS_2          1            5
  CLUS_3          0            5
  CLUS_4          0            3
  CLUS_5          1            2
  CLUS_6          0            1
  CLUS_7          0            3
  CLUS_8          0            2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AR MUTATED        2      0      1      0
  AR WILD-TYPE     14      8     13     16
D78V5, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           14
  CLUS_2          0            8
  CLUS_3          1           13
  CLUS_4          0           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AR MUTATED        2      1      0      0
  AR WILD-TYPE     14     15      4     18
D78V6, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           14
  CLUS_2          1           15
  CLUS_3          0            4
  CLUS_4          0           18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        2      1      0
  AR WILD-TYPE     24     10     18
D78V7, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           24
  CLUS_2          1           10
  CLUS_3          0           18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AR MUTATED        1      1      0      1      0
  AR WILD-TYPE     12     17      8     13      2
D78V8, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           12
  CLUS_2          1           17
  CLUS_3          0            8
  CLUS_4          1           13
  CLUS_5          0            2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        1      2      0
  AR WILD-TYPE     20     12     19
D78V9, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           20
  CLUS_2          2           12
  CLUS_3          0           19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        2      1      0
  AR WILD-TYPE     28     15      8
D78V10, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           28
  CLUS_2          1           15
  CLUS_3          0            8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = VARS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VARS MUTATED        2      2      1      1
  VARS WILD-TYPE     19     18      9      8
D79V1, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VARS MUTATED        0      1      3      2      0
  VARS WILD-TYPE     13      7     11     11      7
D79V2, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            3             11
  CLUS_4            2             11
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V3, binary
                cls
clus              0  1
  VARS MUTATED    0  3
  VARS WILD-TYPE 13 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      0    3
  VARS WILD-TYPE   13   12
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            0             13
  CLUS_2            3             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  VARS MUTATED        0      1      0      0      1      0      0      1
  VARS WILD-TYPE      5      5      5      3      2      1      3      1
D79V4, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            0              5
  CLUS_2            1              5
  CLUS_3            0              5
  CLUS_4            0              3
  CLUS_5            1              2
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            1              1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VARS MUTATED        1      0      4      1
  VARS WILD-TYPE     15      8     10     15
D79V5, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0              8
  CLUS_3            4             10
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VARS MUTATED        0      4      1      1
  VARS WILD-TYPE     16     12      3     17
D79V6, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            0             16
  CLUS_2            4             12
  CLUS_3            1              3
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VARS MUTATED        2      2      2
  VARS WILD-TYPE     24      9     16
D79V7, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            2             24
  CLUS_2            2              9
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VARS MUTATED        2      2      0      2      0
  VARS WILD-TYPE     11     16      8     12      2
D79V8, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             16
  CLUS_3            0              8
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VARS MUTATED        2      1      3
  VARS WILD-TYPE     19     13     16
D79V9, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             13
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VARS MUTATED        3      2      1
  VARS WILD-TYPE     27     14      7
D79V10, multiclass
        clus
vv       VARS MUTATED VARS WILD-TYPE
  CLUS_1            3             27
  CLUS_2            2             14
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = SEZ6L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEZ6L2 MUTATED        2      4      0      2
  SEZ6L2 WILD-TYPE     19     16     10      7
D80V1, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              4               16
  CLUS_3              0               10
  CLUS_4              2                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SEZ6L2 MUTATED        2      2      1      1      0
  SEZ6L2 WILD-TYPE     11      6     13     12      7
D80V2, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2                6
  CLUS_3              1               13
  CLUS_4              1               12
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V3, binary
                  cls
clus                0  1
  SEZ6L2 MUTATED    1  2
  SEZ6L2 WILD-TYPE 12 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEZ6L2 MUTATED      1    2
  SEZ6L2 WILD-TYPE   12   13
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SEZ6L2 MUTATED        0      2      1      0      0      0      0      0
  SEZ6L2 WILD-TYPE      5      4      4      3      3      1      3      2
D80V4, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2                4
  CLUS_3              1                4
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEZ6L2 MUTATED        2      0      2      2
  SEZ6L2 WILD-TYPE     14      8     12     14
D80V5, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEZ6L2 MUTATED        2      2      0      2
  SEZ6L2 WILD-TYPE     14     14      4     16
D80V6, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               14
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEZ6L2 MUTATED        4      0      2
  SEZ6L2 WILD-TYPE     22     11     16
D80V7, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              0               11
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SEZ6L2 MUTATED        1      1      2      2      0
  SEZ6L2 WILD-TYPE     12     17      6     12      2
D80V8, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               17
  CLUS_3              2                6
  CLUS_4              2               12
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEZ6L2 MUTATED        2      2      2
  SEZ6L2 WILD-TYPE     19     12     17
D80V9, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              2               12
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEZ6L2 MUTATED        4      1      1
  SEZ6L2 WILD-TYPE     26     15      7
D80V10, multiclass
        clus
vv       SEZ6L2 MUTATED SEZ6L2 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              1               15
  CLUS_3              1                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = PABPC1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PABPC1 MUTATED        1      1      2      0
  PABPC1 WILD-TYPE     20     19      8      9
D81V1, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              1               19
  CLUS_3              2                8
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PABPC1 MUTATED        1      0      1      0      0
  PABPC1 WILD-TYPE     12      8     13     13      7
D81V2, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JF       TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LA       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" 
D81V3, binary
                  cls
clus                0  1
  PABPC1 MUTATED    1  0
  PABPC1 WILD-TYPE 12 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    0
  PABPC1 WILD-TYPE   12   15
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PABPC1 MUTATED        0      0      0      1      0      0      0      0
  PABPC1 WILD-TYPE      5      6      5      2      3      1      3      2
D81V4, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               27 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LJ       TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LP       TCGA-PA-A5YG       TCGA-PK-A5H8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PABPC1 MUTATED        1      1      0      0
  PABPC1 WILD-TYPE     15      7     14     16
D81V5, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PABPC1 MUTATED        1      1      0      0
  PABPC1 WILD-TYPE     15     15      4     18
D81V6, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        2      0      0
  PABPC1 WILD-TYPE     24     11     18
D81V7, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JF       TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LA       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PABPC1 MUTATED        0      0      0      1      1
  PABPC1 WILD-TYPE     13     18      8     13      1
D81V8, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JF       TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LA       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        0      2      0
  PABPC1 WILD-TYPE     21     12     19
D81V9, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JF       TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LA       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        2      0      0
  PABPC1 WILD-TYPE     28     16      8
D81V10, multiclass
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JF       TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JP       TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LA       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 

Clustering(82) Variable = FANK1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FANK1 MUTATED        1      1      1      0
  FANK1 WILD-TYPE     20     19      9      9
D82V1, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FANK1 MUTATED        0      1      0      1      1
  FANK1 WILD-TYPE     13      7     14     12      6
D82V2, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             1              12
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V3, binary
                 cls
clus               0  1
  FANK1 MUTATED    0  1
  FANK1 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      0    1
  FANK1 WILD-TYPE   13   14
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FANK1 MUTATED        1      0      0      0      0      0      0      0
  FANK1 WILD-TYPE      4      6      5      3      3      1      3      2
D82V4, multiclass
[1] "Remove cluster labels:" "FANK1 MUTATED"         
clus
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5LD      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FANK1 MUTATED        1      1      0      1
  FANK1 WILD-TYPE     15      7     14     15
D82V5, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FANK1 MUTATED        1      0      1      1
  FANK1 WILD-TYPE     15     16      3     17
D82V6, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0              16
  CLUS_3             1               3
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FANK1 MUTATED        1      1      1
  FANK1 WILD-TYPE     25     10     17
D82V7, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              10
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FANK1 MUTATED        0      0      1      2      0
  FANK1 WILD-TYPE     13     18      7     12      2
D82V8, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0              18
  CLUS_3             1               7
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FANK1 MUTATED        2      0      1
  FANK1 WILD-TYPE     19     14     18
D82V9, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              14
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FANK1 MUTATED        2      0      1
  FANK1 WILD-TYPE     28     16      7
D82V10, multiclass
        clus
vv       FANK1 MUTATED FANK1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = NMU MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NMU MUTATED        1      2      1      0
  NMU WILD-TYPE     20     18      9      9
D83V1, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           1            20
  CLUS_2           2            18
  CLUS_3           1             9
  CLUS_4           0             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            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NMU MUTATED        1      1      1      1      0
  NMU WILD-TYPE     12      7     13     12      7
D83V2, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           1            12
  CLUS_2           1             7
  CLUS_3           1            13
  CLUS_4           1            12
  CLUS_5           0             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V3, binary
               cls
clus             0  1
  NMU MUTATED    1  0
  NMU WILD-TYPE 12 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMU MUTATED      1    0
  NMU WILD-TYPE   12   15
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           1            12
  CLUS_2           0            15
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NMU MUTATED        0      0      1      0      0      0      0      0
  NMU WILD-TYPE      5      6      4      3      3      1      3      2
D83V4, multiclass
[1] "Remove cluster labels:" "NMU MUTATED"           
clus
  NMU MUTATED NMU WILD-TYPE 
            1            27 
   TCGA-OR-A5J2    TCGA-OR-A5J3    TCGA-OR-A5J6    TCGA-OR-A5J7    TCGA-OR-A5J8 
"NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" 
   TCGA-OR-A5JA    TCGA-OR-A5JP    TCGA-OR-A5JR    TCGA-OR-A5JV    TCGA-OR-A5JW 
"NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" 
   TCGA-OR-A5JY    TCGA-OR-A5K4    TCGA-OR-A5K5    TCGA-OR-A5K8    TCGA-OR-A5KO 
"NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" 
   TCGA-OR-A5KU    TCGA-OR-A5KW    TCGA-OR-A5KX    TCGA-OR-A5KZ    TCGA-OR-A5LD 
"NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" 
   TCGA-OR-A5LJ    TCGA-OR-A5LK    TCGA-OR-A5LL    TCGA-OR-A5LO    TCGA-OR-A5LP 
"NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" "NMU WILD-TYPE" 
   TCGA-PA-A5YG    TCGA-PK-A5H8 
"NMU WILD-TYPE" "NMU WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NMU MUTATED        0      2      0      1
  NMU WILD-TYPE     16      6     14     15
D83V5, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           0            16
  CLUS_2           2             6
  CLUS_3           0            14
  CLUS_4           1            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NMU MUTATED        0      2      0      1
  NMU WILD-TYPE     16     14      4     17
D83V6, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           0            16
  CLUS_2           2            14
  CLUS_3           0             4
  CLUS_4           1            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NMU MUTATED        2      1      1
  NMU WILD-TYPE     24     10     17
D83V7, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           2            24
  CLUS_2           1            10
  CLUS_3           1            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NMU MUTATED        2      2      0      0      0
  NMU WILD-TYPE     11     16      8     14      2
D83V8, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           2            11
  CLUS_2           2            16
  CLUS_3           0             8
  CLUS_4           0            14
  CLUS_5           0             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NMU MUTATED        1      1      2
  NMU WILD-TYPE     20     13     17
D83V9, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           1            20
  CLUS_2           1            13
  CLUS_3           2            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NMU MUTATED        2      2      0
  NMU WILD-TYPE     28     14      8
D83V10, multiclass
        clus
vv       NMU MUTATED NMU WILD-TYPE
  CLUS_1           2            28
  CLUS_2           2            14
  CLUS_3           0             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = ADAD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAD2 MUTATED        2      0      1      1
  ADAD2 WILD-TYPE     19     20      9      8
D84V1, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              20
  CLUS_3             1               9
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ADAD2 MUTATED        0      0      2      1      1
  ADAD2 WILD-TYPE     13      8     12     12      6
D84V2, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             1              12
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V3, binary
                 cls
clus               0  1
  ADAD2 MUTATED    0  1
  ADAD2 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAD2 MUTATED      0    1
  ADAD2 WILD-TYPE   13   14
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ADAD2 MUTATED        0      1      0      0      0      0      0      0
  ADAD2 WILD-TYPE      5      5      5      3      3      1      3      2
D84V4, multiclass
[1] "Remove cluster labels:" "ADAD2 MUTATED"         
clus
  ADAD2 MUTATED ADAD2 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5KO      TCGA-OR-A5KU 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" "ADAD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAD2 MUTATED        1      0      2      1
  ADAD2 WILD-TYPE     15      8     12     15
D84V5, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0               8
  CLUS_3             2              12
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAD2 MUTATED        0      2      1      1
  ADAD2 WILD-TYPE     16     14      3     17
D84V6, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             2              14
  CLUS_3             1               3
  CLUS_4             1              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ADAD2 MUTATED        0      3      1
  ADAD2 WILD-TYPE     26      8     17
D84V7, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             3               8
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ADAD2 MUTATED        0      3      0      1      0
  ADAD2 WILD-TYPE     13     15      8     13      2
D84V8, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             3              15
  CLUS_3             0               8
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ADAD2 MUTATED        0      3      1
  ADAD2 WILD-TYPE     21     11     18
D84V9, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             0              21
  CLUS_2             3              11
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ADAD2 MUTATED        1      2      1
  ADAD2 WILD-TYPE     29     14      7
D84V10, multiclass
        clus
vv       ADAD2 MUTATED ADAD2 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             2              14
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = CLIC6 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLIC6 MUTATED        2      3      0      0
  CLIC6 WILD-TYPE     19     17     10      9
D85V1, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             3              17
  CLUS_3             0              10
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLIC6 MUTATED        1      1      1      1      0
  CLIC6 WILD-TYPE     12      7     13     12      7
D85V2, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1               7
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V3, binary
                 cls
clus               0  1
  CLIC6 MUTATED    2  0
  CLIC6 WILD-TYPE 11 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIC6 MUTATED      2    0
  CLIC6 WILD-TYPE   11   15
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CLIC6 MUTATED        0      0      1      0      1      0      0      0
  CLIC6 WILD-TYPE      5      6      4      3      2      1      3      2
D85V4, multiclass
[1] "Remove cluster labels:" "CLIC6 MUTATED"         
clus
  CLIC6 MUTATED CLIC6 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J7      TCGA-OR-A5J8 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR      TCGA-OR-A5JT 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KW 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"CLIC6 WILD-TYPE" "CLIC6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLIC6 MUTATED        2      1      0      1
  CLIC6 WILD-TYPE     14      7     14     15
D85V5, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CLIC6 MUTATED        2      1      1      0
  CLIC6 WILD-TYPE     14     15      3     18
D85V6, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             1               3
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CLIC6 MUTATED        2      2      0
  CLIC6 WILD-TYPE     24      9     18
D85V7, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             2               9
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLIC6 MUTATED        0      1      1      2      0
  CLIC6 WILD-TYPE     13     17      7     12      2
D85V8, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              17
  CLUS_3             1               7
  CLUS_4             2              12
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CLIC6 MUTATED        2      2      0
  CLIC6 WILD-TYPE     19     12     19
D85V9, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2              12
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CLIC6 MUTATED        3      1      0
  CLIC6 WILD-TYPE     27     15      8
D85V10, multiclass
        clus
vv       CLIC6 MUTATED CLIC6 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(86) Variable = PCDHB13 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHB13 MUTATED        1      1      2      1
  PCDHB13 WILD-TYPE     20     19      8      8
D86V1, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               1                19
  CLUS_3               2                 8
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHB13 MUTATED        0      1      3      0      0
  PCDHB13 WILD-TYPE     13      7     11     13      7
D86V2, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1                 7
  CLUS_3               3                11
  CLUS_4               0                13
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V3, binary
                   cls
clus                 0  1
  PCDHB13 MUTATED    0  2
  PCDHB13 WILD-TYPE 13 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHB13 MUTATED      0    2
  PCDHB13 WILD-TYPE   13   13
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PCDHB13 MUTATED        0      2      0      0      0      0      0      0
  PCDHB13 WILD-TYPE      5      4      5      3      3      1      3      2
D86V4, multiclass
[1] "Remove cluster labels:" "PCDHB13 MUTATED"       
clus
  PCDHB13 MUTATED PCDHB13 WILD-TYPE 
                2                26 
       TCGA-OR-A5J2        TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5JP        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JY        TCGA-OR-A5K4        TCGA-OR-A5K5 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5K8        TCGA-OR-A5KO        TCGA-OR-A5KU        TCGA-OR-A5KW 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
       TCGA-PA-A5YG        TCGA-PK-A5H8 
"PCDHB13 WILD-TYPE" "PCDHB13 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHB13 MUTATED        0      0      3      1
  PCDHB13 WILD-TYPE     16      8     11     15
D86V5, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                 8
  CLUS_3               3                11
  CLUS_4               1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHB13 MUTATED        0      3      0      1
  PCDHB13 WILD-TYPE     16     13      4     17
D86V6, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                13
  CLUS_3               0                 4
  CLUS_4               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHB13 MUTATED        3      0      1
  PCDHB13 WILD-TYPE     23     11     17
D86V7, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               3                23
  CLUS_2               0                11
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHB13 MUTATED        3      0      1      0      0
  PCDHB13 WILD-TYPE     10     18      7     14      2
D86V8, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               0                18
  CLUS_3               1                 7
  CLUS_4               0                14
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHB13 MUTATED        3      0      1
  PCDHB13 WILD-TYPE     18     14     18
D86V9, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               3                18
  CLUS_2               0                14
  CLUS_3               1                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHB13 MUTATED        3      0      1
  PCDHB13 WILD-TYPE     27     16      7
D86V10, multiclass
        clus
vv       PCDHB13 MUTATED PCDHB13 WILD-TYPE
  CLUS_1               3                27
  CLUS_2               0                16
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = PLEC MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEC MUTATED        4      7      1      1
  PLEC WILD-TYPE     17     13      9      8
D87V1, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            4             17
  CLUS_2            7             13
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLEC MUTATED        2      2      1      3      2
  PLEC WILD-TYPE     11      6     13     10      5
D87V2, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2              6
  CLUS_3            1             13
  CLUS_4            3             10
  CLUS_5            2              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V3, binary
                cls
clus              0  1
  PLEC MUTATED    1  4
  PLEC WILD-TYPE 12 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      1    4
  PLEC WILD-TYPE   12   11
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            1             12
  CLUS_2            4             11
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PLEC MUTATED        0      4      0      0      0      0      1      0
  PLEC WILD-TYPE      5      2      5      3      3      1      2      2
D87V4, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            0              5
  CLUS_2            4              2
  CLUS_3            0              5
  CLUS_4            0              3
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            1              2
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEC MUTATED        2      0      5      3
  PLEC WILD-TYPE     14      8      9     13
D87V5, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0              8
  CLUS_3            5              9
  CLUS_4            3             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEC MUTATED        2      4      0      4
  PLEC WILD-TYPE     14     12      4     14
D87V6, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            2             14
  CLUS_2            4             12
  CLUS_3            0              4
  CLUS_4            4             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PLEC MUTATED        6      2      2
  PLEC WILD-TYPE     20      9     16
D87V7, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            6             20
  CLUS_2            2              9
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLEC MUTATED        4      2      2      2      0
  PLEC WILD-TYPE      9     16      6     12      2
D87V8, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            4              9
  CLUS_2            2             16
  CLUS_3            2              6
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PLEC MUTATED        6      3      1
  PLEC WILD-TYPE     15     11     18
D87V9, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            6             15
  CLUS_2            3             11
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PLEC MUTATED        7      2      1
  PLEC WILD-TYPE     23     14      7
D87V10, multiclass
        clus
vv       PLEC MUTATED PLEC WILD-TYPE
  CLUS_1            7             23
  CLUS_2            2             14
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = AMDHD1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMDHD1 MUTATED        5      2      1      2
  AMDHD1 WILD-TYPE     16     18      9      7
D88V1, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              5               16
  CLUS_2              2               18
  CLUS_3              1                9
  CLUS_4              2                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMDHD1 MUTATED        1      1      4      2      1
  AMDHD1 WILD-TYPE     12      7     10     11      6
D88V2, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1                7
  CLUS_3              4               10
  CLUS_4              2               11
  CLUS_5              1                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V3, binary
                  cls
clus                0  1
  AMDHD1 MUTATED    0  3
  AMDHD1 WILD-TYPE 13 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMDHD1 MUTATED      0    3
  AMDHD1 WILD-TYPE   13   12
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              3               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AMDHD1 MUTATED        1      0      0      0      1      0      0      1
  AMDHD1 WILD-TYPE      4      6      5      3      2      1      3      1
D88V4, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              0                6
  CLUS_3              0                5
  CLUS_4              0                3
  CLUS_5              1                2
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMDHD1 MUTATED        3      2      3      1
  AMDHD1 WILD-TYPE     13      6     11     15
D88V5, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              2                6
  CLUS_3              3               11
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMDHD1 MUTATED        1      4      2      2
  AMDHD1 WILD-TYPE     15     12      2     16
D88V6, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              4               12
  CLUS_3              2                2
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  AMDHD1 MUTATED        3      4      2
  AMDHD1 WILD-TYPE     23      7     16
D88V7, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              3               23
  CLUS_2              4                7
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMDHD1 MUTATED        1      4      1      3      0
  AMDHD1 WILD-TYPE     12     14      7     11      2
D88V8, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               14
  CLUS_3              1                7
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  AMDHD1 MUTATED        3      2      4
  AMDHD1 WILD-TYPE     18     12     15
D88V9, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              3               18
  CLUS_2              2               12
  CLUS_3              4               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  AMDHD1 MUTATED        4      3      2
  AMDHD1 WILD-TYPE     26     13      6
D88V10, multiclass
        clus
vv       AMDHD1 MUTATED AMDHD1 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              3               13
  CLUS_3              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(89) Variable = DSPP MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DSPP MUTATED        4      4      1      0
  DSPP WILD-TYPE     17     16      9      9
D89V1, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            4             17
  CLUS_2            4             16
  CLUS_3            1              9
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DSPP MUTATED        1      4      1      3      0
  DSPP WILD-TYPE     12      4     13     10      7
D89V2, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            1             12
  CLUS_2            4              4
  CLUS_3            1             13
  CLUS_4            3             10
  CLUS_5            0              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V3, binary
                cls
clus              0  1
  DSPP MUTATED    2  2
  DSPP WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      2    2
  DSPP WILD-TYPE   11   13
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  DSPP MUTATED        1      1      0      1      0      0      0      1
  DSPP WILD-TYPE      4      5      5      2      3      1      3      1
D89V4, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1              5
  CLUS_3            0              5
  CLUS_4            1              2
  CLUS_5            0              3
  CLUS_6            0              1
  CLUS_7            0              3
  CLUS_8            1              1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DSPP MUTATED        3      1      2      3
  DSPP WILD-TYPE     13      7     12     13
D89V5, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            3             13
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            3             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DSPP MUTATED        4      1      1      3
  DSPP WILD-TYPE     12     15      3     15
D89V6, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            4             12
  CLUS_2            1             15
  CLUS_3            1              3
  CLUS_4            3             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DSPP MUTATED        3      3      3
  DSPP WILD-TYPE     23      8     15
D89V7, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            3             23
  CLUS_2            3              8
  CLUS_3            3             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DSPP MUTATED        1      4      1      2      1
  DSPP WILD-TYPE     12     14      7     12      1
D89V8, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            1             12
  CLUS_2            4             14
  CLUS_3            1              7
  CLUS_4            2             12
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DSPP MUTATED        3      3      3
  DSPP WILD-TYPE     18     11     16
D89V9, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            3             18
  CLUS_2            3             11
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DSPP MUTATED        5      3      1
  DSPP WILD-TYPE     25     13      7
D89V10, multiclass
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  CLUS_1            5             25
  CLUS_2            3             13
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(90) Variable = TMEM189 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM189 MUTATED        3      0      0      0
  TMEM189 WILD-TYPE     18     20     10      9
D90V1, multiclass
        clus
vv       TMEM189 MUTATED TMEM189 WILD-TYPE
  CLUS_1               3                18
  CLUS_2               0                20
  CLUS_3               0                10
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TMEM189 MUTATED        0      1      1      0      0
  TMEM189 WILD-TYPE     13      7     13     13      7
D90V2, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                53 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" 
D90V3, binary
                   cls
clus                 0  1
  TMEM189 MUTATED    1  0
  TMEM189 WILD-TYPE 12 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM189 MUTATED      1    0
  TMEM189 WILD-TYPE   12   15
        clus
vv       TMEM189 MUTATED TMEM189 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TMEM189 MUTATED        1      0      0      0      0      0      0      0
  TMEM189 WILD-TYPE      4      6      5      3      3      1      3      2
D90V4, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                1                27 
       TCGA-OR-A5J3        TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JA        TCGA-OR-A5JP        TCGA-OR-A5JR        TCGA-OR-A5JT 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JV        TCGA-OR-A5JW        TCGA-OR-A5JY        TCGA-OR-A5K4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5KO        TCGA-OR-A5KU 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-PA-A5YG        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM189 MUTATED        0      1      1      0
  TMEM189 WILD-TYPE     16      7     13     16
D90V5, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                52 
       TCGA-OR-A5J1        TCGA-OR-A5J3        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-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF        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-A5KO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM189 MUTATED        1      1      0      0
  TMEM189 WILD-TYPE     15     15      4     18
D90V6, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                52 
       TCGA-OR-A5J1        TCGA-OR-A5J3        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-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF        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-A5KO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3        TCGA-OR-A5L4 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9        TCGA-OR-A5LA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG        TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM189 MUTATED        0      2      0
  TMEM189 WILD-TYPE     26      9     18
D90V7, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                53 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TMEM189 MUTATED        0      1      0      1      0
  TMEM189 WILD-TYPE     13     17      8     13      2
D90V8, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                53 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-PK-A5H8 
"TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM189 MUTATED        0      2      0
  TMEM189 WILD-TYPE     21     12     19
D90V9, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                52 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM189 MUTATED        1      1      0
  TMEM189 WILD-TYPE     29     15      8
D90V10, multiclass
[1] "Remove cluster labels:" "TMEM189 MUTATED"       
clus
  TMEM189 MUTATED TMEM189 WILD-TYPE 
                2                52 
       TCGA-OR-A5J1        TCGA-OR-A5J3        TCGA-OR-A5J4        TCGA-OR-A5J5 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JA 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JD        TCGA-OR-A5JF 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JI        TCGA-OR-A5JK        TCGA-OR-A5JL        TCGA-OR-A5JP 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JQ        TCGA-OR-A5JR        TCGA-OR-A5JT        TCGA-OR-A5JV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JX        TCGA-OR-A5JY        TCGA-OR-A5K2 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5K4        TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5K9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KO        TCGA-OR-A5KT        TCGA-OR-A5KU        TCGA-OR-A5KV 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5L3 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5L4        TCGA-OR-A5L5        TCGA-OR-A5L6        TCGA-OR-A5L9 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LA        TCGA-OR-A5LB        TCGA-OR-A5LC        TCGA-OR-A5LD 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LJ        TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 
       TCGA-OR-A5LP        TCGA-OR-A5LR        TCGA-P6-A5OF        TCGA-PA-A5YG 
"TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" "TMEM189 WILD-TYPE" 

Clustering(91) Variable = CRIPAK MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        2      4      1      3
  CRIPAK WILD-TYPE     19     16      9      6
D91V1, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               19
  CLUS_2              4               16
  CLUS_3              1                9
  CLUS_4              3                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CRIPAK MUTATED        2      1      2      2      2
  CRIPAK WILD-TYPE     11      7     12     11      5
D91V2, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               11
  CLUS_2              1                7
  CLUS_3              2               12
  CLUS_4              2               11
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V3, binary
                  cls
clus                0  1
  CRIPAK MUTATED    1  3
  CRIPAK WILD-TYPE 12 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      1    3
  CRIPAK WILD-TYPE   12   12
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1               12
  CLUS_2              3               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CRIPAK MUTATED        1      2      1      0      0      0      0      0
  CRIPAK WILD-TYPE      4      4      4      3      3      1      3      2
D91V4, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1                4
  CLUS_2              2                4
  CLUS_3              1                4
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              0                1
  CLUS_7              0                3
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        2      0      3      4
  CRIPAK WILD-TYPE     14      8     11     12
D91V5, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               14
  CLUS_2              0                8
  CLUS_3              3               11
  CLUS_4              4               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        2      2      1      4
  CRIPAK WILD-TYPE     14     14      3     14
D91V6, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               14
  CLUS_3              1                3
  CLUS_4              4               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        5      1      3
  CRIPAK WILD-TYPE     21     10     15
D91V7, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              5               21
  CLUS_2              1               10
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CRIPAK MUTATED        1      4      3      1      0
  CRIPAK WILD-TYPE     12     14      5     13      2
D91V8, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               14
  CLUS_3              3                5
  CLUS_4              1               13
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        5      1      3
  CRIPAK WILD-TYPE     16     13     16
D91V9, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              5               16
  CLUS_2              1               13
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        5      4      0
  CRIPAK WILD-TYPE     25     12      8
D91V10, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              5               25
  CLUS_2              4               12
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(92) Variable = PDCD6 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDCD6 MUTATED        0      1      1      1
  PDCD6 WILD-TYPE     21     19      9      8
D92V1, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             0              21
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PDCD6 MUTATED        1      0      0      1      1
  PDCD6 WILD-TYPE     12      8     14     12      6
D92V2, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             0              14
  CLUS_4             1              12
  CLUS_5             1               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V3, binary
                 cls
clus               0  1
  PDCD6 MUTATED    1  0
  PDCD6 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD6 MUTATED      1    0
  PDCD6 WILD-TYPE   12   15
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PDCD6 MUTATED        0      0      0      0      0      1      0      0
  PDCD6 WILD-TYPE      5      6      5      3      3      0      3      2
D92V4, multiclass
[1] "Remove cluster labels:" "PDCD6 MUTATED"         
clus
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JT 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDCD6 MUTATED        0      0      1      1
  PDCD6 WILD-TYPE     16      8     13     15
D92V5, multiclass
[1] "Remove cluster labels:" "PDCD6 MUTATED"         
clus
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JP      TCGA-OR-A5JQ 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDCD6 MUTATED        0      0      0      2
  PDCD6 WILD-TYPE     16     16      4     16
D92V6, multiclass
[1] "Remove cluster labels:" "PDCD6 MUTATED"         
clus
  PDCD6 MUTATED PDCD6 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JP      TCGA-OR-A5JQ 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" "PDCD6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PDCD6 MUTATED        2      0      1
  PDCD6 WILD-TYPE     24     11     17
D92V7, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             0              11
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PDCD6 MUTATED        1      1      1      0      0
  PDCD6 WILD-TYPE     12     17      7     14      2
D92V8, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              17
  CLUS_3             1               7
  CLUS_4             0              14
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PDCD6 MUTATED        1      1      1
  PDCD6 WILD-TYPE     20     13     18
D92V9, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              13
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PDCD6 MUTATED        2      1      0
  PDCD6 WILD-TYPE     28     15      8
D92V10, multiclass
        clus
vv       PDCD6 MUTATED PDCD6 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(93) Variable = MAP7 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP7 MUTATED        2      1      0      0
  MAP7 WILD-TYPE     19     19     10      9
D93V1, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            1             19
  CLUS_3            0             10
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAP7 MUTATED        1      0      0      1      1
  MAP7 WILD-TYPE     12      8     14     12      6
D93V2, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0              8
  CLUS_3            0             14
  CLUS_4            1             12
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V3, binary
                cls
clus              0  1
  MAP7 MUTATED    1  0
  MAP7 WILD-TYPE 12 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      1    0
  MAP7 WILD-TYPE   12   15
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0             15
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MAP7 MUTATED        0      0      0      0      0      0      1      0
  MAP7 WILD-TYPE      5      6      5      3      3      1      2      2
D93V4, multiclass
[1] "Remove cluster labels:" "MAP7 MUTATED"          
clus
  MAP7 MUTATED MAP7 WILD-TYPE 
             1             27 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
    TCGA-OR-A5LP     TCGA-PA-A5YG     TCGA-PK-A5H8 
"MAP7 WILD-TYPE" "MAP7 WILD-TYPE" "MAP7 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP7 MUTATED        1      0      1      1
  MAP7 WILD-TYPE     15      8     13     15
D93V5, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0              8
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP7 MUTATED        1      0      0      2
  MAP7 WILD-TYPE     15     16      4     16
D93V6, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0             16
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAP7 MUTATED        1      0      2
  MAP7 WILD-TYPE     25     11     16
D93V7, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            0             11
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAP7 MUTATED        0      1      1      1      0
  MAP7 WILD-TYPE     13     17      7     13      2
D93V8, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1             17
  CLUS_3            1              7
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAP7 MUTATED        1      1      1
  MAP7 WILD-TYPE     20     13     18
D93V9, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             13
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MAP7 MUTATED        1      1      1
  MAP7 WILD-TYPE     29     15      7
D93V10, multiclass
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  CLUS_1            1             29
  CLUS_2            1             15
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(94) Variable = NOM1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOM1 MUTATED        2      2      1      1
  NOM1 WILD-TYPE     19     18      9      8
D94V1, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            1              9
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOM1 MUTATED        1      1      1      0      2
  NOM1 WILD-TYPE     12      7     13     13      5
D94V2, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            0             13
  CLUS_5            2              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V3, binary
                cls
clus              0  1
  NOM1 MUTATED    1  1
  NOM1 WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      1    1
  NOM1 WILD-TYPE   12   14
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NOM1 MUTATED        1      0      1      0      0      0      0      0
  NOM1 WILD-TYPE      4      6      4      3      3      1      3      2
D94V4, multiclass
[1] "Remove cluster labels:" "NOM1 MUTATED"          
clus
  NOM1 MUTATED NOM1 WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5LD 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOM1 MUTATED        2      0      1      2
  NOM1 WILD-TYPE     14      8     13     14
D94V5, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0              8
  CLUS_3            1             13
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOM1 MUTATED        2      1      0      2
  NOM1 WILD-TYPE     14     15      4     16
D94V6, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             15
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NOM1 MUTATED        2      1      2
  NOM1 WILD-TYPE     24     10     16
D94V7, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            1             10
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOM1 MUTATED        2      1      1      1      0
  NOM1 WILD-TYPE     11     17      7     13      2
D94V8, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1             17
  CLUS_3            1              7
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NOM1 MUTATED        3      0      2
  NOM1 WILD-TYPE     18     14     17
D94V9, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            3             18
  CLUS_2            0             14
  CLUS_3            2             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NOM1 MUTATED        3      1      1
  NOM1 WILD-TYPE     27     15      7
D94V10, multiclass
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  CLUS_1            3             27
  CLUS_2            1             15
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(95) Variable = SHOX2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHOX2 MUTATED        2      0      0      1
  SHOX2 WILD-TYPE     19     20     10      8
D95V1, multiclass
        clus
vv       SHOX2 MUTATED SHOX2 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              20
  CLUS_3             0              10
  CLUS_4             1               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHOX2 MUTATED        1      0      0      1      0
  SHOX2 WILD-TYPE     12      8     14     12      7
D95V2, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" 
D95V3, binary
                 cls
clus               0  1
  SHOX2 MUTATED    1  0
  SHOX2 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHOX2 MUTATED      1    0
  SHOX2 WILD-TYPE   12   15
        clus
vv       SHOX2 MUTATED SHOX2 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SHOX2 MUTATED        0      0      1      0      0      0      0      0
  SHOX2 WILD-TYPE      5      6      4      3      3      1      3      2
D95V4, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHOX2 MUTATED        1      0      0      1
  SHOX2 WILD-TYPE     15      8     14     15
D95V5, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KW 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHOX2 MUTATED        1      0      0      1
  SHOX2 WILD-TYPE     15     16      4     17
D95V6, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KW 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SHOX2 MUTATED        1      0      1
  SHOX2 WILD-TYPE     25     11     17
D95V7, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHOX2 MUTATED        0      1      0      1      0
  SHOX2 WILD-TYPE     13     17      8     13      2
D95V8, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SHOX2 MUTATED        1      0      1
  SHOX2 WILD-TYPE     20     14     18
D95V9, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SHOX2 MUTATED        1      1      0
  SHOX2 WILD-TYPE     29     15      8
D95V10, multiclass
[1] "Remove cluster labels:" "SHOX2 MUTATED"         
clus
  SHOX2 MUTATED SHOX2 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K8 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5HB 
"SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" "SHOX2 WILD-TYPE" 

Clustering(96) Variable = HSD17B1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HSD17B1 MUTATED        2      2      0      0
  HSD17B1 WILD-TYPE     19     18     10      9
D96V1, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               2                18
  CLUS_3               0                10
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HSD17B1 MUTATED        0      0      0      3      1
  HSD17B1 WILD-TYPE     13      8     14     10      6
D96V2, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               0                 8
  CLUS_3               0                14
  CLUS_4               3                10
  CLUS_5               1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V3, binary
                   cls
clus                 0  1
  HSD17B1 MUTATED    2  1
  HSD17B1 WILD-TYPE 11 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B1 MUTATED      2    1
  HSD17B1 WILD-TYPE   11   14
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  HSD17B1 MUTATED        0      0      1      0      1      0      1      0
  HSD17B1 WILD-TYPE      5      6      4      3      2      1      2      2
D96V4, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 6
  CLUS_3               1                 4
  CLUS_4               0                 3
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               1                 2
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HSD17B1 MUTATED        2      0      1      1
  HSD17B1 WILD-TYPE     14      8     13     15
D96V5, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                 8
  CLUS_3               1                13
  CLUS_4               1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HSD17B1 MUTATED        0      0      2      2
  HSD17B1 WILD-TYPE     16     16      2     16
D96V6, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                16
  CLUS_3               2                 2
  CLUS_4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  HSD17B1 MUTATED        2      1      1
  HSD17B1 WILD-TYPE     24     10     17
D96V7, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               1                10
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HSD17B1 MUTATED        1      1      0      2      0
  HSD17B1 WILD-TYPE     12     17      8     12      2
D96V8, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                17
  CLUS_3               0                 8
  CLUS_4               2                12
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  HSD17B1 MUTATED        2      0      2
  HSD17B1 WILD-TYPE     19     14     17
D96V9, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               0                14
  CLUS_3               2                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  HSD17B1 MUTATED        2      1      1
  HSD17B1 WILD-TYPE     28     15      7
D96V10, multiclass
        clus
vv       HSD17B1 MUTATED HSD17B1 WILD-TYPE
  CLUS_1               2                28
  CLUS_2               1                15
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(97) Variable = PRKAR1A MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKAR1A MUTATED        2      1      2      1
  PRKAR1A WILD-TYPE     19     19      8      8
D97V1, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               2                19
  CLUS_2               1                19
  CLUS_3               2                 8
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRKAR1A MUTATED        1      1      2      1      1
  PRKAR1A WILD-TYPE     12      7     12     12      6
D97V2, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                 7
  CLUS_3               2                12
  CLUS_4               1                12
  CLUS_5               1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V3, binary
                   cls
clus                 0  1
  PRKAR1A MUTATED    1  3
  PRKAR1A WILD-TYPE 12 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1A MUTATED      1    3
  PRKAR1A WILD-TYPE   12   12
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PRKAR1A MUTATED        1      2      0      0      1      0      0      0
  PRKAR1A WILD-TYPE      4      4      5      3      2      1      3      2
D97V4, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               2                 4
  CLUS_3               0                 5
  CLUS_4               0                 3
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKAR1A MUTATED        2      1      3      0
  PRKAR1A WILD-TYPE     14      7     11     16
D97V5, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                 7
  CLUS_3               3                11
  CLUS_4               0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKAR1A MUTATED        1      3      1      1
  PRKAR1A WILD-TYPE     15     13      3     17
D97V6, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               1                15
  CLUS_2               3                13
  CLUS_3               1                 3
  CLUS_4               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PRKAR1A MUTATED        5      1      0
  PRKAR1A WILD-TYPE     21     10     18
D97V7, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               5                21
  CLUS_2               1                10
  CLUS_3               0                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRKAR1A MUTATED        3      1      1      1      0
  PRKAR1A WILD-TYPE     10     17      7     13      2
D97V8, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                17
  CLUS_3               1                 7
  CLUS_4               1                13
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PRKAR1A MUTATED        5      1      0
  PRKAR1A WILD-TYPE     16     13     19
D97V9, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               5                16
  CLUS_2               1                13
  CLUS_3               0                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PRKAR1A MUTATED        5      1      0
  PRKAR1A WILD-TYPE     25     15      8
D97V10, multiclass
        clus
vv       PRKAR1A MUTATED PRKAR1A WILD-TYPE
  CLUS_1               5                25
  CLUS_2               1                15
  CLUS_3               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(98) Variable = KRTAP5-5 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        1      1      1      0
  KRTAP5-5 WILD-TYPE     20     19      9      9
D98V1, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 20
  CLUS_2                1                 19
  CLUS_3                1                  9
  CLUS_4                0                  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                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRTAP5-5 MUTATED        1      0      1      0      0
  KRTAP5-5 WILD-TYPE     12      8     13     13      7
D98V2, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 53 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JF         TCGA-OR-A5JI         TCGA-OR-A5JK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JL         TCGA-OR-A5JP         TCGA-OR-A5JQ 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5JT         TCGA-OR-A5JV 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JW         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KT 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5L3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L4         TCGA-OR-A5L5         TCGA-OR-A5L6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LA         TCGA-OR-A5LC 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LR         TCGA-P6-A5OF         TCGA-PA-A5YG 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5H8         TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
D98V3, binary
                    cls
clus                  0  1
  KRTAP5-5 MUTATED    0  0
  KRTAP5-5 WILD-TYPE 13 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      0    0
  KRTAP5-5 WILD-TYPE   13   15
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRTAP5-5 MUTATED        0      0      0      0      0      0      0      0
  KRTAP5-5 WILD-TYPE      5      6      5      3      3      1      3      2
D98V4, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        1      1      0      0
  KRTAP5-5 WILD-TYPE     15      7     14     16
D98V5, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 52 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J5         TCGA-OR-A5J6         TCGA-OR-A5J7 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J8         TCGA-OR-A5JA         TCGA-OR-A5JB 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JC         TCGA-OR-A5JD         TCGA-OR-A5JF 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JI         TCGA-OR-A5JK         TCGA-OR-A5JL 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JP         TCGA-OR-A5JQ         TCGA-OR-A5JR 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JX         TCGA-OR-A5JY         TCGA-OR-A5K2 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K4         TCGA-OR-A5K5         TCGA-OR-A5K8 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KO         TCGA-OR-A5KT         TCGA-OR-A5KU 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KX 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KZ         TCGA-OR-A5L3         TCGA-OR-A5L4 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L5         TCGA-OR-A5L6         TCGA-OR-A5L9 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LA         TCGA-OR-A5LC         TCGA-OR-A5LD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LJ         TCGA-OR-A5LK         TCGA-OR-A5LL 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LR 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-P6-A5OF         TCGA-PA-A5YG         TCGA-PK-A5H8 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        1      1      0      0
  KRTAP5-5 WILD-TYPE     15     15      4     18
D98V6, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 52 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J5         TCGA-OR-A5J6         TCGA-OR-A5J7 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J8         TCGA-OR-A5JA         TCGA-OR-A5JB 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JC         TCGA-OR-A5JD         TCGA-OR-A5JF 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JI         TCGA-OR-A5JK         TCGA-OR-A5JL 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JP         TCGA-OR-A5JQ         TCGA-OR-A5JR 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JX         TCGA-OR-A5JY         TCGA-OR-A5K2 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K4         TCGA-OR-A5K5         TCGA-OR-A5K8 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KO         TCGA-OR-A5KT         TCGA-OR-A5KU 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KX 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KZ         TCGA-OR-A5L3         TCGA-OR-A5L4 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L5         TCGA-OR-A5L6         TCGA-OR-A5L9 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LA         TCGA-OR-A5LC         TCGA-OR-A5LD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LJ         TCGA-OR-A5LK         TCGA-OR-A5LL 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LR 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-P6-A5OF         TCGA-PA-A5YG         TCGA-PK-A5H8 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP5-5 MUTATED        2      0      0
  KRTAP5-5 WILD-TYPE     24     11     18
D98V7, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 53 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JF         TCGA-OR-A5JI         TCGA-OR-A5JK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JL         TCGA-OR-A5JP         TCGA-OR-A5JQ 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5JT         TCGA-OR-A5JV 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JW         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KT 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5L3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L4         TCGA-OR-A5L5         TCGA-OR-A5L6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LA         TCGA-OR-A5LC 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LR         TCGA-P6-A5OF         TCGA-PA-A5YG 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5H8         TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRTAP5-5 MUTATED        0      0      0      1      1
  KRTAP5-5 WILD-TYPE     13     18      8     13      1
D98V8, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 53 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JF         TCGA-OR-A5JI         TCGA-OR-A5JK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JL         TCGA-OR-A5JP         TCGA-OR-A5JQ 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5JT         TCGA-OR-A5JV 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JW         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KT 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5L3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L4         TCGA-OR-A5L5         TCGA-OR-A5L6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LA         TCGA-OR-A5LC 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LR         TCGA-P6-A5OF         TCGA-PA-A5YG 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5H8         TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP5-5 MUTATED        1      1      0
  KRTAP5-5 WILD-TYPE     20     13     19
D98V9, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 52 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JF         TCGA-OR-A5JI         TCGA-OR-A5JK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JL         TCGA-OR-A5JP         TCGA-OR-A5JQ 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5JT         TCGA-OR-A5JV 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JW         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KT 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5L3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L4         TCGA-OR-A5L5         TCGA-OR-A5L6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LA         TCGA-OR-A5LC 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LR         TCGA-P6-A5OF         TCGA-PA-A5YG 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP5-5 MUTATED        2      0      0
  KRTAP5-5 WILD-TYPE     28     16      8
D98V10, multiclass
[1] "Remove cluster labels:" "KRTAP5-5 MUTATED"      
clus
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                 52 
        TCGA-OR-A5J1         TCGA-OR-A5J2         TCGA-OR-A5J3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J5         TCGA-OR-A5J6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5J7         TCGA-OR-A5J8         TCGA-OR-A5JA 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JD 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JF         TCGA-OR-A5JI         TCGA-OR-A5JK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JL         TCGA-OR-A5JP         TCGA-OR-A5JQ 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5JT         TCGA-OR-A5JV 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5JW         TCGA-OR-A5JX         TCGA-OR-A5JY 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K4         TCGA-OR-A5K5 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5K8         TCGA-OR-A5KO         TCGA-OR-A5KT 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5KX         TCGA-OR-A5KZ         TCGA-OR-A5L3 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L4         TCGA-OR-A5L5         TCGA-OR-A5L6 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LA         TCGA-OR-A5LC 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LD         TCGA-OR-A5LJ         TCGA-OR-A5LK 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LO         TCGA-OR-A5LP 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-OR-A5LR         TCGA-P6-A5OF         TCGA-PA-A5YG 
"KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" "KRTAP5-5 WILD-TYPE" 
        TCGA-PK-A5HB 
"KRTAP5-5 WILD-TYPE" 

Clustering(99) Variable = DLEU7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DLEU7 MUTATED        2      0      1      0
  DLEU7 WILD-TYPE     19     20      9      9
D99V1, multiclass
        clus
vv       DLEU7 MUTATED DLEU7 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              20
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DLEU7 MUTATED        0      0      1      0      0
  DLEU7 WILD-TYPE     13      8     13     13      7
D99V2, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              54 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5H8      TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
D99V3, binary
                 cls
clus               0  1
  DLEU7 MUTATED    0  1
  DLEU7 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEU7 MUTATED      0    1
  DLEU7 WILD-TYPE   13   14
        clus
vv       DLEU7 MUTATED DLEU7 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  DLEU7 MUTATED        0      1      0      0      0      0      0      0
  DLEU7 WILD-TYPE      5      5      5      3      3      1      3      2
D99V4, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              27 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JP      TCGA-OR-A5JR 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5KO      TCGA-OR-A5KU 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-PA-A5YG      TCGA-PK-A5H8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DLEU7 MUTATED        0      0      1      0
  DLEU7 WILD-TYPE     16      8     13     16
D99V5, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DLEU7 MUTATED        0      1      0      0
  DLEU7 WILD-TYPE     16     15      4     18
D99V6, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8      TCGA-OR-A5JA 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JP 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9      TCGA-OR-A5KO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DLEU7 MUTATED        0      1      0
  DLEU7 WILD-TYPE     26     10     18
D99V7, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              54 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5H8      TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DLEU7 MUTATED        0      1      0      0      0
  DLEU7 WILD-TYPE     13     17      8     14      2
D99V8, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              54 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5H8      TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DLEU7 MUTATED        0      1      0
  DLEU7 WILD-TYPE     21     13     19
D99V9, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DLEU7 MUTATED        0      1      0
  DLEU7 WILD-TYPE     30     15      8
D99V10, multiclass
[1] "Remove cluster labels:" "DLEU7 MUTATED"         
clus
  DLEU7 MUTATED DLEU7 WILD-TYPE 
              1              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J7      TCGA-OR-A5J8 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JF      TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JP      TCGA-OR-A5JQ      TCGA-OR-A5JR      TCGA-OR-A5JT 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX      TCGA-OR-A5JY 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5      TCGA-OR-A5K9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KO      TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5KW      TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5L4      TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LA      TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LJ      TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-OR-A5LP      TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG 
"DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" "DLEU7 WILD-TYPE" 
     TCGA-PK-A5HB 
"DLEU7 WILD-TYPE" 

Clustering(100) Variable = FEZ2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FEZ2 MUTATED        0      2      1      0
  FEZ2 WILD-TYPE     21     18      9      9
D100V1, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             21
  CLUS_2            2             18
  CLUS_3            1              9
  CLUS_4            0              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FEZ2 MUTATED        0      1      1      0      1
  FEZ2 WILD-TYPE     13      7     13     13      6
D100V2, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            0             13
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V3, binary
                cls
clus              0  1
  FEZ2 MUTATED    0  1
  FEZ2 WILD-TYPE 13 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FEZ2 MUTATED      0    1
  FEZ2 WILD-TYPE   13   14
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FEZ2 MUTATED        1      0      0      0      0      0      0      0
  FEZ2 WILD-TYPE      4      6      5      3      3      1      3      2
D100V4, multiclass
[1] "Remove cluster labels:" "FEZ2 MUTATED"          
clus
  FEZ2 MUTATED FEZ2 WILD-TYPE 
             1             27 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JA     TCGA-OR-A5JP     TCGA-OR-A5JR 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5JT     TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5K4     TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5KU     TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5LD     TCGA-OR-A5LK     TCGA-OR-A5LL     TCGA-OR-A5LO 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
    TCGA-OR-A5LP     TCGA-PA-A5YG     TCGA-PK-A5H8 
"FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" "FEZ2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FEZ2 MUTATED        0      1      0      2
  FEZ2 WILD-TYPE     16      7     14     14
D100V5, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            0             14
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FEZ2 MUTATED        1      0      0      2
  FEZ2 WILD-TYPE     15     16      4     16
D100V6, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0             16
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FEZ2 MUTATED        0      1      2
  FEZ2 WILD-TYPE     26     10     16
D100V7, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            1             10
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FEZ2 MUTATED        0      1      1      1      0
  FEZ2 WILD-TYPE     13     17      7     13      2
D100V8, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1             17
  CLUS_3            1              7
  CLUS_4            1             13
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FEZ2 MUTATED        2      0      1
  FEZ2 WILD-TYPE     19     14     18
D100V9, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            0             14
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FEZ2 MUTATED        1      1      1
  FEZ2 WILD-TYPE     29     15      7
D100V10, multiclass
        clus
vv       FEZ2 MUTATED FEZ2 WILD-TYPE
  CLUS_1            1             29
  CLUS_2            1             15
  CLUS_3            1              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(101) Variable = RASIP1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RASIP1 MUTATED        1      3      2      0
  RASIP1 WILD-TYPE     20     17      8      9
D101V1, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              3               17
  CLUS_3              2                8
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RASIP1 MUTATED        2      2      2      0      0
  RASIP1 WILD-TYPE     11      6     12     13      7
D101V2, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2                6
  CLUS_3              2               12
  CLUS_4              0               13
  CLUS_5              0                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V3, binary
                  cls
clus                0  1
  RASIP1 MUTATED    1  1
  RASIP1 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASIP1 MUTATED      1    1
  RASIP1 WILD-TYPE   12   14
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RASIP1 MUTATED        1      0      0      0      1      0      0      0
  RASIP1 WILD-TYPE      4      6      5      3      2      1      3      2
D101V4, multiclass
[1] "Remove cluster labels:" "RASIP1 MUTATED"        
clus
  RASIP1 MUTATED RASIP1 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"RASIP1 WILD-TYPE" "RASIP1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RASIP1 MUTATED        2      3      1      0
  RASIP1 WILD-TYPE     14      5     13     16
D101V5, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              3                5
  CLUS_3              1               13
  CLUS_4              0               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RASIP1 MUTATED        3      3      0      0
  RASIP1 WILD-TYPE     13     13      4     18
D101V6, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              3               13
  CLUS_3              0                4
  CLUS_4              0               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RASIP1 MUTATED        3      3      0
  RASIP1 WILD-TYPE     23      8     18
D101V7, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              3               23
  CLUS_2              3                8
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RASIP1 MUTATED        1      2      0      3      0
  RASIP1 WILD-TYPE     12     16      8     11      2
D101V8, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              2               16
  CLUS_3              0                8
  CLUS_4              3               11
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RASIP1 MUTATED        2      3      1
  RASIP1 WILD-TYPE     19     11     18
D101V9, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              3               11
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RASIP1 MUTATED        4      2      0
  RASIP1 WILD-TYPE     26     14      8
D101V10, multiclass
        clus
vv       RASIP1 MUTATED RASIP1 WILD-TYPE
  CLUS_1              4               26
  CLUS_2              2               14
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(102) Variable = JMJD4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  JMJD4 MUTATED        1      1      1      0
  JMJD4 WILD-TYPE     20     19      9      9
D102V1, multiclass
        clus
vv       JMJD4 MUTATED JMJD4 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  JMJD4 MUTATED        2      0      0      0      0
  JMJD4 WILD-TYPE     11      8     14     13      7
D102V2, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" 
D102V3, binary
                 cls
clus               0  1
  JMJD4 MUTATED    0  2
  JMJD4 WILD-TYPE 13 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD4 MUTATED      0    2
  JMJD4 WILD-TYPE   13   13
        clus
vv       JMJD4 MUTATED JMJD4 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  JMJD4 MUTATED        0      0      0      2      0      0      0      0
  JMJD4 WILD-TYPE      5      6      5      1      3      1      3      2
D102V4, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J8 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4      TCGA-OR-A5K5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  JMJD4 MUTATED        2      0      0      0
  JMJD4 WILD-TYPE     14      8     14     16
D102V5, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JI 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ      TCGA-OR-A5JR 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  JMJD4 MUTATED        2      0      0      0
  JMJD4 WILD-TYPE     14     16      4     18
D102V6, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA      TCGA-OR-A5JB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF      TCGA-OR-A5JI 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ      TCGA-OR-A5JR 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JX 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4      TCGA-OR-A5K5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO      TCGA-OR-A5KT 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW      TCGA-OR-A5KX 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4      TCGA-OR-A5L5 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA      TCGA-OR-A5LB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ      TCGA-OR-A5LK 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP      TCGA-OR-A5LR 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8      TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  JMJD4 MUTATED        2      0      0
  JMJD4 WILD-TYPE     24     11     18
D102V7, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  JMJD4 MUTATED        0      0      0      2      0
  JMJD4 WILD-TYPE     13     18      8     12      2
D102V8, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              53 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5H8 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  JMJD4 MUTATED        1      1      0
  JMJD4 WILD-TYPE     20     13     19
D102V9, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  JMJD4 MUTATED        2      0      0
  JMJD4 WILD-TYPE     28     16      8
D102V10, multiclass
[1] "Remove cluster labels:" "JMJD4 MUTATED"         
clus
  JMJD4 MUTATED JMJD4 WILD-TYPE 
              2              52 
     TCGA-OR-A5J1      TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5J5      TCGA-OR-A5J6      TCGA-OR-A5J8      TCGA-OR-A5JA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JB      TCGA-OR-A5JC      TCGA-OR-A5JD      TCGA-OR-A5JF 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JI      TCGA-OR-A5JK      TCGA-OR-A5JL      TCGA-OR-A5JQ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV      TCGA-OR-A5JW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5JX      TCGA-OR-A5JY      TCGA-OR-A5K2      TCGA-OR-A5K4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5K9      TCGA-OR-A5KO 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KT      TCGA-OR-A5KU      TCGA-OR-A5KV      TCGA-OR-A5KW 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5L3      TCGA-OR-A5L4 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5L5      TCGA-OR-A5L6      TCGA-OR-A5L9      TCGA-OR-A5LA 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LB      TCGA-OR-A5LC      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 
     TCGA-OR-A5LR      TCGA-P6-A5OF      TCGA-PA-A5YG      TCGA-PK-A5HB 
"JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" "JMJD4 WILD-TYPE" 

Clustering(103) Variable = COQ2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COQ2 MUTATED        1      1      1      2
  COQ2 WILD-TYPE     20     19      9      7
D103V1, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             19
  CLUS_3            1              9
  CLUS_4            2              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  COQ2 MUTATED        0      1      1      1      1
  COQ2 WILD-TYPE     13      7     13     12      6
D103V2, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1              7
  CLUS_3            1             13
  CLUS_4            1             12
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V3, binary
                cls
clus              0  1
  COQ2 MUTATED    1  1
  COQ2 WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ2 MUTATED      1    1
  COQ2 WILD-TYPE   12   14
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  COQ2 MUTATED        0      1      1      0      0      0      0      0
  COQ2 WILD-TYPE      5      5      4      3      3      1      3      2
D103V4, multiclass
[1] "Remove cluster labels:" "COQ2 MUTATED"          
clus
  COQ2 MUTATED COQ2 WILD-TYPE 
             2             26 
    TCGA-OR-A5J2     TCGA-OR-A5J3     TCGA-OR-A5J6     TCGA-OR-A5J7 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-OR-A5J8     TCGA-OR-A5JP     TCGA-OR-A5JR     TCGA-OR-A5JT 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-OR-A5JV     TCGA-OR-A5JW     TCGA-OR-A5JY     TCGA-OR-A5K4 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-OR-A5K5     TCGA-OR-A5K8     TCGA-OR-A5KO     TCGA-OR-A5KU 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-OR-A5KW     TCGA-OR-A5KX     TCGA-OR-A5KZ     TCGA-OR-A5LD 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-OR-A5LJ     TCGA-OR-A5LL     TCGA-OR-A5LO     TCGA-OR-A5LP 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
    TCGA-PA-A5YG     TCGA-PK-A5H8 
"COQ2 WILD-TYPE" "COQ2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COQ2 MUTATED        0      1      2      1
  COQ2 WILD-TYPE     16      7     12     15
D103V5, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1              7
  CLUS_3            2             12
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COQ2 MUTATED        0      2      0      2
  COQ2 WILD-TYPE     16     14      4     16
D103V6, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            2             14
  CLUS_3            0              4
  CLUS_4            2             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  COQ2 MUTATED        2      1      1
  COQ2 WILD-TYPE     24     10     17
D103V7, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            1             10
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  COQ2 MUTATED        1      2      1      0      0
  COQ2 WILD-TYPE     12     16      7     14      2
D103V8, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             16
  CLUS_3            1              7
  CLUS_4            0             14
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  COQ2 MUTATED        2      0      2
  COQ2 WILD-TYPE     19     14     17
D103V9, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            0             14
  CLUS_3            2             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  COQ2 MUTATED        2      2      0
  COQ2 WILD-TYPE     28     14      8
D103V10, multiclass
        clus
vv       COQ2 MUTATED COQ2 WILD-TYPE
  CLUS_1            2             28
  CLUS_2            2             14
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(104) Variable = UQCRFS1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UQCRFS1 MUTATED        1      1      1      1
  UQCRFS1 WILD-TYPE     20     19      9      8
D104V1, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               1                19
  CLUS_3               1                 9
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  UQCRFS1 MUTATED        2      1      2      0      0
  UQCRFS1 WILD-TYPE     11      7     12     13      7
D104V2, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                 7
  CLUS_3               2                12
  CLUS_4               0                13
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V3, binary
                   cls
clus                 0  1
  UQCRFS1 MUTATED    0  2
  UQCRFS1 WILD-TYPE 13 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UQCRFS1 MUTATED      0    2
  UQCRFS1 WILD-TYPE   13   13
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  UQCRFS1 MUTATED        1      1      0      0      0      0      0      0
  UQCRFS1 WILD-TYPE      4      5      5      3      3      1      3      2
D104V4, multiclass
[1] "Remove cluster labels:" "UQCRFS1 MUTATED"       
clus
  UQCRFS1 MUTATED UQCRFS1 WILD-TYPE 
                2                26 
       TCGA-OR-A5J2        TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5JA        TCGA-OR-A5JP        TCGA-OR-A5JR        TCGA-OR-A5JT 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5JV        TCGA-OR-A5JW        TCGA-OR-A5JY        TCGA-OR-A5K4 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5K8        TCGA-OR-A5KO        TCGA-OR-A5KU 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5KW        TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LJ 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
       TCGA-PA-A5YG        TCGA-PK-A5H8 
"UQCRFS1 WILD-TYPE" "UQCRFS1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UQCRFS1 MUTATED        1      1      1      1
  UQCRFS1 WILD-TYPE     15      7     13     15
D104V5, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                 7
  CLUS_3               1                13
  CLUS_4               1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UQCRFS1 MUTATED        1      2      0      1
  UQCRFS1 WILD-TYPE     15     14      4     17
D104V6, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                14
  CLUS_3               0                 4
  CLUS_4               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  UQCRFS1 MUTATED        4      0      1
  UQCRFS1 WILD-TYPE     22     11     17
D104V7, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               4                22
  CLUS_2               0                11
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  UQCRFS1 MUTATED        3      0      1      1      0
  UQCRFS1 WILD-TYPE     10     18      7     13      2
D104V8, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               0                18
  CLUS_3               1                 7
  CLUS_4               1                13
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  UQCRFS1 MUTATED        2      2      1
  UQCRFS1 WILD-TYPE     19     12     18
D104V9, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               2                12
  CLUS_3               1                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  UQCRFS1 MUTATED        4      0      1
  UQCRFS1 WILD-TYPE     26     16      7
D104V10, multiclass
        clus
vv       UQCRFS1 MUTATED UQCRFS1 WILD-TYPE
  CLUS_1               4                26
  CLUS_2               0                16
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(105) Variable = C9ORF66 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C9ORF66 MUTATED        2      2      1      0
  C9ORF66 WILD-TYPE     19     18      9      9
D105V1, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               2                18
  CLUS_3               1                 9
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C9ORF66 MUTATED        1      1      1      2      0
  C9ORF66 WILD-TYPE     12      7     13     11      7
D105V2, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                 7
  CLUS_3               1                13
  CLUS_4               2                11
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V3, binary
                   cls
clus                 0  1
  C9ORF66 MUTATED    1  1
  C9ORF66 WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF66 MUTATED      1    1
  C9ORF66 WILD-TYPE   12   14
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C9ORF66 MUTATED        0      0      0      0      1      1      0      0
  C9ORF66 WILD-TYPE      5      6      5      3      2      0      3      2
D105V4, multiclass
[1] "Remove cluster labels:" "C9ORF66 MUTATED"       
clus
  C9ORF66 MUTATED C9ORF66 WILD-TYPE 
                2                26 
       TCGA-OR-A5J2        TCGA-OR-A5J3        TCGA-OR-A5J6        TCGA-OR-A5J7 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5JA        TCGA-OR-A5JP        TCGA-OR-A5JT        TCGA-OR-A5JV 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5JW        TCGA-OR-A5JY        TCGA-OR-A5K4        TCGA-OR-A5K5 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5K8        TCGA-OR-A5KO        TCGA-OR-A5KU        TCGA-OR-A5KW 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
       TCGA-PA-A5YG        TCGA-PK-A5H8 
"C9ORF66 WILD-TYPE" "C9ORF66 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C9ORF66 MUTATED        2      1      1      1
  C9ORF66 WILD-TYPE     14      7     13     15
D105V5, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                 7
  CLUS_3               1                13
  CLUS_4               1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C9ORF66 MUTATED        1      2      1      1
  C9ORF66 WILD-TYPE     15     14      3     17
D105V6, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                14
  CLUS_3               1                 3
  CLUS_4               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C9ORF66 MUTATED        2      2      1
  C9ORF66 WILD-TYPE     24      9     17
D105V7, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               2                 9
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C9ORF66 MUTATED        1      2      0      2      0
  C9ORF66 WILD-TYPE     12     16      8     12      2
D105V8, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                 8
  CLUS_4               2                12
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C9ORF66 MUTATED        2      0      3
  C9ORF66 WILD-TYPE     19     14     16
D105V9, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               0                14
  CLUS_3               3                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C9ORF66 MUTATED        2      2      1
  C9ORF66 WILD-TYPE     28     14      7
D105V10, multiclass
        clus
vv       C9ORF66 MUTATED C9ORF66 WILD-TYPE
  CLUS_1               2                28
  CLUS_2               2                14
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(106) Variable = POLRMT MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POLRMT MUTATED        1      1      0      2
  POLRMT WILD-TYPE     20     19     10      7
D106V1, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              1               20
  CLUS_2              1               19
  CLUS_3              0               10
  CLUS_4              2                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  POLRMT MUTATED        0      0      0      2      2
  POLRMT WILD-TYPE     13      8     14     11      5
D106V2, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              0               13
  CLUS_2              0                8
  CLUS_3              0               14
  CLUS_4              2               11
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V3, binary
                  cls
clus                0  1
  POLRMT MUTATED    3  0
  POLRMT WILD-TYPE 10 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLRMT MUTATED      3    0
  POLRMT WILD-TYPE   10   15
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              3               10
  CLUS_2              0               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  POLRMT MUTATED        0      0      2      0      0      0      1      0
  POLRMT WILD-TYPE      5      6      3      3      3      1      2      2
D106V4, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              0                5
  CLUS_2              0                6
  CLUS_3              2                3
  CLUS_4              0                3
  CLUS_5              0                3
  CLUS_6              0                1
  CLUS_7              1                2
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POLRMT MUTATED        0      0      2      2
  POLRMT WILD-TYPE     16      8     12     14
D106V5, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              0               16
  CLUS_2              0                8
  CLUS_3              2               12
  CLUS_4              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POLRMT MUTATED        0      0      0      4
  POLRMT WILD-TYPE     16     16      4     14
D106V6, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              0               16
  CLUS_2              0               16
  CLUS_3              0                4
  CLUS_4              4               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLRMT MUTATED        1      0      3
  POLRMT WILD-TYPE     25     11     15
D106V7, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              1               25
  CLUS_2              0               11
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  POLRMT MUTATED        0      3      1      0      0
  POLRMT WILD-TYPE     13     15      7     14      2
D106V8, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              0               13
  CLUS_2              3               15
  CLUS_3              1                7
  CLUS_4              0               14
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLRMT MUTATED        1      0      3
  POLRMT WILD-TYPE     20     14     16
D106V9, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              1               20
  CLUS_2              0               14
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLRMT MUTATED        1      3      0
  POLRMT WILD-TYPE     29     13      8
D106V10, multiclass
        clus
vv       POLRMT MUTATED POLRMT WILD-TYPE
  CLUS_1              1               29
  CLUS_2              3               13
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(107) Variable = ADAMTS7 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAMTS7 MUTATED        0      3      0      1
  ADAMTS7 WILD-TYPE     21     17     10      8
D107V1, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                21
  CLUS_2               3                17
  CLUS_3               0                10
  CLUS_4               1                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ADAMTS7 MUTATED        0      0      1      2      1
  ADAMTS7 WILD-TYPE     13      8     13     11      6
D107V2, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               0                 8
  CLUS_3               1                13
  CLUS_4               2                11
  CLUS_5               1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V3, binary
                   cls
clus                 0  1
  ADAMTS7 MUTATED    3  0
  ADAMTS7 WILD-TYPE 10 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS7 MUTATED      3    0
  ADAMTS7 WILD-TYPE   10   15
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               3                10
  CLUS_2               0                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ADAMTS7 MUTATED        0      0      2      0      1      0      0      0
  ADAMTS7 WILD-TYPE      5      6      3      3      2      1      3      2
D107V4, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 6
  CLUS_3               2                 3
  CLUS_4               0                 3
  CLUS_5               1                 2
  CLUS_6               0                 1
  CLUS_7               0                 3
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAMTS7 MUTATED        0      1      0      3
  ADAMTS7 WILD-TYPE     16      7     14     13
D107V5, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                 7
  CLUS_3               0                14
  CLUS_4               3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ADAMTS7 MUTATED        0      1      0      3
  ADAMTS7 WILD-TYPE     16     15      4     15
D107V6, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                15
  CLUS_3               0                 4
  CLUS_4               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ADAMTS7 MUTATED        0      1      3
  ADAMTS7 WILD-TYPE     26     10     15
D107V7, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                26
  CLUS_2               1                10
  CLUS_3               3                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ADAMTS7 MUTATED        0      3      1      0      0
  ADAMTS7 WILD-TYPE     13     15      7     14      2
D107V8, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               1                 7
  CLUS_4               0                14
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ADAMTS7 MUTATED        0      1      3
  ADAMTS7 WILD-TYPE     21     13     16
D107V9, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                21
  CLUS_2               1                13
  CLUS_3               3                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ADAMTS7 MUTATED        0      3      1
  ADAMTS7 WILD-TYPE     30     13      7
D107V10, multiclass
        clus
vv       ADAMTS7 MUTATED ADAMTS7 WILD-TYPE
  CLUS_1               0                30
  CLUS_2               3                13
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(108) Variable = BTNL9 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTNL9 MUTATED        2      1      1      0
  BTNL9 WILD-TYPE     19     19      9      9
D108V1, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              19
  CLUS_3             1               9
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BTNL9 MUTATED        0      0      3      0      0
  BTNL9 WILD-TYPE     13      8     11     13      7
D108V2, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0               8
  CLUS_3             3              11
  CLUS_4             0              13
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V3, binary
                 cls
clus               0  1
  BTNL9 MUTATED    1  1
  BTNL9 WILD-TYPE 12 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL9 MUTATED      1    1
  BTNL9 WILD-TYPE   12   14
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  BTNL9 MUTATED        0      1      0      0      1      0      0      0
  BTNL9 WILD-TYPE      5      5      5      3      2      1      3      2
D108V4, multiclass
[1] "Remove cluster labels:" "BTNL9 MUTATED"         
clus
  BTNL9 MUTATED BTNL9 WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J6      TCGA-OR-A5J7 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5J8      TCGA-OR-A5JP      TCGA-OR-A5JR      TCGA-OR-A5JT 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5JV      TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5K5      TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KW 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"BTNL9 WILD-TYPE" "BTNL9 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTNL9 MUTATED        0      1      2      0
  BTNL9 WILD-TYPE     16      7     12     16
D108V5, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1               7
  CLUS_3             2              12
  CLUS_4             0              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BTNL9 MUTATED        0      3      0      0
  BTNL9 WILD-TYPE     16     13      4     18
D108V6, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             3              13
  CLUS_3             0               4
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BTNL9 MUTATED        1      2      0
  BTNL9 WILD-TYPE     25      9     18
D108V7, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             2               9
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BTNL9 MUTATED        1      1      0      1      0
  BTNL9 WILD-TYPE     12     17      8     13      2
D108V8, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              17
  CLUS_3             0               8
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BTNL9 MUTATED        1      2      0
  BTNL9 WILD-TYPE     20     12     19
D108V9, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             2              12
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BTNL9 MUTATED        2      1      0
  BTNL9 WILD-TYPE     28     15      8
D108V10, multiclass
        clus
vv       BTNL9 MUTATED BTNL9 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             1              15
  CLUS_3             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(109) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        4      1      0      2
  NF1 WILD-TYPE     17     19     10      7
D109V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            17
  CLUS_2           1            19
  CLUS_3           0            10
  CLUS_4           2             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            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        2      0      2      2      1
  NF1 WILD-TYPE     11      8     12     11      6
D109V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            11
  CLUS_2           0             8
  CLUS_3           2            12
  CLUS_4           2            11
  CLUS_5           1             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V3, binary
               cls
clus             0  1
  NF1 MUTATED    0  4
  NF1 WILD-TYPE 13 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0    4
  NF1 WILD-TYPE   13   11
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            13
  CLUS_2           4            11
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NF1 MUTATED        1      0      0      1      1      0      0      1
  NF1 WILD-TYPE      4      6      5      2      2      1      3      1
D109V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1             4
  CLUS_2           0             6
  CLUS_3           0             5
  CLUS_4           1             2
  CLUS_5           1             2
  CLUS_6           0             1
  CLUS_7           0             3
  CLUS_8           1             1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        4      0      2      1
  NF1 WILD-TYPE     12      8     12     15
D109V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            12
  CLUS_2           0             8
  CLUS_3           2            12
  CLUS_4           1            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        2      2      2      1
  NF1 WILD-TYPE     14     14      2     17
D109V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            14
  CLUS_2           2            14
  CLUS_3           2             2
  CLUS_4           1            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        2      3      2
  NF1 WILD-TYPE     24      8     16
D109V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            24
  CLUS_2           3             8
  CLUS_3           2            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        1      2      1      3      0
  NF1 WILD-TYPE     12     16      7     11      2
D109V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            12
  CLUS_2           2            16
  CLUS_3           1             7
  CLUS_4           3            11
  CLUS_5           0             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        3      2      2
  NF1 WILD-TYPE     18     12     17
D109V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            18
  CLUS_2           2            12
  CLUS_3           2            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        3      1      3
  NF1 WILD-TYPE     27     15      5
D109V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            27
  CLUS_2           1            15
  CLUS_3           3             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(110) Variable = ZNF814 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        1      1      1      0
  ZNF814 WILD-TYPE     20     19      9      9
D110V1, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              1               19
  CLUS_3              1                9
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF814 MUTATED        0      0      1      1      0
  ZNF814 WILD-TYPE     13      8     13     12      7
D110V2, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" 
D110V3, binary
                  cls
clus                0  1
  ZNF814 MUTATED    1  1
  ZNF814 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      1    1
  ZNF814 WILD-TYPE   12   14
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF814 MUTATED        0      1      0      0      0      1      0      0
  ZNF814 WILD-TYPE      5      5      5      3      3      0      3      2
D110V4, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J7 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J8       TCGA-OR-A5JP       TCGA-OR-A5JT       TCGA-OR-A5JV 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4       TCGA-OR-A5K5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      0      1      1
  ZNF814 WILD-TYPE     16      8     13     15
D110V5, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF       TCGA-OR-A5JI 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP       TCGA-OR-A5JQ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KX 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4       TCGA-OR-A5L5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA       TCGA-OR-A5LB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      1      0      1
  ZNF814 WILD-TYPE     16     15      4     17
D110V6, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF       TCGA-OR-A5JI 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP       TCGA-OR-A5JQ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JX 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4       TCGA-OR-A5K5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO       TCGA-OR-A5KT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW       TCGA-OR-A5KX 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4       TCGA-OR-A5L5 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA       TCGA-OR-A5LB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      0      1
  ZNF814 WILD-TYPE     25     11     17
D110V7, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF814 MUTATED        1      1      0      0      0
  ZNF814 WILD-TYPE     12     17      8     14      2
D110V8, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      0      1
  ZNF814 WILD-TYPE     20     14     18
D110V9, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      1      0
  ZNF814 WILD-TYPE     29     15      8
D110V10, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J6       TCGA-OR-A5J7       TCGA-OR-A5J8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5L9       TCGA-OR-A5LA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 

Clustering(111) Variable = RNF135 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF135 MUTATED        1      2      0      0
  RNF135 WILD-TYPE     20     18     10      9
D111V1, multiclass
        clus
vv       RNF135 MUTATED RNF135 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              2               18
  CLUS_3              0               10
  CLUS_4              0                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF135 MUTATED        0      0      0      2      0
  RNF135 WILD-TYPE     13      8     14     11      7
D111V2, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-PK-A5HB 
"RNF135 WILD-TYPE" 
D111V3, binary
                  cls
clus                0  1
  RNF135 MUTATED    1  0
  RNF135 WILD-TYPE 12 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF135 MUTATED      1    0
  RNF135 WILD-TYPE   12   15
        clus
vv       RNF135 MUTATED RNF135 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RNF135 MUTATED        0      0      1      0      0      0      0      0
  RNF135 WILD-TYPE      5      6      4      3      3      1      3      2
D111V4, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               1               27 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J7       TCGA-OR-A5J8 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LJ       TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LP       TCGA-PA-A5YG       TCGA-PK-A5H8 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF135 MUTATED        0      0      0      2
  RNF135 WILD-TYPE     16      8     14     14
D111V5, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF       TCGA-OR-A5JI 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP       TCGA-OR-A5JQ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA       TCGA-OR-A5LB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF135 MUTATED        0      0      1      1
  RNF135 WILD-TYPE     16     16      3     17
D111V6, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J5 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA       TCGA-OR-A5JB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF       TCGA-OR-A5JI 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP       TCGA-OR-A5JQ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV       TCGA-OR-A5JW 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2       TCGA-OR-A5K4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9       TCGA-OR-A5KO 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV       TCGA-OR-A5KW 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3       TCGA-OR-A5L4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA       TCGA-OR-A5LB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ       TCGA-OR-A5LK 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP       TCGA-OR-A5LR 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8       TCGA-PK-A5HB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF135 MUTATED        1      0      1
  RNF135 WILD-TYPE     25     11     17
D111V7, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-PK-A5HB 
"RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF135 MUTATED        0      1      1      0      0
  RNF135 WILD-TYPE     13     17      7     14      2
D111V8, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               53 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5H8 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-PK-A5HB 
"RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF135 MUTATED        1      0      1
  RNF135 WILD-TYPE     20     14     18
D111V9, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RNF135 MUTATED        1      1      0
  RNF135 WILD-TYPE     29     15      8
D111V10, multiclass
[1] "Remove cluster labels:" "RNF135 MUTATED"        
clus
  RNF135 MUTATED RNF135 WILD-TYPE 
               2               52 
      TCGA-OR-A5J1       TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J4 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5J5       TCGA-OR-A5J7       TCGA-OR-A5J8       TCGA-OR-A5JA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JD       TCGA-OR-A5JF 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JI       TCGA-OR-A5JK       TCGA-OR-A5JL       TCGA-OR-A5JP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JQ       TCGA-OR-A5JR       TCGA-OR-A5JT       TCGA-OR-A5JV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5JW       TCGA-OR-A5JX       TCGA-OR-A5JY       TCGA-OR-A5K2 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5K4       TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5K9 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KO       TCGA-OR-A5KT       TCGA-OR-A5KU       TCGA-OR-A5KV 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5L3 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5L4       TCGA-OR-A5L5       TCGA-OR-A5L6       TCGA-OR-A5LA 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LB       TCGA-OR-A5LC       TCGA-OR-A5LD       TCGA-OR-A5LJ 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO       TCGA-OR-A5LP 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 
      TCGA-OR-A5LR       TCGA-P6-A5OF       TCGA-PA-A5YG       TCGA-PK-A5HB 
"RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" "RNF135 WILD-TYPE" 

Clustering(112) Variable = CSGALNACT2 MUTATION ANALYSIS
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSGALNACT2 MUTATED        0      3      0      0
  CSGALNACT2 WILD-TYPE     21     17     10      9
D112V1, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                   21
  CLUS_2                  3                   17
  CLUS_3                  0                   10
  CLUS_4                  0                    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                   CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CSGALNACT2 MUTATED        1      0      0      0      2
  CSGALNACT2 WILD-TYPE     12      8     14     13      5
D112V2, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   12
  CLUS_2                  0                    8
  CLUS_3                  0                   14
  CLUS_4                  0                   13
  CLUS_5                  2                    5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V3, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    1  0
  CSGALNACT2 WILD-TYPE 12 15
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      1    0
  CSGALNACT2 WILD-TYPE   12   15
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   12
  CLUS_2                  0                   15
[1] 2 2
[1] FALSE
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CSGALNACT2 MUTATED        0      0      1      0      0      0      0      0
  CSGALNACT2 WILD-TYPE      5      6      4      3      3      1      3      2
D112V4, multiclass
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   27 
          TCGA-OR-A5J2           TCGA-OR-A5J3           TCGA-OR-A5J6 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5J7           TCGA-OR-A5J8           TCGA-OR-A5JA 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5JP           TCGA-OR-A5JR           TCGA-OR-A5JT 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5JV           TCGA-OR-A5JW           TCGA-OR-A5JY 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5K4           TCGA-OR-A5K5           TCGA-OR-A5K8 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5KO           TCGA-OR-A5KU           TCGA-OR-A5KW 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5KX           TCGA-OR-A5KZ           TCGA-OR-A5LD 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5LJ           TCGA-OR-A5LK           TCGA-OR-A5LL 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-OR-A5LO           TCGA-PA-A5YG           TCGA-PK-A5H8 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSGALNACT2 MUTATED        1      0      0      2
  CSGALNACT2 WILD-TYPE     15      8     14     14
D112V5, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   15
  CLUS_2                  0                    8
  CLUS_3                  0                   14
  CLUS_4                  2                   14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSGALNACT2 MUTATED        1      0      0      2
  CSGALNACT2 WILD-TYPE     15     16      4     16
D112V6, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   15
  CLUS_2                  0                   16
  CLUS_3                  0                    4
  CLUS_4                  2                   16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3
  CSGALNACT2 MUTATED        1      0      2
  CSGALNACT2 WILD-TYPE     25     11     16
D112V7, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   25
  CLUS_2                  0                   11
  CLUS_3                  2                   16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CSGALNACT2 MUTATED        0      2      0      1      0
  CSGALNACT2 WILD-TYPE     13     16      8     13      2
D112V8, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                   13
  CLUS_2                  2                   16
  CLUS_3                  0                    8
  CLUS_4                  1                   13
  CLUS_5                  0                    2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3
  CSGALNACT2 MUTATED        0      1      2
  CSGALNACT2 WILD-TYPE     21     13     17
D112V9, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                   21
  CLUS_2                  1                   13
  CLUS_3                  2                   17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3
  CSGALNACT2 MUTATED        1      2      0
  CSGALNACT2 WILD-TYPE     29     14      8
D112V10, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   29
  CLUS_2                  2                   14
  CLUS_3                  0                    8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(113) Variable = SPIRE2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SPIRE2 MUTATED        0      1      1      1
  SPIRE2 WILD-TYPE     21     19      9      8
D113V1, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              1               19
  CLUS_3              1                9
  CLUS_4              1                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               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPIRE2 MUTATED        1      0      0      0      2
  SPIRE2 WILD-TYPE     12      8     14     13      5
D113V2, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              0                8
  CLUS_3              0               14
  CLUS_4              0               13
  CLUS_5              2                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V3, binary
                  cls
clus                0  1
  SPIRE2 MUTATED    1  1
  SPIRE2 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIRE2 MUTATED      1    1
  SPIRE2 WILD-TYPE   12   14
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SPIRE2 MUTATED        0      0      1      1      0      0      0      0
  SPIRE2 WILD-TYPE      5      6      4      2      3      1      3      2
D113V4, multiclass
[1] "Remove cluster labels:" "SPIRE2 MUTATED"        
clus
  SPIRE2 MUTATED SPIRE2 WILD-TYPE 
               2               26 
      TCGA-OR-A5J2       TCGA-OR-A5J3       TCGA-OR-A5J6       TCGA-OR-A5J8 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5JA       TCGA-OR-A5JP       TCGA-OR-A5JR       TCGA-OR-A5JT 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5JV       TCGA-OR-A5JW       TCGA-OR-A5JY       TCGA-OR-A5K4 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5K5       TCGA-OR-A5K8       TCGA-OR-A5KO       TCGA-OR-A5KU 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5KW       TCGA-OR-A5KX       TCGA-OR-A5KZ       TCGA-OR-A5LD 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-OR-A5LJ       TCGA-OR-A5LK       TCGA-OR-A5LL       TCGA-OR-A5LO 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
      TCGA-PA-A5YG       TCGA-PK-A5H8 
"SPIRE2 WILD-TYPE" "SPIRE2 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SPIRE2 MUTATED        1      0      1      1
  SPIRE2 WILD-TYPE     15      8     13     15
D113V5, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              0                8
  CLUS_3              1               13
  CLUS_4              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SPIRE2 MUTATED        1      0      0      2
  SPIRE2 WILD-TYPE     15     16      4     16
D113V6, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              0               16
  CLUS_3              0                4
  CLUS_4              2               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SPIRE2 MUTATED        2      0      1
  SPIRE2 WILD-TYPE     24     11     17
D113V7, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              2               24
  CLUS_2              0               11
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPIRE2 MUTATED        0      1      1      1      0
  SPIRE2 WILD-TYPE     13     17      7     13      2
D113V8, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1               17
  CLUS_3              1                7
  CLUS_4              1               13
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SPIRE2 MUTATED        1      1      1
  SPIRE2 WILD-TYPE     20     13     18
D113V9, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              1               13
  CLUS_3              1               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SPIRE2 MUTATED        2      1      0
  SPIRE2 WILD-TYPE     28     15      8
D113V10, multiclass
        clus
vv       SPIRE2 MUTATED SPIRE2 WILD-TYPE
  CLUS_1              2               28
  CLUS_2              1               15
  CLUS_3              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(114) Variable = CYP4A22 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP4A22 MUTATED        2      0      2      0
  CYP4A22 WILD-TYPE     19     20      8      9
D114V1, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               2                19
  CLUS_2               0                20
  CLUS_3               2                 8
  CLUS_4               0                 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                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CYP4A22 MUTATED        1      1      2      0      0
  CYP4A22 WILD-TYPE     12      7     12     13      7
D114V2, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                 7
  CLUS_3               2                12
  CLUS_4               0                13
  CLUS_5               0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V3, binary
                   cls
clus                 0  1
  CYP4A22 MUTATED    1  1
  CYP4A22 WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      1    1
  CYP4A22 WILD-TYPE   12   14
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CYP4A22 MUTATED        1      1      0      0      0      0      0      0
  CYP4A22 WILD-TYPE      4      5      5      3      3      1      3      2
D114V4, multiclass
[1] "Remove cluster labels:" "CYP4A22 MUTATED"       
clus
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                2                26 
       TCGA-OR-A5J3        TCGA-OR-A5J6        TCGA-OR-A5J7        TCGA-OR-A5J8 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5JA        TCGA-OR-A5JP        TCGA-OR-A5JR        TCGA-OR-A5JT 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5JV        TCGA-OR-A5JW        TCGA-OR-A5JY        TCGA-OR-A5K4 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5K5        TCGA-OR-A5KO        TCGA-OR-A5KU        TCGA-OR-A5KW 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5KX        TCGA-OR-A5KZ        TCGA-OR-A5LD        TCGA-OR-A5LJ 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-OR-A5LK        TCGA-OR-A5LL        TCGA-OR-A5LO        TCGA-OR-A5LP 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
       TCGA-PA-A5YG        TCGA-PK-A5H8 
"CYP4A22 WILD-TYPE" "CYP4A22 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP4A22 MUTATED        1      2      1      0
  CYP4A22 WILD-TYPE     15      6     13     16
D114V5, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                 6
  CLUS_3               1                13
  CLUS_4               0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP4A22 MUTATED        2      2      0      0
  CYP4A22 WILD-TYPE     14     14      4     18
D114V6, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                14
  CLUS_3               0                 4
  CLUS_4               0                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP4A22 MUTATED        2      2      0
  CYP4A22 WILD-TYPE     24      9     18
D114V7, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               2                 9
  CLUS_3               0                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CYP4A22 MUTATED        0      2      0      1      1
  CYP4A22 WILD-TYPE     13     16      8     13      1
D114V8, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                16
  CLUS_3               0                 8
  CLUS_4               1                13
  CLUS_5               1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP4A22 MUTATED        1      3      0
  CYP4A22 WILD-TYPE     20     11     19
D114V9, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               1                20
  CLUS_2               3                11
  CLUS_3               0                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP4A22 MUTATED        2      2      0
  CYP4A22 WILD-TYPE     28     14      8
D114V10, multiclass
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  CLUS_1               2                28
  CLUS_2               2                14
  CLUS_3               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(115) Variable = HLA-A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-A MUTATED        2      1      0      0
  HLA-A WILD-TYPE     19     19     10      9
D115V1, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              19
  CLUS_2             1              19
  CLUS_3             0              10
  CLUS_4             0               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              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-A MUTATED        1      0      1      1      0
  HLA-A WILD-TYPE     12      8     13     12      7
D115V2, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0               8
  CLUS_3             1              13
  CLUS_4             1              12
  CLUS_5             0               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V3, binary
                 cls
clus               0  1
  HLA-A MUTATED    1  1
  HLA-A WILD-TYPE 12 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    1
  HLA-A WILD-TYPE   12   14
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  HLA-A MUTATED        0      0      1      1      0      0      0      0
  HLA-A WILD-TYPE      5      6      4      2      3      1      3      2
D115V4, multiclass
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              2              26 
     TCGA-OR-A5J2      TCGA-OR-A5J3      TCGA-OR-A5J7      TCGA-OR-A5J8 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5JA      TCGA-OR-A5JR      TCGA-OR-A5JT      TCGA-OR-A5JV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5JW      TCGA-OR-A5JY      TCGA-OR-A5K4      TCGA-OR-A5K5 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5K8      TCGA-OR-A5KO      TCGA-OR-A5KU      TCGA-OR-A5KW 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5KX      TCGA-OR-A5KZ      TCGA-OR-A5LD      TCGA-OR-A5LJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-OR-A5LK      TCGA-OR-A5LL      TCGA-OR-A5LO      TCGA-OR-A5LP 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-PA-A5YG      TCGA-PK-A5H8 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-A MUTATED        1      1      0      1
  HLA-A WILD-TYPE     15      7     14     15
D115V5, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1               7
  CLUS_3             0              14
  CLUS_4             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-A MUTATED        1      1      1      0
  HLA-A WILD-TYPE     15     15      3     18
D115V6, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              15
  CLUS_3             1               3
  CLUS_4             0              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        2      0      1
  HLA-A WILD-TYPE     24     11     17
D115V7, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              24
  CLUS_2             0              11
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-A MUTATED        1      0      1      1      0
  HLA-A WILD-TYPE     12     18      7     13      2
D115V8, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              12
  CLUS_2             0              18
  CLUS_3             1               7
  CLUS_4             1              13
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        2      0      1
  HLA-A WILD-TYPE     19     14     18
D115V9, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              19
  CLUS_2             0              14
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        2      0      1
  HLA-A WILD-TYPE     28     16      7
D115V10, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              28
  CLUS_2             0              16
  CLUS_3             1               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(116) Variable = GLI3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLI3 MUTATED        2      2      0      1
  GLI3 WILD-TYPE     19     18     10      8
D116V1, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             18
  CLUS_3            0             10
  CLUS_4            1              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             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GLI3 MUTATED        2      0      0      1      1
  GLI3 WILD-TYPE     11      8     14     12      6
D116V2, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            0              8
  CLUS_3            0             14
  CLUS_4            1             12
  CLUS_5            1              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V3, binary
                cls
clus              0  1
  GLI3 MUTATED    0  0
  GLI3 WILD-TYPE 13 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI3 MUTATED      0    0
  GLI3 WILD-TYPE   13   15
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GLI3 MUTATED        0      0      0      0      0      0      0      0
  GLI3 WILD-TYPE      5      6      5      3      3      1      3      2
D116V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLI3 MUTATED        2      0      1      1
  GLI3 WILD-TYPE     14      8     13     15
D116V5, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            0              8
  CLUS_3            1             13
  CLUS_4            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GLI3 MUTATED        2      1      0      1
  GLI3 WILD-TYPE     14     15      4     17
D116V6, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             15
  CLUS_3            0              4
  CLUS_4            1             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GLI3 MUTATED        4      0      0
  GLI3 WILD-TYPE     22     11     18
D116V7, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            4             22
  CLUS_2            0             11
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GLI3 MUTATED        1      0      1      2      0
  GLI3 WILD-TYPE     12     18      7     12      2
D116V8, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            0             18
  CLUS_3            1              7
  CLUS_4            2             12
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GLI3 MUTATED        2      2      0
  GLI3 WILD-TYPE     19     12     19
D116V9, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2             12
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GLI3 MUTATED        4      0      0
  GLI3 WILD-TYPE     26     16      8
D116V10, multiclass
        clus
vv       GLI3 MUTATED GLI3 WILD-TYPE
  CLUS_1            4             26
  CLUS_2            0             16
  CLUS_3            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
