[1] "ofn"        "-oTDLBC-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/DLBC-TP/20125263/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/19899503/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=41, common to both=41
[1] "Reduce the number of clustering variables from 110 to 94."
[1] 94 41
[1] "MYD88 MUTATION ANALYSIS"
[1] 3
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              38 
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              38 
[1] "FRG1 MUTATION ANALYSIS"
[1] 3
  FRG1 MUTATED FRG1 WILD-TYPE 
             9             32 
  FRG1 MUTATED FRG1 WILD-TYPE 
             9             32 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             27 
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             27 
[1] "TPPP MUTATION ANALYSIS"
[1] 3
  TPPP MUTATED TPPP WILD-TYPE 
             5             36 
  TPPP MUTATED TPPP WILD-TYPE 
             5             36 
[1] "CHIT1 MUTATION ANALYSIS"
[1] 3
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              6              35 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              6              35 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
            8            33 
  B2M MUTATED B2M WILD-TYPE 
            8            33 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              30 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              30 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6              35 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6              35 
[1] "FOXD4L1 MUTATION ANALYSIS"
[1] 3
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                7                34 
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                7                34 
[1] "DND1 MUTATION ANALYSIS"
[1] 3
  DND1 MUTATED DND1 WILD-TYPE 
             5             36 
  DND1 MUTATED DND1 WILD-TYPE 
             5             36 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7              34 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7              34 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             6             35 
  TP53 MUTATED TP53 WILD-TYPE 
             6             35 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             10              31 
  CDC27 MUTATED CDC27 WILD-TYPE 
             10              31 
[1] "EPB41L4A MUTATION ANALYSIS"
[1] 3
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 4                 37 
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 4                 37 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 4                 37 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 4                 37 
[1] "KRT3 MUTATION ANALYSIS"
[1] 3
  KRT3 MUTATED KRT3 WILD-TYPE 
             4             37 
  KRT3 MUTATED KRT3 WILD-TYPE 
             4             37 
[1] "OR1S2 MUTATION ANALYSIS"
[1] 3
  OR1S2 MUTATED OR1S2 WILD-TYPE 
             10              31 
  OR1S2 MUTATED OR1S2 WILD-TYPE 
             10              31 
[1] "RGPD5 MUTATION ANALYSIS"
[1] 3
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5              36 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5              36 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                6                35 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                6                35 
[1] "RBMXL1 MUTATION ANALYSIS"
[1] 3
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               4               37 
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               4               37 
[1] "CCDC66 MUTATION ANALYSIS"
[1] 3
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               37 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               37 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               7               34 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               7               34 
[1] "PCMTD1 MUTATION ANALYSIS"
[1] 3
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               6               35 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               6               35 
[1] "FAM120B MUTATION ANALYSIS"
[1] 3
  FAM120B MUTATED FAM120B WILD-TYPE 
                5                36 
  FAM120B MUTATED FAM120B WILD-TYPE 
                5                36 
[1] "SMARCA2 MUTATION ANALYSIS"
[1] 3
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4                37 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4                37 
[1] "C11ORF40 MUTATION ANALYSIS"
[1] 3
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 4                 37 
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 4                 37 
[1] "ZSCAN5A MUTATION ANALYSIS"
[1] 3
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                3                38 
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                3                38 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 37 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 37 
[1] "DEFA1 MUTATION ANALYSIS"
[1] 3
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              4              37 
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              4              37 
[1] "SIRPA MUTATION ANALYSIS"
[1] 3
  SIRPA MUTATED SIRPA WILD-TYPE 
              5              36 
  SIRPA MUTATED SIRPA WILD-TYPE 
              5              36 
[1] "TMPRSS13 MUTATION ANALYSIS"
[1] 3
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 3                 38 
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 3                 38 
[1] "CYP2A6 MUTATION ANALYSIS"
[1] 3
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               37 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               37 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
           7           34 
  AR MUTATED AR WILD-TYPE 
           7           34 
[1] "ARHGEF5 MUTATION ANALYSIS"
[1] 3
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3                38 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3                38 
[1] "RNF39 MUTATION ANALYSIS"
[1] 3
  RNF39 MUTATED RNF39 WILD-TYPE 
              3              38 
  RNF39 MUTATED RNF39 WILD-TYPE 
              3              38 
[1] "ABCA1 MUTATION ANALYSIS"
[1] 3
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              5              36 
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              5              36 
[1] "CS MUTATION ANALYSIS"
[1] 3
  CS MUTATED CS WILD-TYPE 
           3           38 
  CS MUTATED CS WILD-TYPE 
           3           38 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               4               37 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               4               37 
[1] "RANBP2 MUTATION ANALYSIS"
[1] 3
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               6               35 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               6               35 
[1] "KLHL6 MUTATION ANALYSIS"
[1] 3
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              6              35 
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              6              35 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              10               31 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              10               31 
[1] "CYP4A11 MUTATION ANALYSIS"
[1] 3
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                4                37 
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                4                37 
[1] "PIM1 MUTATION ANALYSIS"
[1] 3
  PIM1 MUTATED PIM1 WILD-TYPE 
             8             33 
  PIM1 MUTATED PIM1 WILD-TYPE 
             8             33 
[1] "POTEE MUTATION ANALYSIS"
[1] 3
  POTEE MUTATED POTEE WILD-TYPE 
              7              34 
  POTEE MUTATED POTEE WILD-TYPE 
              7              34 
[1] "OR52E6 MUTATION ANALYSIS"
[1] 3
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               3               38 
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               3               38 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9               32 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9               32 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             9             32 
  PRB2 MUTATED PRB2 WILD-TYPE 
             9             32 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             20 
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             20 
[1] "SALL1 MUTATION ANALYSIS"
[1] 3
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              36 
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              36 
[1] "PAK2 MUTATION ANALYSIS"
[1] 3
  PAK2 MUTATED PAK2 WILD-TYPE 
             7             34 
  PAK2 MUTATED PAK2 WILD-TYPE 
             7             34 
[1] "FLG MUTATION ANALYSIS"
[1] 3
  FLG MUTATED FLG WILD-TYPE 
           17            24 
  FLG MUTATED FLG WILD-TYPE 
           17            24 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             13              28 
  MUC17 MUTATED MUC17 WILD-TYPE 
             13              28 
[1] "OR2T4 MUTATION ANALYSIS"
[1] 3
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              8              33 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              8              33 
[1] "AMAC1L3 MUTATION ANALYSIS"
[1] 3
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                36 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                36 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
             3             38 
  APOB MUTATED APOB WILD-TYPE 
             3             38 
[1] "KRTAP4-7 MUTATION ANALYSIS"
[1] 3
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 8                 33 
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 8                 33 
[1] "MUC16 MUTATION ANALYSIS"
[1] 3
  MUC16 MUTATED MUC16 WILD-TYPE 
             13              28 
  MUC16 MUTATED MUC16 WILD-TYPE 
             13              28 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6             35 
  NEFH MUTATED NEFH WILD-TYPE 
             6             35 
[1] "KCNN3 MUTATION ANALYSIS"
[1] 3
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7              34 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7              34 
[1] "RNASEH2B MUTATION ANALYSIS"
[1] 3
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                 38 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                 38 
[1] "FAM153B MUTATION ANALYSIS"
[1] 3
  FAM153B MUTATED FAM153B WILD-TYPE 
                3                38 
  FAM153B MUTATED FAM153B WILD-TYPE 
                3                38 
[1] "OTOP1 MUTATION ANALYSIS"
[1] 3
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              37 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              37 
[1] "AATK MUTATION ANALYSIS"
[1] 3
  AATK MUTATED AATK WILD-TYPE 
             3             38 
  AATK MUTATED AATK WILD-TYPE 
             3             38 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               36 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               36 
[1] "GUCA1C MUTATION ANALYSIS"
[1] 3
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               3               38 
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               3               38 
[1] "TRIM48 MUTATION ANALYSIS"
[1] 3
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               8               33 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               8               33 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                   36 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                   36 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               6               35 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               6               35 
[1] "DHRS4 MUTATION ANALYSIS"
[1] 3
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              4              37 
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              4              37 
[1] "FAM21A MUTATION ANALYSIS"
[1] 3
  FAM21A MUTATED FAM21A WILD-TYPE 
               4               37 
  FAM21A MUTATED FAM21A WILD-TYPE 
               4               37 
[1] "KIAA1529 MUTATION ANALYSIS"
[1] 3
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 4                 37 
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 4                 37 
[1] "OR2M5 MUTATION ANALYSIS"
[1] 3
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              4              37 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              4              37 
[1] "KRT6A MUTATION ANALYSIS"
[1] 3
  KRT6A MUTATED KRT6A WILD-TYPE 
              4              37 
  KRT6A MUTATED KRT6A WILD-TYPE 
              4              37 
[1] "CYP2F1 MUTATION ANALYSIS"
[1] 3
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               4               37 
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               4               37 
[1] "FCGBP MUTATION ANALYSIS"
[1] 3
  FCGBP MUTATED FCGBP WILD-TYPE 
              5              36 
  FCGBP MUTATED FCGBP WILD-TYPE 
              5              36 
[1] "ZNF493 MUTATION ANALYSIS"
[1] 3
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               4               37 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               4               37 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              7              34 
  HLA-B MUTATED HLA-B WILD-TYPE 
              7              34 
[1] "FCRLA MUTATION ANALYSIS"
[1] 3
  FCRLA MUTATED FCRLA WILD-TYPE 
              3              38 
  FCRLA MUTATED FCRLA WILD-TYPE 
              3              38 
[1] "KLRC2 MUTATION ANALYSIS"
[1] 3
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              5              36 
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              5              36 
[1] "CD79B MUTATION ANALYSIS"
[1] 3
  CD79B MUTATED CD79B WILD-TYPE 
              5              36 
  CD79B MUTATED CD79B WILD-TYPE 
              5              36 
[1] "TMSB4X MUTATION ANALYSIS"
[1] 3
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               5               36 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               5               36 
[1] "PRB1 MUTATION ANALYSIS"
[1] 3
  PRB1 MUTATED PRB1 WILD-TYPE 
             5             36 
  PRB1 MUTATED PRB1 WILD-TYPE 
             5             36 
[1] "PCDHA7 MUTATION ANALYSIS"
[1] 3
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               4               37 
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               4               37 
[1] "OR5H14 MUTATION ANALYSIS"
[1] 3
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               3               38 
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               3               38 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
             4             37 
  PER3 MUTATED PER3 WILD-TYPE 
             4             37 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               34 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               34 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              38 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              38 
[1] "IGSF3 MUTATION ANALYSIS"
[1] 3
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              6              35 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              6              35 
[1] "KRTAP1-1 MUTATION ANALYSIS"
[1] 3
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                 38 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                 38 
[1] "C15ORF39 MUTATION ANALYSIS"
[1] 3
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 3                 38 
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 3                 38 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               3               38 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               3               38 
[1] "ZNF880 MUTATION ANALYSIS"
[1] 3
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               8               33 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               8               33 
[1] "NBPF15 MUTATION ANALYSIS"
[1] 3
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               4               37 
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               4               37 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 38 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 38 
[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 41 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	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 41 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=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MYD88 MUTATION ANALYSIS
D1V1, binary
                 cls
clus               0  1
  MYD88 MUTATED    3  0
  MYD88 WILD-TYPE 20 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      3    0
  MYD88 WILD-TYPE   20   18
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             0              18
[1] 2 2
[1] FALSE
D1V2, binary
                 cls
clus               0  1
  MYD88 MUTATED    0  3
  MYD88 WILD-TYPE 20 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      0    3
  MYD88 WILD-TYPE   20   18
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D1V3, binary
                 cls
clus               0  1
  MYD88 MUTATED    2  1
  MYD88 WILD-TYPE 13 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      2    1
  MYD88 WILD-TYPE   13   13
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MYD88 MUTATED        1      1      1
  MYD88 WILD-TYPE      4     12     10
D1V4, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1              12
  CLUS_3             1              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"
D1V5, binary
                 cls
clus               0  1
  MYD88 MUTATED    1  0
  MYD88 WILD-TYPE  8 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      1    0
  MYD88 WILD-TYPE    8   12
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MYD88 MUTATED        0      0      1
  MYD88 WILD-TYPE      7      9      4
D1V6, multiclass
[1] "Remove cluster labels:" "MYD88 MUTATED"         
clus
  MYD88 MUTATED MYD88 WILD-TYPE 
              1              20 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" 
     TCGA-FM-8000      TCGA-G8-6324      TCGA-GR-7353      TCGA-GR-A4D4 
"MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" 
     TCGA-GR-A4D5      TCGA-GR-A4D6      TCGA-GR-A4D9      TCGA-RQ-A68N 
"MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" "MYD88 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MYD88 MUTATED        1      0      2      0
  MYD88 WILD-TYPE     10     11      8      9
D1V7, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             0              11
  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
  MYD88 MUTATED        1      0      1      1      0
  MYD88 WILD-TYPE      5     11      6     11      5
D1V8, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             0              11
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             0               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"
D1V9, binary
                 cls
clus               0  1
  MYD88 MUTATED    2  1
  MYD88 WILD-TYPE 15 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      2    1
  MYD88 WILD-TYPE   15   18
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             1              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MYD88 MUTATED        0      0      0      2      0      0      1      0
  MYD88 WILD-TYPE      4      5      5      4      7      1      3      1
                 vv
clus              CLUS_9
  MYD88 MUTATED        0
  MYD88 WILD-TYPE      3
D1V10, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             2               4
  CLUS_5             0               7
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = FRG1 MUTATION ANALYSIS
D2V1, binary
                cls
clus              0  1
  FRG1 MUTATED    6  3
  FRG1 WILD-TYPE 17 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      6    3
  FRG1 WILD-TYPE   17   15
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            6             17
  CLUS_2            3             15
[1] 2 2
[1] FALSE
D2V2, binary
                cls
clus              0  1
  FRG1 MUTATED    5  4
  FRG1 WILD-TYPE 15 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      5    4
  FRG1 WILD-TYPE   15   17
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            5             15
  CLUS_2            4             17
[1] 2 2
[1] FALSE
D2V3, binary
                cls
clus              0  1
  FRG1 MUTATED    5  2
  FRG1 WILD-TYPE 10 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      5    2
  FRG1 WILD-TYPE   10   12
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            5             10
  CLUS_2            2             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FRG1 MUTATED        1      4      2
  FRG1 WILD-TYPE      4      9      9
D2V4, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            4              9
  CLUS_3            2              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                cls
clus             0 1
  FRG1 MUTATED   3 4
  FRG1 WILD-TYPE 6 8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      3    4
  FRG1 WILD-TYPE    6    8
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            3              6
  CLUS_2            4              8
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FRG1 MUTATED        4      2      1
  FRG1 WILD-TYPE      3      7      4
D2V6, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            4              3
  CLUS_2            2              7
  CLUS_3            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FRG1 MUTATED        3      3      0      3
  FRG1 WILD-TYPE      8      8     10      6
D2V7, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            3              8
  CLUS_3            0             10
  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
  FRG1 MUTATED        3      3      1      0      2
  FRG1 WILD-TYPE      3      8      6     12      3
D2V8, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            3              3
  CLUS_2            3              8
  CLUS_3            1              6
  CLUS_4            0             12
  CLUS_5            2              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"
D2V9, binary
                cls
clus              0  1
  FRG1 MUTATED    4  5
  FRG1 WILD-TYPE 13 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      4    5
  FRG1 WILD-TYPE   13   14
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            4             13
  CLUS_2            5             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  FRG1 MUTATED        2      3      0      0      3      1      0      0      0
  FRG1 WILD-TYPE      2      2      5      6      4      0      4      1      3
D2V10, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            2              2
  CLUS_2            3              2
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            3              4
  CLUS_6            1              0
  CLUS_7            0              4
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = MLL2 MUTATION ANALYSIS
D3V1, binary
                cls
clus              0  1
  MLL2 MUTATED    5  9
  MLL2 WILD-TYPE 18  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      5    9
  MLL2 WILD-TYPE   18    9
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             18
  CLUS_2            9              9
[1] 2 2
[1] FALSE
D3V2, binary
                cls
clus              0  1
  MLL2 MUTATED    5  9
  MLL2 WILD-TYPE 15 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      5    9
  MLL2 WILD-TYPE   15   12
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             15
  CLUS_2            9             12
[1] 2 2
[1] FALSE
D3V3, binary
                cls
clus              0  1
  MLL2 MUTATED    5  5
  MLL2 WILD-TYPE 10  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      5    5
  MLL2 WILD-TYPE   10    9
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             10
  CLUS_2            5              9
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        2      4      4
  MLL2 WILD-TYPE      3      9      7
D3V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              3
  CLUS_2            4              9
  CLUS_3            4              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"
D3V5, binary
                cls
clus             0 1
  MLL2 MUTATED   2 5
  MLL2 WILD-TYPE 7 7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2    5
  MLL2 WILD-TYPE    7    7
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            5              7
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        2      5      0
  MLL2 WILD-TYPE      5      4      5
D3V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              5
  CLUS_2            5              4
  CLUS_3            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        2      3      4      5
  MLL2 WILD-TYPE      9      8      6      4
D3V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            3              8
  CLUS_3            4              6
  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
  MLL2 MUTATED        1      4      1      4      4
  MLL2 WILD-TYPE      5      7      6      8      1
D3V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            4              7
  CLUS_3            1              6
  CLUS_4            4              8
  CLUS_5            4              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"
D3V9, binary
                cls
clus              0  1
  MLL2 MUTATED    5  8
  MLL2 WILD-TYPE 12 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      5    8
  MLL2 WILD-TYPE   12   11
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             12
  CLUS_2            8             11
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  MLL2 MUTATED        1      2      0      4      4      0      1      1      0
  MLL2 WILD-TYPE      3      3      5      2      3      1      3      0      3
D3V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            2              3
  CLUS_3            0              5
  CLUS_4            4              2
  CLUS_5            4              3
  CLUS_6            0              1
  CLUS_7            1              3
  CLUS_8            1              0
  CLUS_9            0              3
[1] 9 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 = TPPP MUTATION ANALYSIS
D4V1, binary
                cls
clus              0  1
  TPPP MUTATED    3  2
  TPPP WILD-TYPE 20 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      3    2
  TPPP WILD-TYPE   20   16
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            3             20
  CLUS_2            2             16
[1] 2 2
[1] FALSE
D4V2, binary
                cls
clus              0  1
  TPPP MUTATED    4  1
  TPPP WILD-TYPE 16 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      4    1
  TPPP WILD-TYPE   16   20
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            4             16
  CLUS_2            1             20
[1] 2 2
[1] FALSE
D4V3, binary
                cls
clus              0  1
  TPPP MUTATED    1  2
  TPPP WILD-TYPE 14 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      1    2
  TPPP WILD-TYPE   14   12
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            1             14
  CLUS_2            2             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TPPP MUTATED        0      1      2
  TPPP WILD-TYPE      5     12      9
D4V4, multiclass
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            0              5
  CLUS_2            1             12
  CLUS_3            2              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                cls
clus             0 1
  TPPP MUTATED   1 3
  TPPP WILD-TYPE 8 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      1    3
  TPPP WILD-TYPE    8    9
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            1              8
  CLUS_2            3              9
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TPPP MUTATED        0      3      1
  TPPP WILD-TYPE      7      6      4
D4V6, multiclass
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            0              7
  CLUS_2            3              6
  CLUS_3            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TPPP MUTATED        2      2      0      1
  TPPP WILD-TYPE      9      9     10      8
D4V7, multiclass
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            2              9
  CLUS_2            2              9
  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
  TPPP MUTATED        1      2      0      1      1
  TPPP WILD-TYPE      5      9      7     11      4
D4V8, multiclass
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2              9
  CLUS_3            0              7
  CLUS_4            1             11
  CLUS_5            1              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"
D4V9, binary
                cls
clus              0  1
  TPPP MUTATED    1  2
  TPPP WILD-TYPE 16 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      1    2
  TPPP WILD-TYPE   16   17
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            1             16
  CLUS_2            2             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  TPPP MUTATED        0      1      0      0      2      0      0      0      0
  TPPP WILD-TYPE      4      4      5      6      5      1      4      1      3
D4V10, multiclass
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  CLUS_1            0              4
  CLUS_2            1              4
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            2              5
  CLUS_6            0              1
  CLUS_7            0              4
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = CHIT1 MUTATION ANALYSIS
D5V1, binary
                 cls
clus               0  1
  CHIT1 MUTATED    3  3
  CHIT1 WILD-TYPE 20 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      3    3
  CHIT1 WILD-TYPE   20   15
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D5V2, binary
                 cls
clus               0  1
  CHIT1 MUTATED    3  3
  CHIT1 WILD-TYPE 17 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      3    3
  CHIT1 WILD-TYPE   17   18
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D5V3, binary
                 cls
clus               0  1
  CHIT1 MUTATED    2  3
  CHIT1 WILD-TYPE 13 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      2    3
  CHIT1 WILD-TYPE   13   11
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHIT1 MUTATED        1      1      3
  CHIT1 WILD-TYPE      4     12      8
D5V4, multiclass
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1              12
  CLUS_3             3               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"
D5V5, binary
                 cls
clus               0  1
  CHIT1 MUTATED    0  2
  CHIT1 WILD-TYPE  9 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      0    2
  CHIT1 WILD-TYPE    9   10
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHIT1 MUTATED        0      2      0
  CHIT1 WILD-TYPE      7      7      5
D5V6, multiclass
[1] "Remove cluster labels:" "CHIT1 MUTATED"         
clus
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              2              19 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HO 
"CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8047 
"CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" 
     TCGA-FF-8061      TCGA-FF-8062      TCGA-FM-8000      TCGA-G8-6324 
"CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" 
     TCGA-GR-7353      TCGA-GR-A4D4      TCGA-GR-A4D5      TCGA-GR-A4D6 
"CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" 
     TCGA-GR-A4D9      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" "CHIT1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHIT1 MUTATED        3      1      2      0
  CHIT1 WILD-TYPE      8     10      8      9
D5V7, multiclass
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             1              10
  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
  CHIT1 MUTATED        1      1      2      2      0
  CHIT1 WILD-TYPE      5     10      5     10      5
D5V8, multiclass
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              10
  CLUS_3             2               5
  CLUS_4             2              10
  CLUS_5             0               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"
D5V9, binary
                 cls
clus               0  1
  CHIT1 MUTATED    4  1
  CHIT1 WILD-TYPE 13 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      4    1
  CHIT1 WILD-TYPE   13   18
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             4              13
  CLUS_2             1              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CHIT1 MUTATED        1      1      0      1      2      0      0      0
  CHIT1 WILD-TYPE      3      4      5      5      5      1      4      1
                 vv
clus              CLUS_9
  CHIT1 MUTATED        0
  CHIT1 WILD-TYPE      3
D5V10, multiclass
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               5
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = B2M MUTATION ANALYSIS
D6V1, binary
               cls
clus             0  1
  B2M MUTATED    7  1
  B2M WILD-TYPE 16 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      7    1
  B2M WILD-TYPE   16   17
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           7            16
  CLUS_2           1            17
[1] 2 2
[1] FALSE
D6V2, binary
               cls
clus             0  1
  B2M MUTATED    3  5
  B2M WILD-TYPE 17 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      3    5
  B2M WILD-TYPE   17   16
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           3            17
  CLUS_2           5            16
[1] 2 2
[1] FALSE
D6V3, binary
               cls
clus             0  1
  B2M MUTATED    5  2
  B2M WILD-TYPE 10 12
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      5    2
  B2M WILD-TYPE   10   12
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           5            10
  CLUS_2           2            12
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  B2M MUTATED        1      4      2
  B2M WILD-TYPE      4      9      9
D6V4, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             4
  CLUS_2           4             9
  CLUS_3           2             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
               cls
clus            0 1
  B2M MUTATED   3 3
  B2M WILD-TYPE 6 9
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      3    3
  B2M WILD-TYPE    6    9
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           3             6
  CLUS_2           3             9
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  B2M MUTATED        3      1      2
  B2M WILD-TYPE      4      8      3
D6V6, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           3             4
  CLUS_2           1             8
  CLUS_3           2             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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  B2M MUTATED        2      2      0      4
  B2M WILD-TYPE      9      9     10      5
D6V7, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           2             9
  CLUS_2           2             9
  CLUS_3           0            10
  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
  B2M MUTATED        1      2      1      2      2
  B2M WILD-TYPE      5      9      6     10      3
D6V8, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             5
  CLUS_2           2             9
  CLUS_3           1             6
  CLUS_4           2            10
  CLUS_5           2             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"
D6V9, binary
               cls
clus             0  1
  B2M MUTATED    2  5
  B2M WILD-TYPE 15 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      2    5
  B2M WILD-TYPE   15   14
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           2            15
  CLUS_2           5            14
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  B2M MUTATED        1      1      1      0      1      1      2      0      0
  B2M WILD-TYPE      3      4      4      6      6      0      2      1      3
D6V10, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             3
  CLUS_2           1             4
  CLUS_3           1             4
  CLUS_4           0             6
  CLUS_5           1             6
  CLUS_6           1             0
  CLUS_7           2             2
  CLUS_8           0             1
  CLUS_9           0             3
[1] 9 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 = TPTE2 MUTATION ANALYSIS
D7V1, binary
                 cls
clus               0  1
  TPTE2 MUTATED    6  5
  TPTE2 WILD-TYPE 17 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      6    5
  TPTE2 WILD-TYPE   17   13
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             6              17
  CLUS_2             5              13
[1] 2 2
[1] FALSE
D7V2, binary
                 cls
clus               0  1
  TPTE2 MUTATED    5  6
  TPTE2 WILD-TYPE 15 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      5    6
  TPTE2 WILD-TYPE   15   15
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             5              15
  CLUS_2             6              15
[1] 2 2
[1] FALSE
D7V3, binary
                 cls
clus               0  1
  TPTE2 MUTATED    1  4
  TPTE2 WILD-TYPE 14 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      1    4
  TPTE2 WILD-TYPE   14   10
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             4              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TPTE2 MUTATED        1      1      3
  TPTE2 WILD-TYPE      4     12      8
D7V4, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1              12
  CLUS_3             3               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"
D7V5, binary
                 cls
clus              0 1
  TPTE2 MUTATED   2 4
  TPTE2 WILD-TYPE 7 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      2    4
  TPTE2 WILD-TYPE    7    8
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TPTE2 MUTATED        1      4      1
  TPTE2 WILD-TYPE      6      5      4
D7V6, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             4               5
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TPTE2 MUTATED        3      4      4      0
  TPTE2 WILD-TYPE      8      7      6      9
D7V7, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             4               7
  CLUS_3             4               6
  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
  TPTE2 MUTATED        1      4      2      4      0
  TPTE2 WILD-TYPE      5      7      5      8      5
D7V8, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             4               7
  CLUS_3             2               5
  CLUS_4             4               8
  CLUS_5             0               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"
D7V9, binary
                 cls
clus               0  1
  TPTE2 MUTATED    3  5
  TPTE2 WILD-TYPE 14 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      3    5
  TPTE2 WILD-TYPE   14   14
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             5              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TPTE2 MUTATED        0      1      2      2      0      0      1      1
  TPTE2 WILD-TYPE      4      4      3      4      7      1      3      0
                 vv
clus              CLUS_9
  TPTE2 MUTATED        1
  TPTE2 WILD-TYPE      2
D7V10, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             2               3
  CLUS_4             2               4
  CLUS_5             0               7
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             1               2
[1] 9 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 = RHPN2 MUTATION ANALYSIS
D8V1, binary
                 cls
clus               0  1
  RHPN2 MUTATED    4  2
  RHPN2 WILD-TYPE 19 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      4    2
  RHPN2 WILD-TYPE   19   16
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D8V2, binary
                 cls
clus               0  1
  RHPN2 MUTATED    3  3
  RHPN2 WILD-TYPE 17 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      3    3
  RHPN2 WILD-TYPE   17   18
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D8V3, binary
                 cls
clus               0  1
  RHPN2 MUTATED    4  0
  RHPN2 WILD-TYPE 11 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      4    0
  RHPN2 WILD-TYPE   11   14
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             4              11
  CLUS_2             0              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RHPN2 MUTATED        0      4      0
  RHPN2 WILD-TYPE      5      9     11
D8V4, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             4               9
  CLUS_3             0              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"
D8V5, binary
                 cls
clus              0 1
  RHPN2 MUTATED   2 3
  RHPN2 WILD-TYPE 7 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      2    3
  RHPN2 WILD-TYPE    7    9
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             3               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RHPN2 MUTATED        3      2      0
  RHPN2 WILD-TYPE      4      7      5
D8V6, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             3               4
  CLUS_2             2               7
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RHPN2 MUTATED        1      1      1      3
  RHPN2 WILD-TYPE     10     10      9      6
D8V7, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              10
  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
  RHPN2 MUTATED        2      1      0      1      2
  RHPN2 WILD-TYPE      4     10      7     11      3
D8V8, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             2               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"
D8V9, binary
                 cls
clus               0  1
  RHPN2 MUTATED    2  4
  RHPN2 WILD-TYPE 15 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      2    4
  RHPN2 WILD-TYPE   15   15
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RHPN2 MUTATED        0      0      0      0      3      1      0      1
  RHPN2 WILD-TYPE      4      5      5      6      4      0      4      0
                 vv
clus              CLUS_9
  RHPN2 MUTATED        1
  RHPN2 WILD-TYPE      2
D8V10, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             3               4
  CLUS_6             1               0
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             1               2
[1] 9 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 = FOXD4L1 MUTATION ANALYSIS
D9V1, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    5  2
  FOXD4L1 WILD-TYPE 18 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      5    2
  FOXD4L1 WILD-TYPE   18   16
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               5                18
  CLUS_2               2                16
[1] 2 2
[1] FALSE
D9V2, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    4  3
  FOXD4L1 WILD-TYPE 16 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      4    3
  FOXD4L1 WILD-TYPE   16   18
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               4                16
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D9V3, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    2  2
  FOXD4L1 WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      2    2
  FOXD4L1 WILD-TYPE   13   12
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FOXD4L1 MUTATED        2      1      1
  FOXD4L1 WILD-TYPE      3     12     10
D9V4, multiclass
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               2                 3
  CLUS_2               1                12
  CLUS_3               1                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"
D9V5, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    2  2
  FOXD4L1 WILD-TYPE  7 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      2    2
  FOXD4L1 WILD-TYPE    7   10
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FOXD4L1 MUTATED        0      2      2
  FOXD4L1 WILD-TYPE      7      7      3
D9V6, multiclass
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                 7
  CLUS_3               2                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXD4L1 MUTATED        2      2      1      2
  FOXD4L1 WILD-TYPE      9      9      9      7
D9V7, multiclass
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 9
  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
  FOXD4L1 MUTATED        1      2      1      3      0
  FOXD4L1 WILD-TYPE      5      9      6      9      5
D9V8, multiclass
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                 9
  CLUS_3               1                 6
  CLUS_4               3                 9
  CLUS_5               0                 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"
D9V9, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    1  5
  FOXD4L1 WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      1    5
  FOXD4L1 WILD-TYPE   16   14
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               1                16
  CLUS_2               5                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FOXD4L1 MUTATED        1      1      1      1      0      0      1      1
  FOXD4L1 WILD-TYPE      3      4      4      5      7      1      3      0
                   vv
clus                CLUS_9
  FOXD4L1 MUTATED        0
  FOXD4L1 WILD-TYPE      3
D9V10, multiclass
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 4
  CLUS_3               1                 4
  CLUS_4               1                 5
  CLUS_5               0                 7
  CLUS_6               0                 1
  CLUS_7               1                 3
  CLUS_8               1                 0
  CLUS_9               0                 3
[1] 9 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 = DND1 MUTATION ANALYSIS
D10V1, binary
                cls
clus              0  1
  DND1 MUTATED    2  3
  DND1 WILD-TYPE 21 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      2    3
  DND1 WILD-TYPE   21   15
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            2             21
  CLUS_2            3             15
[1] 2 2
[1] FALSE
D10V2, binary
                cls
clus              0  1
  DND1 MUTATED    2  3
  DND1 WILD-TYPE 18 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      2    3
  DND1 WILD-TYPE   18   18
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            3             18
[1] 2 2
[1] FALSE
D10V3, binary
                cls
clus              0  1
  DND1 MUTATED    2  1
  DND1 WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      2    1
  DND1 WILD-TYPE   13   13
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            1             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DND1 MUTATED        1      2      0
  DND1 WILD-TYPE      4     11     11
D10V4, multiclass
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            2             11
  CLUS_3            0             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"
D10V5, binary
                cls
clus              0  1
  DND1 MUTATED    2  2
  DND1 WILD-TYPE  7 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      2    2
  DND1 WILD-TYPE    7   10
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            2             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DND1 MUTATED        0      2      2
  DND1 WILD-TYPE      7      7      3
D10V6, multiclass
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2              7
  CLUS_3            2              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DND1 MUTATED        2      1      0      2
  DND1 WILD-TYPE      9     10     10      7
D10V7, multiclass
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             10
  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
  DND1 MUTATED        1      1      1      1      1
  DND1 WILD-TYPE      5     10      6     11      4
D10V8, multiclass
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            1             10
  CLUS_3            1              6
  CLUS_4            1             11
  CLUS_5            1              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"
D10V9, binary
                cls
clus              0  1
  DND1 MUTATED    1  3
  DND1 WILD-TYPE 16 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      1    3
  DND1 WILD-TYPE   16   16
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            1             16
  CLUS_2            3             16
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  DND1 MUTATED        1      1      0      0      0      0      2      0      0
  DND1 WILD-TYPE      3      4      5      6      7      1      2      1      3
D10V10, multiclass
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            1              4
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            0              7
  CLUS_6            0              1
  CLUS_7            2              2
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = ATXN1 MUTATION ANALYSIS
D11V1, binary
                 cls
clus               0  1
  ATXN1 MUTATED    4  3
  ATXN1 WILD-TYPE 19 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      4    3
  ATXN1 WILD-TYPE   19   15
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D11V2, binary
                 cls
clus               0  1
  ATXN1 MUTATED    4  3
  ATXN1 WILD-TYPE 16 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      4    3
  ATXN1 WILD-TYPE   16   18
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D11V3, binary
                 cls
clus               0  1
  ATXN1 MUTATED    3  1
  ATXN1 WILD-TYPE 12 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      3    1
  ATXN1 WILD-TYPE   12   13
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ATXN1 MUTATED        0      3      1
  ATXN1 WILD-TYPE      5     10     10
D11V4, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             3              10
  CLUS_3             1              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"
D11V5, binary
                 cls
clus               0  1
  ATXN1 MUTATED    2  2
  ATXN1 WILD-TYPE  7 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      2    2
  ATXN1 WILD-TYPE    7   10
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ATXN1 MUTATED        1      2      1
  ATXN1 WILD-TYPE      6      7      4
D11V6, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             2               7
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATXN1 MUTATED        0      2      2      3
  ATXN1 WILD-TYPE     11      9      8      6
D11V7, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             2               9
  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
  ATXN1 MUTATED        2      2      0      1      2
  ATXN1 WILD-TYPE      4      9      7     11      3
D11V8, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             2               9
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             2               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"
D11V9, binary
                 cls
clus               0  1
  ATXN1 MUTATED    2  5
  ATXN1 WILD-TYPE 15 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      2    5
  ATXN1 WILD-TYPE   15   14
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             5              14
[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        0      1      0      2      2      0      1      1
  ATXN1 WILD-TYPE      4      4      5      4      5      1      3      0
                 vv
clus              CLUS_9
  ATXN1 MUTATED        0
  ATXN1 WILD-TYPE      3
D11V10, multiclass
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             2               4
  CLUS_5             2               5
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = TP53 MUTATION ANALYSIS
D12V1, binary
                cls
clus              0  1
  TP53 MUTATED    1  5
  TP53 WILD-TYPE 22 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1    5
  TP53 WILD-TYPE   22   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             22
  CLUS_2            5             13
[1] 2 2
[1] FALSE
D12V2, binary
                cls
clus              0  1
  TP53 MUTATED    2  4
  TP53 WILD-TYPE 18 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    4
  TP53 WILD-TYPE   18   17
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            4             17
[1] 2 2
[1] FALSE
D12V3, binary
                cls
clus              0  1
  TP53 MUTATED    2  1
  TP53 WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    1
  TP53 WILD-TYPE   13   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            1             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        1      1      1
  TP53 WILD-TYPE      4     12     10
D12V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            1             12
  CLUS_3            1             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"
D12V5, binary
                cls
clus              0  1
  TP53 MUTATED    2  0
  TP53 WILD-TYPE  7 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    0
  TP53 WILD-TYPE    7   12
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            0             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        1      0      1
  TP53 WILD-TYPE      6      9      4
D12V6, multiclass
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             2             19 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8046 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FM-8000 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G8-6324     TCGA-GR-7353     TCGA-GR-A4D5     TCGA-GR-A4D6 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GR-A4D9     TCGA-RQ-A68N     TCGA-RQ-A6JB 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      1      0      3
  TP53 WILD-TYPE      9     10     10      6
D12V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             10
  CLUS_3            0             10
  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        1      2      2      0      1
  TP53 WILD-TYPE      5      9      5     12      4
D12V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2              9
  CLUS_3            2              5
  CLUS_4            0             12
  CLUS_5            1              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"
D12V9, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE 15 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE   15   16
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             15
  CLUS_2            3             16
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  TP53 MUTATED        1      1      1      0      1      0      1      0      0
  TP53 WILD-TYPE      3      4      4      6      6      1      3      1      3
D12V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            1              4
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            1              3
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = CDC27 MUTATION ANALYSIS
D13V1, binary
                 cls
clus               0  1
  CDC27 MUTATED    6  4
  CDC27 WILD-TYPE 17 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      6    4
  CDC27 WILD-TYPE   17   14
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             6              17
  CLUS_2             4              14
[1] 2 2
[1] FALSE
D13V2, binary
                 cls
clus               0  1
  CDC27 MUTATED    6  4
  CDC27 WILD-TYPE 14 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      6    4
  CDC27 WILD-TYPE   14   17
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             6              14
  CLUS_2             4              17
[1] 2 2
[1] FALSE
D13V3, binary
                 cls
clus               0  1
  CDC27 MUTATED    4  3
  CDC27 WILD-TYPE 11 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      4    3
  CDC27 WILD-TYPE   11   11
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              11
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDC27 MUTATED        2      2      3
  CDC27 WILD-TYPE      3     11      8
D13V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             2              11
  CLUS_3             3               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"
D13V5, binary
                 cls
clus              0 1
  CDC27 MUTATED   3 5
  CDC27 WILD-TYPE 6 7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    5
  CDC27 WILD-TYPE    6    7
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             5               7
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDC27 MUTATED        2      4      2
  CDC27 WILD-TYPE      5      5      3
D13V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             4               5
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDC27 MUTATED        2      3      1      4
  CDC27 WILD-TYPE      9      8      9      5
D13V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               9
  CLUS_2             3               8
  CLUS_3             1               9
  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
  CDC27 MUTATED        1      3      1      1      4
  CDC27 WILD-TYPE      5      8      6     11      1
D13V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             3               8
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             4               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"
D13V9, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  8
  CDC27 WILD-TYPE 15 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    8
  CDC27 WILD-TYPE   15   11
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             8              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDC27 MUTATED        1      2      0      0      3      0      2      1
  CDC27 WILD-TYPE      3      3      5      6      4      1      2      0
                 vv
clus              CLUS_9
  CDC27 MUTATED        1
  CDC27 WILD-TYPE      2
D13V10, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             2               3
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             3               4
  CLUS_6             0               1
  CLUS_7             2               2
  CLUS_8             1               0
  CLUS_9             1               2
[1] 9 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 = EPB41L4A MUTATION ANALYSIS
D14V1, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    3  1
  EPB41L4A WILD-TYPE 20 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      3    1
  EPB41L4A WILD-TYPE   20   17
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                3                 20
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
D14V2, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    3  1
  EPB41L4A WILD-TYPE 17 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      3    1
  EPB41L4A WILD-TYPE   17   20
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D14V3, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    1  2
  EPB41L4A WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      1    2
  EPB41L4A WILD-TYPE   14   12
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  EPB41L4A MUTATED        0      1      2
  EPB41L4A WILD-TYPE      5     12      9
D14V4, multiclass
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                 12
  CLUS_3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    0  2
  EPB41L4A WILD-TYPE  9 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      0    2
  EPB41L4A WILD-TYPE    9   10
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  EPB41L4A MUTATED        1      1      0
  EPB41L4A WILD-TYPE      6      8      5
D14V6, multiclass
[1] "Remove cluster labels:" "EPB41L4A MUTATED"      
clus
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 2                 19 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FM-8000 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-G8-6324         TCGA-GR-A4D4         TCGA-GR-A4D5 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-GR-A4D6         TCGA-GR-A4D9         TCGA-RQ-A68N 
"EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" "EPB41L4A WILD-TYPE" 
        TCGA-RQ-A6JB 
"EPB41L4A WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EPB41L4A MUTATED        0      2      1      1
  EPB41L4A WILD-TYPE     11      9      9      8
D14V7, multiclass
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  9
  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
  EPB41L4A MUTATED        0      2      0      1      1
  EPB41L4A WILD-TYPE      6      9      7     11      4
D14V8, multiclass
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                2                  9
  CLUS_3                0                  7
  CLUS_4                1                 11
  CLUS_5                1                  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"
D14V9, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    1  3
  EPB41L4A WILD-TYPE 16 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      1    3
  EPB41L4A WILD-TYPE   16   16
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  EPB41L4A MUTATED        1      1      0      1      1      0      0      0
  EPB41L4A WILD-TYPE      3      4      5      5      6      1      4      1
                    vv
clus                 CLUS_9
  EPB41L4A MUTATED        0
  EPB41L4A WILD-TYPE      3
D14V10, multiclass
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  4
  CLUS_3                0                  5
  CLUS_4                1                  5
  CLUS_5                1                  6
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                0                  1
  CLUS_9                0                  3
[1] 9 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 = NOTCH2NL MUTATION ANALYSIS
D15V1, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    2  2
  NOTCH2NL WILD-TYPE 21 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      2    2
  NOTCH2NL WILD-TYPE   21   16
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D15V2, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    3  1
  NOTCH2NL WILD-TYPE 17 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3    1
  NOTCH2NL WILD-TYPE   17   20
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D15V3, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    0  1
  NOTCH2NL WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      0    1
  NOTCH2NL WILD-TYPE   15   13
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  NOTCH2NL MUTATED        0      0      1
  NOTCH2NL WILD-TYPE      5     13     10
D15V4, multiclass
[1] "Remove cluster labels:" "NOTCH2NL MUTATED"      
clus
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                 28 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FF-8041 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FM-8000         TCGA-GS-A9TT         TCGA-GS-A9TV 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-VB-A8QN 
"NOTCH2NL WILD-TYPE" 
D15V5, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    0  1
  NOTCH2NL WILD-TYPE  9 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      0    1
  NOTCH2NL WILD-TYPE    9   11
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  NOTCH2NL MUTATED        0      1      0
  NOTCH2NL WILD-TYPE      7      8      5
D15V6, multiclass
[1] "Remove cluster labels:" "NOTCH2NL MUTATED"      
clus
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                 20 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-FM-8000         TCGA-GR-7353         TCGA-GR-A4D4 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"NOTCH2NL WILD-TYPE" "NOTCH2NL WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH2NL MUTATED        1      2      1      0
  NOTCH2NL WILD-TYPE     10      9      9      9
D15V7, multiclass
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                  9
  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
  NOTCH2NL MUTATED        0      2      1      1      0
  NOTCH2NL WILD-TYPE      6      9      6     11      5
D15V8, multiclass
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                2                  9
  CLUS_3                1                  6
  CLUS_4                1                 11
  CLUS_5                0                  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"
D15V9, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    1  3
  NOTCH2NL WILD-TYPE 16 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      1    3
  NOTCH2NL WILD-TYPE   16   16
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NOTCH2NL MUTATED        0      1      1      0      0      0      0      1
  NOTCH2NL WILD-TYPE      4      4      4      6      7      1      4      0
                    vv
clus                 CLUS_9
  NOTCH2NL MUTATED        1
  NOTCH2NL WILD-TYPE      2
D15V10, multiclass
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  4
  CLUS_3                1                  4
  CLUS_4                0                  6
  CLUS_5                0                  7
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                1                  2
[1] 9 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 = KRT3 MUTATION ANALYSIS
D16V1, binary
                cls
clus              0  1
  KRT3 MUTATED    2  2
  KRT3 WILD-TYPE 21 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      2    2
  KRT3 WILD-TYPE   21   16
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            2             21
  CLUS_2            2             16
[1] 2 2
[1] FALSE
D16V2, binary
                cls
clus              0  1
  KRT3 MUTATED    2  2
  KRT3 WILD-TYPE 18 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      2    2
  KRT3 WILD-TYPE   18   19
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            2             19
[1] 2 2
[1] FALSE
D16V3, binary
                cls
clus              0  1
  KRT3 MUTATED    0  2
  KRT3 WILD-TYPE 15 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      0    2
  KRT3 WILD-TYPE   15   12
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            0             15
  CLUS_2            2             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT3 MUTATED        0      0      2
  KRT3 WILD-TYPE      5     13      9
D16V4, multiclass
[1] "Remove cluster labels:" "KRT3 MUTATED"          
clus
  KRT3 MUTATED KRT3 WILD-TYPE 
             2             27 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A82F     TCGA-FA-A86F 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-A7CR     TCGA-FF-A7CW 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FF-A7CX     TCGA-FM-8000     TCGA-GS-A9TT     TCGA-GS-A9TV 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
D16V5, binary
                cls
clus              0  1
  KRT3 MUTATED    0  2
  KRT3 WILD-TYPE  9 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      0    2
  KRT3 WILD-TYPE    9   10
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT3 MUTATED        1      1      0
  KRT3 WILD-TYPE      6      8      5
D16V6, multiclass
[1] "Remove cluster labels:" "KRT3 MUTATED"          
clus
  KRT3 MUTATED KRT3 WILD-TYPE 
             2             19 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FM-8000 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
    TCGA-GR-A4D9     TCGA-RQ-A68N     TCGA-RQ-A6JB 
"KRT3 WILD-TYPE" "KRT3 WILD-TYPE" "KRT3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRT3 MUTATED        1      2      1      0
  KRT3 WILD-TYPE     10      9      9      9
D16V7, multiclass
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            2              9
  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
  KRT3 MUTATED        0      2      1      1      0
  KRT3 WILD-TYPE      6      9      6     11      5
D16V8, multiclass
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            2              9
  CLUS_3            1              6
  CLUS_4            1             11
  CLUS_5            0              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"
D16V9, binary
                cls
clus              0  1
  KRT3 MUTATED    2  2
  KRT3 WILD-TYPE 15 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      2    2
  KRT3 WILD-TYPE   15   17
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            2             15
  CLUS_2            2             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  KRT3 MUTATED        1      0      0      1      1      0      0      1      0
  KRT3 WILD-TYPE      3      5      5      5      6      1      4      0      3
D16V10, multiclass
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            0              5
  CLUS_3            0              5
  CLUS_4            1              5
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            0              4
  CLUS_8            1              0
  CLUS_9            0              3
[1] 9 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 = OR1S2 MUTATION ANALYSIS
D17V1, binary
                 cls
clus               0  1
  OR1S2 MUTATED    7  3
  OR1S2 WILD-TYPE 16 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      7    3
  OR1S2 WILD-TYPE   16   15
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             7              16
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D17V2, binary
                 cls
clus               0  1
  OR1S2 MUTATED    5  5
  OR1S2 WILD-TYPE 15 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      5    5
  OR1S2 WILD-TYPE   15   16
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             5              15
  CLUS_2             5              16
[1] 2 2
[1] FALSE
D17V3, binary
                 cls
clus               0  1
  OR1S2 MUTATED    4  2
  OR1S2 WILD-TYPE 11 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      4    2
  OR1S2 WILD-TYPE   11   12
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             4              11
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR1S2 MUTATED        2      2      2
  OR1S2 WILD-TYPE      3     11      9
D17V4, multiclass
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             2              11
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                 cls
clus               0  1
  OR1S2 MUTATED    3  2
  OR1S2 WILD-TYPE  6 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      3    2
  OR1S2 WILD-TYPE    6   10
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR1S2 MUTATED        1      2      2
  OR1S2 WILD-TYPE      6      7      3
D17V6, multiclass
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             2               7
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR1S2 MUTATED        4      2      3      1
  OR1S2 WILD-TYPE      7      9      7      8
D17V7, multiclass
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             4               7
  CLUS_2             2               9
  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
  OR1S2 MUTATED        2      2      2      4      0
  OR1S2 WILD-TYPE      4      9      5      8      5
D17V8, multiclass
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             2               9
  CLUS_3             2               5
  CLUS_4             4               8
  CLUS_5             0               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"
D17V9, binary
                 cls
clus               0  1
  OR1S2 MUTATED    5  3
  OR1S2 WILD-TYPE 12 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      5    3
  OR1S2 WILD-TYPE   12   16
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             5              12
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OR1S2 MUTATED        1      1      0      1      2      0      1      1
  OR1S2 WILD-TYPE      3      4      5      5      5      1      3      0
                 vv
clus              CLUS_9
  OR1S2 MUTATED        1
  OR1S2 WILD-TYPE      2
D17V10, multiclass
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               5
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             1               2
[1] 9 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 = RGPD5 MUTATION ANALYSIS
D18V1, binary
                 cls
clus               0  1
  RGPD5 MUTATED    5  0
  RGPD5 WILD-TYPE 18 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      5    0
  RGPD5 WILD-TYPE   18   18
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             5              18
  CLUS_2             0              18
[1] 2 2
[1] FALSE
D18V2, binary
                 cls
clus               0  1
  RGPD5 MUTATED    4  1
  RGPD5 WILD-TYPE 16 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      4    1
  RGPD5 WILD-TYPE   16   20
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             1              20
[1] 2 2
[1] FALSE
D18V3, binary
                 cls
clus               0  1
  RGPD5 MUTATED    2  2
  RGPD5 WILD-TYPE 13 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      2    2
  RGPD5 WILD-TYPE   13   12
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RGPD5 MUTATED        2      1      1
  RGPD5 WILD-TYPE      3     12     10
D18V4, multiclass
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1              12
  CLUS_3             1              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"
D18V5, binary
                 cls
clus               0  1
  RGPD5 MUTATED    1  1
  RGPD5 WILD-TYPE  8 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      1    1
  RGPD5 WILD-TYPE    8   11
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RGPD5 MUTATED        1      1      0
  RGPD5 WILD-TYPE      6      8      5
D18V6, multiclass
[1] "Remove cluster labels:" "RGPD5 MUTATED"         
clus
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              2              19 
     TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN      TCGA-FA-A6HO 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FM-8000 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-GR-7353      TCGA-GR-A4D4      TCGA-GR-A4D5      TCGA-GR-A4D6 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-GR-A4D9      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RGPD5 MUTATED        1      1      2      1
  RGPD5 WILD-TYPE     10     10      8      8
D18V7, multiclass
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              10
  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
  RGPD5 MUTATED        1      1      0      3      0
  RGPD5 WILD-TYPE      5     10      7      9      5
D18V8, multiclass
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             3               9
  CLUS_5             0               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"
D18V9, binary
                 cls
clus               0  1
  RGPD5 MUTATED    2  3
  RGPD5 WILD-TYPE 15 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      2    3
  RGPD5 WILD-TYPE   15   16
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RGPD5 MUTATED        1      0      2      1      0      0      0      1
  RGPD5 WILD-TYPE      3      5      3      5      7      1      4      0
                 vv
clus              CLUS_9
  RGPD5 MUTATED        0
  RGPD5 WILD-TYPE      3
D18V10, multiclass
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               5
  CLUS_3             2               3
  CLUS_4             1               5
  CLUS_5             0               7
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = TNFAIP3 MUTATION ANALYSIS
D19V1, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    6  0
  TNFAIP3 WILD-TYPE 17 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      6    0
  TNFAIP3 WILD-TYPE   17   18
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               6                17
  CLUS_2               0                18
[1] 2 2
[1] FALSE
D19V2, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    3  3
  TNFAIP3 WILD-TYPE 17 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      3    3
  TNFAIP3 WILD-TYPE   17   18
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D19V3, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    2  3
  TNFAIP3 WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      2    3
  TNFAIP3 WILD-TYPE   13   11
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               2                13
  CLUS_2               3                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TNFAIP3 MUTATED        0      3      2
  TNFAIP3 WILD-TYPE      5     10      9
D19V4, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                10
  CLUS_3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    0  2
  TNFAIP3 WILD-TYPE  9 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      0    2
  TNFAIP3 WILD-TYPE    9   10
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TNFAIP3 MUTATED        1      1      0
  TNFAIP3 WILD-TYPE      6      8      5
D19V6, multiclass
[1] "Remove cluster labels:" "TNFAIP3 MUTATED"       
clus
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                2                19 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" "TNFAIP3 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNFAIP3 MUTATED        0      3      2      1
  TNFAIP3 WILD-TYPE     11      8      8      8
D19V7, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                11
  CLUS_2               3                 8
  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
  TNFAIP3 MUTATED        1      3      0      1      1
  TNFAIP3 WILD-TYPE      5      8      7     11      4
D19V8, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                 8
  CLUS_3               0                 7
  CLUS_4               1                11
  CLUS_5               1                 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"
D19V9, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    1  4
  TNFAIP3 WILD-TYPE 16 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      1    4
  TNFAIP3 WILD-TYPE   16   15
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               1                16
  CLUS_2               4                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TNFAIP3 MUTATED        0      1      0      2      0      1      0      1
  TNFAIP3 WILD-TYPE      4      4      5      4      7      0      4      0
                   vv
clus                CLUS_9
  TNFAIP3 MUTATED        0
  TNFAIP3 WILD-TYPE      3
D19V10, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               0                 5
  CLUS_4               2                 4
  CLUS_5               0                 7
  CLUS_6               1                 0
  CLUS_7               0                 4
  CLUS_8               1                 0
  CLUS_9               0                 3
[1] 9 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 = RBMXL1 MUTATION ANALYSIS
D20V1, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  2
  RBMXL1 WILD-TYPE 21 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    2
  RBMXL1 WILD-TYPE   21   16
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              2               21
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D20V2, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    3  1
  RBMXL1 WILD-TYPE 17 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      3    1
  RBMXL1 WILD-TYPE   17   20
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D20V3, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  1
  RBMXL1 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    1
  RBMXL1 WILD-TYPE   13   13
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RBMXL1 MUTATED        0      2      1
  RBMXL1 WILD-TYPE      5     11     10
D20V4, multiclass
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2               11
  CLUS_3              1               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"
D20V5, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    1  1
  RBMXL1 WILD-TYPE  8 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      1    1
  RBMXL1 WILD-TYPE    8   11
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               11
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RBMXL1 MUTATED        1      1      0
  RBMXL1 WILD-TYPE      6      8      5
D20V6, multiclass
[1] "Remove cluster labels:" "RBMXL1 MUTATED"        
clus
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               2               19 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FF-8041       TCGA-FF-8043       TCGA-FF-8047 
"RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" 
      TCGA-FF-8061       TCGA-FF-8062       TCGA-FM-8000       TCGA-G8-6324 
"RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" 
      TCGA-GR-7353       TCGA-GR-A4D4       TCGA-GR-A4D5       TCGA-GR-A4D6 
"RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" 
      TCGA-GR-A4D9       TCGA-RQ-A68N       TCGA-RQ-A6JB 
"RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" "RBMXL1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBMXL1 MUTATED        2      1      1      0
  RBMXL1 WILD-TYPE      9     10      9      9
D20V7, multiclass
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              1               10
  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
  RBMXL1 MUTATED        2      1      0      1      0
  RBMXL1 WILD-TYPE      4     10      7     11      5
D20V8, multiclass
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              2                4
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              0                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"
D20V9, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  2
  RBMXL1 WILD-TYPE 15 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    2
  RBMXL1 WILD-TYPE   15   17
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              2               17
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RBMXL1 MUTATED        0      1      0      0      2      0      0      0
  RBMXL1 WILD-TYPE      4      4      5      6      5      1      4      1
                  vv
clus               CLUS_9
  RBMXL1 MUTATED        1
  RBMXL1 WILD-TYPE      2
D20V10, multiclass
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              0                1
  CLUS_9              1                2
[1] 9 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 = CCDC66 MUTATION ANALYSIS
D21V1, binary
                  cls
clus                0  1
  CCDC66 MUTATED    2  2
  CCDC66 WILD-TYPE 21 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      2    2
  CCDC66 WILD-TYPE   21   16
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              2               21
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D21V2, binary
                  cls
clus                0  1
  CCDC66 MUTATED    4  0
  CCDC66 WILD-TYPE 16 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      4    0
  CCDC66 WILD-TYPE   16   21
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              4               16
  CLUS_2              0               21
[1] 2 2
[1] FALSE
D21V3, binary
                  cls
clus                0  1
  CCDC66 MUTATED    0  2
  CCDC66 WILD-TYPE 15 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      0    2
  CCDC66 WILD-TYPE   15   12
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0               15
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CCDC66 MUTATED        0      0      2
  CCDC66 WILD-TYPE      5     13      9
D21V4, multiclass
[1] "Remove cluster labels:" "CCDC66 MUTATED"        
clus
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A7DS 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-FA-A7Q1       TCGA-FA-A82F       TCGA-FA-A86F       TCGA-FF-8041 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046       TCGA-FF-8047 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR       TCGA-FF-A7CW 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT       TCGA-GS-A9TV 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" "CCDC66 WILD-TYPE" 
D21V5, binary
                  cls
clus               0 1
  CCDC66 MUTATED   0 4
  CCDC66 WILD-TYPE 9 8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      0    4
  CCDC66 WILD-TYPE    9    8
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              4                8
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CCDC66 MUTATED        0      4      0
  CCDC66 WILD-TYPE      7      5      5
D21V6, multiclass
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              4                5
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC66 MUTATED        0      3      0      1
  CCDC66 WILD-TYPE     11      8     10      8
D21V7, multiclass
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              3                8
  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
  CCDC66 MUTATED        0      3      0      0      1
  CCDC66 WILD-TYPE      6      8      7     12      4
D21V8, multiclass
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              3                8
  CLUS_3              0                7
  CLUS_4              0               12
  CLUS_5              1                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"
D21V9, binary
                  cls
clus                0  1
  CCDC66 MUTATED    0  3
  CCDC66 WILD-TYPE 17 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      0    3
  CCDC66 WILD-TYPE   17   16
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0               17
  CLUS_2              3               16
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CCDC66 MUTATED        0      1      0      0      1      0      0      1
  CCDC66 WILD-TYPE      4      4      5      6      6      1      4      0
                  vv
clus               CLUS_9
  CCDC66 MUTATED        0
  CCDC66 WILD-TYPE      3
D21V10, multiclass
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = NOTCH2 MUTATION ANALYSIS
D22V1, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    5  2
  NOTCH2 WILD-TYPE 18 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      5    2
  NOTCH2 WILD-TYPE   18   16
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              5               18
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D22V2, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    3  4
  NOTCH2 WILD-TYPE 17 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      3    4
  NOTCH2 WILD-TYPE   17   17
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              4               17
[1] 2 2
[1] FALSE
D22V3, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    2  2
  NOTCH2 WILD-TYPE 13 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      2    2
  NOTCH2 WILD-TYPE   13   12
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH2 MUTATED        1      2      1
  NOTCH2 WILD-TYPE      4     11     10
D22V4, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              2               11
  CLUS_3              1               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"
D22V5, binary
                  cls
clus               0 1
  NOTCH2 MUTATED   1 4
  NOTCH2 WILD-TYPE 8 8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      1    4
  NOTCH2 WILD-TYPE    8    8
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              4                8
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH2 MUTATED        0      3      2
  NOTCH2 WILD-TYPE      7      6      3
D22V6, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              3                6
  CLUS_3              2                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH2 MUTATED        2      3      1      1
  NOTCH2 WILD-TYPE      9      8      9      8
D22V7, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              3                8
  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
  NOTCH2 MUTATED        1      3      1      1      1
  NOTCH2 WILD-TYPE      5      8      6     11      4
D22V8, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              3                8
  CLUS_3              1                6
  CLUS_4              1               11
  CLUS_5              1                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"
D22V9, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    2  4
  NOTCH2 WILD-TYPE 15 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      2    4
  NOTCH2 WILD-TYPE   15   15
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              4               15
[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      3      1      1      0      0      1      0
  NOTCH2 WILD-TYPE      4      2      4      5      7      1      3      1
                  vv
clus               CLUS_9
  NOTCH2 MUTATED        0
  NOTCH2 WILD-TYPE      3
D22V10, multiclass
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              3                2
  CLUS_3              1                4
  CLUS_4              1                5
  CLUS_5              0                7
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              0                1
  CLUS_9              0                3
[1] 9 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 = PCMTD1 MUTATION ANALYSIS
D23V1, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    3  3
  PCMTD1 WILD-TYPE 20 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      3    3
  PCMTD1 WILD-TYPE   20   15
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              3               20
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D23V2, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    3  3
  PCMTD1 WILD-TYPE 17 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      3    3
  PCMTD1 WILD-TYPE   17   18
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              3               18
[1] 2 2
[1] FALSE
D23V3, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    2  3
  PCMTD1 WILD-TYPE 13 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      2    3
  PCMTD1 WILD-TYPE   13   11
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              3               11
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PCMTD1 MUTATED        0      2      3
  PCMTD1 WILD-TYPE      5     11      8
D23V4, multiclass
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2               11
  CLUS_3              3                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"
D23V5, binary
                  cls
clus               0 1
  PCMTD1 MUTATED   2 3
  PCMTD1 WILD-TYPE 7 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      2    3
  PCMTD1 WILD-TYPE    7    9
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PCMTD1 MUTATED        3      2      0
  PCMTD1 WILD-TYPE      4      7      5
D23V6, multiclass
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              3                4
  CLUS_2              2                7
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCMTD1 MUTATED        2      3      0      1
  PCMTD1 WILD-TYPE      9      8     10      8
D23V7, multiclass
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              3                8
  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
  PCMTD1 MUTATED        1      3      1      0      1
  PCMTD1 WILD-TYPE      5      8      6     12      4
D23V8, multiclass
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              3                8
  CLUS_3              1                6
  CLUS_4              0               12
  CLUS_5              1                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"
D23V9, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    2  4
  PCMTD1 WILD-TYPE 15 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      2    4
  PCMTD1 WILD-TYPE   15   15
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PCMTD1 MUTATED        1      1      1      0      1      0      1      1
  PCMTD1 WILD-TYPE      3      4      4      6      6      1      3      0
                  vv
clus               CLUS_9
  PCMTD1 MUTATED        0
  PCMTD1 WILD-TYPE      3
D23V10, multiclass
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              1                4
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = FAM120B MUTATION ANALYSIS
D24V1, binary
                   cls
clus                 0  1
  FAM120B MUTATED    3  2
  FAM120B WILD-TYPE 20 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      3    2
  FAM120B WILD-TYPE   20   16
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               3                20
  CLUS_2               2                16
[1] 2 2
[1] FALSE
D24V2, binary
                   cls
clus                 0  1
  FAM120B MUTATED    2  3
  FAM120B WILD-TYPE 18 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      2    3
  FAM120B WILD-TYPE   18   18
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               2                18
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D24V3, binary
                   cls
clus                 0  1
  FAM120B MUTATED    3  0
  FAM120B WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      3    0
  FAM120B WILD-TYPE   12   14
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               3                12
  CLUS_2               0                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        0      3      0
  FAM120B WILD-TYPE      5     10     11
D24V4, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                10
  CLUS_3               0                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"
D24V5, binary
                   cls
clus                 0  1
  FAM120B MUTATED    2  2
  FAM120B WILD-TYPE  7 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      2    2
  FAM120B WILD-TYPE    7   10
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        1      2      1
  FAM120B WILD-TYPE      6      7      4
D24V6, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                 7
  CLUS_3               1                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM120B MUTATED        3      1      1      0
  FAM120B WILD-TYPE      8     10      9      9
D24V7, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               1                10
  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
  FAM120B MUTATED        3      1      0      1      0
  FAM120B WILD-TYPE      3     10      7     11      5
D24V8, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               1                11
  CLUS_5               0                 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"
D24V9, binary
                   cls
clus                 0  1
  FAM120B MUTATED    3  1
  FAM120B WILD-TYPE 14 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      3    1
  FAM120B WILD-TYPE   14   18
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               3                14
  CLUS_2               1                18
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FAM120B MUTATED        0      0      0      1      2      0      1      0
  FAM120B WILD-TYPE      4      5      5      5      5      1      3      1
                   vv
clus                CLUS_9
  FAM120B MUTATED        0
  FAM120B WILD-TYPE      3
D24V10, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               0                 5
  CLUS_4               1                 5
  CLUS_5               2                 5
  CLUS_6               0                 1
  CLUS_7               1                 3
  CLUS_8               0                 1
  CLUS_9               0                 3
[1] 9 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 = SMARCA2 MUTATION ANALYSIS
D25V1, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    2  2
  SMARCA2 WILD-TYPE 21 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      2    2
  SMARCA2 WILD-TYPE   21   16
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               2                21
  CLUS_2               2                16
[1] 2 2
[1] FALSE
D25V2, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    3  1
  SMARCA2 WILD-TYPE 17 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      3    1
  SMARCA2 WILD-TYPE   17   20
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D25V3, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    0  2
  SMARCA2 WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      0    2
  SMARCA2 WILD-TYPE   15   12
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               0                15
  CLUS_2               2                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA2 MUTATED        0      0      2
  SMARCA2 WILD-TYPE      5     13      9
D25V4, multiclass
[1] "Remove cluster labels:" "SMARCA2 MUTATED"       
clus
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                27 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8061        TCGA-FF-A7CR        TCGA-FF-A7CW 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-FF-A7CX        TCGA-FM-8000        TCGA-GS-A9TT        TCGA-GS-A9TV 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ        TCGA-GS-A9U4 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
D25V5, binary
                   cls
clus                0 1
  SMARCA2 MUTATED   1 3
  SMARCA2 WILD-TYPE 8 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      1    3
  SMARCA2 WILD-TYPE    8    9
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               3                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA2 MUTATED        1      1      2
  SMARCA2 WILD-TYPE      6      8      3
D25V6, multiclass
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 8
  CLUS_3               2                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCA2 MUTATED        0      2      0      2
  SMARCA2 WILD-TYPE     11      9     10      7
D25V7, multiclass
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                 9
  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
  SMARCA2 MUTATED        1      2      0      0      1
  SMARCA2 WILD-TYPE      5      9      7     12      4
D25V8, multiclass
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                 9
  CLUS_3               0                 7
  CLUS_4               0                12
  CLUS_5               1                 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"
D25V9, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    0  4
  SMARCA2 WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      0    4
  SMARCA2 WILD-TYPE   17   15
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               4                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SMARCA2 MUTATED        1      1      0      0      1      0      1      0
  SMARCA2 WILD-TYPE      3      4      5      6      6      1      3      1
                   vv
clus                CLUS_9
  SMARCA2 MUTATED        0
  SMARCA2 WILD-TYPE      3
D25V10, multiclass
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 4
  CLUS_3               0                 5
  CLUS_4               0                 6
  CLUS_5               1                 6
  CLUS_6               0                 1
  CLUS_7               1                 3
  CLUS_8               0                 1
  CLUS_9               0                 3
[1] 9 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 = C11ORF40 MUTATION ANALYSIS
D26V1, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    2  2
  C11ORF40 WILD-TYPE 21 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      2    2
  C11ORF40 WILD-TYPE   21   16
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D26V2, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    2  2
  C11ORF40 WILD-TYPE 18 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      2    2
  C11ORF40 WILD-TYPE   18   19
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D26V3, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    1  1
  C11ORF40 WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      1    1
  C11ORF40 WILD-TYPE   14   13
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C11ORF40 MUTATED        1      0      1
  C11ORF40 WILD-TYPE      4     13     10
D26V4, multiclass
[1] "Remove cluster labels:" "C11ORF40 MUTATED"      
clus
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 2                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A86F         TCGA-FF-8041 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CX         TCGA-FM-8000 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TV         TCGA-GS-A9TW 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9TZ         TCGA-GS-A9U4 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB         TCGA-VB-A8QN 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
D26V5, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    0  1
  C11ORF40 WILD-TYPE  9 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      0    1
  C11ORF40 WILD-TYPE    9   11
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C11ORF40 MUTATED        0      1      0
  C11ORF40 WILD-TYPE      7      8      5
D26V6, multiclass
[1] "Remove cluster labels:" "C11ORF40 MUTATED"      
clus
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 1                 20 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-FM-8000         TCGA-GR-7353         TCGA-GR-A4D4 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"C11ORF40 WILD-TYPE" "C11ORF40 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C11ORF40 MUTATED        1      1      2      0
  C11ORF40 WILD-TYPE     10     10      8      9
D26V7, multiclass
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 10
  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
  C11ORF40 MUTATED        0      1      1      2      0
  C11ORF40 WILD-TYPE      6     10      6     10      5
D26V8, multiclass
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 10
  CLUS_3                1                  6
  CLUS_4                2                 10
  CLUS_5                0                  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"
D26V9, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    2  1
  C11ORF40 WILD-TYPE 15 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      2    1
  C11ORF40 WILD-TYPE   15   18
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C11ORF40 MUTATED        1      0      0      1      0      0      0      1
  C11ORF40 WILD-TYPE      3      5      5      5      7      1      4      0
                    vv
clus                 CLUS_9
  C11ORF40 MUTATED        0
  C11ORF40 WILD-TYPE      3
D26V10, multiclass
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                1                  5
  CLUS_5                0                  7
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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 = ZSCAN5A MUTATION ANALYSIS
D27V1, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    1  2
  ZSCAN5A WILD-TYPE 22 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      1    2
  ZSCAN5A WILD-TYPE   22   16
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               1                22
  CLUS_2               2                16
[1] 2 2
[1] FALSE
D27V2, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    3  0
  ZSCAN5A WILD-TYPE 17 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      3    0
  ZSCAN5A WILD-TYPE   17   21
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               3                17
  CLUS_2               0                21
[1] 2 2
[1] FALSE
D27V3, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    0  0
  ZSCAN5A WILD-TYPE 15 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      0    0
  ZSCAN5A WILD-TYPE   15   14
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ZSCAN5A MUTATED        0      0      0
  ZSCAN5A WILD-TYPE      5     13     11
D27V4, multiclass
D27V5, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    0  2
  ZSCAN5A WILD-TYPE  9 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      0    2
  ZSCAN5A WILD-TYPE    9   10
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ZSCAN5A MUTATED        0      2      0
  ZSCAN5A WILD-TYPE      7      7      5
D27V6, multiclass
[1] "Remove cluster labels:" "ZSCAN5A MUTATED"       
clus
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                2                19 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-GR-A4D4        TCGA-GR-A4D5 
"ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" "ZSCAN5A WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZSCAN5A MUTATED        0      2      0      1
  ZSCAN5A WILD-TYPE     11      9     10      8
D27V7, multiclass
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                 9
  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
  ZSCAN5A MUTATED        0      1      0      1      1
  ZSCAN5A WILD-TYPE      6     10      7     11      4
D27V8, multiclass
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               1                11
  CLUS_5               1                 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"
D27V9, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    0  3
  ZSCAN5A WILD-TYPE 17 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      0    3
  ZSCAN5A WILD-TYPE   17   16
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               0                17
  CLUS_2               3                16
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZSCAN5A MUTATED        0      0      0      0      1      0      1      0
  ZSCAN5A WILD-TYPE      4      5      5      6      6      1      3      1
                   vv
clus                CLUS_9
  ZSCAN5A MUTATED        1
  ZSCAN5A WILD-TYPE      2
D27V10, multiclass
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               0                 5
  CLUS_4               0                 6
  CLUS_5               1                 6
  CLUS_6               0                 1
  CLUS_7               1                 3
  CLUS_8               0                 1
  CLUS_9               1                 2
[1] 9 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 = KRTAP4-5 MUTATION ANALYSIS
D28V1, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    2  2
  KRTAP4-5 WILD-TYPE 21 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      2    2
  KRTAP4-5 WILD-TYPE   21   16
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D28V2, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    3  1
  KRTAP4-5 WILD-TYPE 17 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      3    1
  KRTAP4-5 WILD-TYPE   17   20
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D28V3, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    1  0
  KRTAP4-5 WILD-TYPE 14 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      1    0
  KRTAP4-5 WILD-TYPE   14   14
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        1      0      0
  KRTAP4-5 WILD-TYPE      4     13     11
D28V4, multiclass
[1] "Remove cluster labels:" "KRTAP4-5 MUTATED"      
clus
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 1                 28 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-GS-A9TT 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-GS-A9TV         TCGA-GS-A9TW         TCGA-GS-A9TX 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-GS-A9TZ         TCGA-GS-A9U4         TCGA-RQ-A68N 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-VB-A8QN 
"KRTAP4-5 WILD-TYPE" 
D28V5, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    2  2
  KRTAP4-5 WILD-TYPE  7 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      2    2
  KRTAP4-5 WILD-TYPE    7   10
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        0      2      2
  KRTAP4-5 WILD-TYPE      7      7      3
D28V6, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                  7
  CLUS_3                2                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-5 MUTATED        1      1      0      2
  KRTAP4-5 WILD-TYPE     10     10     10      7
D28V7, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 10
  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
  KRTAP4-5 MUTATED        1      1      1      0      1
  KRTAP4-5 WILD-TYPE      5     10      6     12      4
D28V8, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 10
  CLUS_3                1                  6
  CLUS_4                0                 12
  CLUS_5                1                  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"
D28V9, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    1  3
  KRTAP4-5 WILD-TYPE 16 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      1    3
  KRTAP4-5 WILD-TYPE   16   16
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 16
[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      0      0      0      1      0      2      1
  KRTAP4-5 WILD-TYPE      4      5      5      6      6      1      2      0
                    vv
clus                 CLUS_9
  KRTAP4-5 MUTATED        0
  KRTAP4-5 WILD-TYPE      3
D28V10, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                0                  6
  CLUS_5                1                  6
  CLUS_6                0                  1
  CLUS_7                2                  2
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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 = DEFA1 MUTATION ANALYSIS
D29V1, binary
                 cls
clus               0  1
  DEFA1 MUTATED    2  2
  DEFA1 WILD-TYPE 21 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      2    2
  DEFA1 WILD-TYPE   21   16
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D29V2, binary
                 cls
clus               0  1
  DEFA1 MUTATED    2  2
  DEFA1 WILD-TYPE 18 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      2    2
  DEFA1 WILD-TYPE   18   19
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D29V3, binary
                 cls
clus               0  1
  DEFA1 MUTATED    1  1
  DEFA1 WILD-TYPE 14 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      1    1
  DEFA1 WILD-TYPE   14   13
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DEFA1 MUTATED        0      1      1
  DEFA1 WILD-TYPE      5     12     10
D29V4, multiclass
[1] "Remove cluster labels:" "DEFA1 MUTATED"         
clus
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              2              27 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-FA-A86F      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-GS-A9TT      TCGA-GS-A9TV 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" "DEFA1 WILD-TYPE" 
D29V5, binary
                 cls
clus              0 1
  DEFA1 MUTATED   0 3
  DEFA1 WILD-TYPE 9 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      0    3
  DEFA1 WILD-TYPE    9    9
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DEFA1 MUTATED        0      3      0
  DEFA1 WILD-TYPE      7      6      5
D29V6, multiclass
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             3               6
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEFA1 MUTATED        0      1      1      2
  DEFA1 WILD-TYPE     11     10      9      7
D29V7, multiclass
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             1              10
  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
  DEFA1 MUTATED        0      1      0      1      2
  DEFA1 WILD-TYPE      6     10      7     11      3
D29V8, multiclass
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             2               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"
D29V9, binary
                 cls
clus               0  1
  DEFA1 MUTATED    0  4
  DEFA1 WILD-TYPE 17 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      0    4
  DEFA1 WILD-TYPE   17   15
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  DEFA1 MUTATED        0      0      0      1      1      0      1      1
  DEFA1 WILD-TYPE      4      5      5      5      6      1      3      0
                 vv
clus              CLUS_9
  DEFA1 MUTATED        0
  DEFA1 WILD-TYPE      3
D29V10, multiclass
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = SIRPA MUTATION ANALYSIS
D30V1, binary
                 cls
clus               0  1
  SIRPA MUTATED    3  2
  SIRPA WILD-TYPE 20 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      3    2
  SIRPA WILD-TYPE   20   16
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             3              20
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D30V2, binary
                 cls
clus               0  1
  SIRPA MUTATED    3  2
  SIRPA WILD-TYPE 17 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      3    2
  SIRPA WILD-TYPE   17   19
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             3              17
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D30V3, binary
                 cls
clus               0  1
  SIRPA MUTATED    1  2
  SIRPA WILD-TYPE 14 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      1    2
  SIRPA WILD-TYPE   14   12
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             1              14
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SIRPA MUTATED        0      1      2
  SIRPA WILD-TYPE      5     12      9
D30V4, multiclass
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1              12
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                 cls
clus              0 1
  SIRPA MUTATED   1 4
  SIRPA WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      1    4
  SIRPA WILD-TYPE    8    8
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             1               8
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SIRPA MUTATED        2      3      0
  SIRPA WILD-TYPE      5      6      5
D30V6, multiclass
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             2               5
  CLUS_2             3               6
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SIRPA MUTATED        1      2      0      2
  SIRPA WILD-TYPE     10      9     10      7
D30V7, multiclass
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2               9
  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
  SIRPA MUTATED        0      2      1      0      2
  SIRPA WILD-TYPE      6      9      6     12      3
D30V8, multiclass
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2               9
  CLUS_3             1               6
  CLUS_4             0              12
  CLUS_5             2               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"
D30V9, binary
                 cls
clus               0  1
  SIRPA MUTATED    1  4
  SIRPA WILD-TYPE 16 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      1    4
  SIRPA WILD-TYPE   16   15
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             1              16
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SIRPA MUTATED        0      1      1      0      1      1      0      1
  SIRPA WILD-TYPE      4      4      4      6      6      0      4      0
                 vv
clus              CLUS_9
  SIRPA MUTATED        0
  SIRPA WILD-TYPE      3
D30V10, multiclass
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             1               4
  CLUS_4             0               6
  CLUS_5             1               6
  CLUS_6             1               0
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = TMPRSS13 MUTATION ANALYSIS
D31V1, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    1  2
  TMPRSS13 WILD-TYPE 22 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      1    2
  TMPRSS13 WILD-TYPE   22   16
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D31V2, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    2  1
  TMPRSS13 WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      2    1
  TMPRSS13 WILD-TYPE   18   20
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D31V3, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    1  1
  TMPRSS13 WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      1    1
  TMPRSS13 WILD-TYPE   14   13
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  TMPRSS13 MUTATED        1      0      1
  TMPRSS13 WILD-TYPE      4     13     10
D31V4, multiclass
[1] "Remove cluster labels:" "TMPRSS13 MUTATED"      
clus
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 2                 27 
        TCGA-FA-A4BB         TCGA-FA-A4XK         TCGA-FA-A6HN 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-FA-A6HO         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CR 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TV         TCGA-GS-A9TW 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9TZ         TCGA-GS-A9U4 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB         TCGA-VB-A8QN 
"TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" "TMPRSS13 WILD-TYPE" 
D31V5, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    1  2
  TMPRSS13 WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      1    2
  TMPRSS13 WILD-TYPE    8   10
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  TMPRSS13 MUTATED        1      2      0
  TMPRSS13 WILD-TYPE      6      7      5
D31V6, multiclass
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                  7
  CLUS_3                0                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMPRSS13 MUTATED        1      0      0      2
  TMPRSS13 WILD-TYPE     10     11     10      7
D31V7, multiclass
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                0                 11
  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
  TMPRSS13 MUTATED        1      0      0      0      2
  TMPRSS13 WILD-TYPE      5     11      7     12      3
D31V8, multiclass
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                 11
  CLUS_3                0                  7
  CLUS_4                0                 12
  CLUS_5                2                  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"
D31V9, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    1  2
  TMPRSS13 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      1    2
  TMPRSS13 WILD-TYPE   16   17
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TMPRSS13 MUTATED        1      0      0      0      2      0      0      0
  TMPRSS13 WILD-TYPE      3      5      5      6      5      1      4      1
                    vv
clus                 CLUS_9
  TMPRSS13 MUTATED        0
  TMPRSS13 WILD-TYPE      3
D31V10, multiclass
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                0                  6
  CLUS_5                2                  5
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                0                  1
  CLUS_9                0                  3
[1] 9 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 = CYP2A6 MUTATION ANALYSIS
D32V1, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  3
  CYP2A6 WILD-TYPE 22 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    3
  CYP2A6 WILD-TYPE   22   15
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D32V2, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    2  2
  CYP2A6 WILD-TYPE 18 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      2    2
  CYP2A6 WILD-TYPE   18   19
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D32V3, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  1
  CYP2A6 WILD-TYPE 14 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    1
  CYP2A6 WILD-TYPE   14   13
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CYP2A6 MUTATED        0      1      1
  CYP2A6 WILD-TYPE      5     12     10
D32V4, multiclass
[1] "Remove cluster labels:" "CYP2A6 MUTATED"        
clus
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-FF-8046       TCGA-FF-8062       TCGA-FF-A7CR       TCGA-FF-A7CW 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT       TCGA-GS-A9TV 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" "CYP2A6 WILD-TYPE" 
D32V5, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  2
  CYP2A6 WILD-TYPE  8 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    2
  CYP2A6 WILD-TYPE    8   10
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CYP2A6 MUTATED        1      2      0
  CYP2A6 WILD-TYPE      6      7      5
D32V6, multiclass
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              2                7
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP2A6 MUTATED        0      0      1      3
  CYP2A6 WILD-TYPE     11     11      9      6
D32V7, multiclass
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              0               11
  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
  CYP2A6 MUTATED        1      0      0      1      2
  CYP2A6 WILD-TYPE      5     11      7     11      3
D32V8, multiclass
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              0               11
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              2                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"
D32V9, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  3
  CYP2A6 WILD-TYPE 16 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    3
  CYP2A6 WILD-TYPE   16   16
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              3               16
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CYP2A6 MUTATED        0      0      0      0      3      0      0      0
  CYP2A6 WILD-TYPE      4      5      5      6      4      1      4      1
                  vv
clus               CLUS_9
  CYP2A6 MUTATED        1
  CYP2A6 WILD-TYPE      2
D32V10, multiclass
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              3                4
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              0                1
  CLUS_9              1                2
[1] 9 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 = AR MUTATION ANALYSIS
D33V1, binary
              cls
clus            0  1
  AR MUTATED    4  3
  AR WILD-TYPE 19 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      4    3
  AR WILD-TYPE   19   15
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          4           19
  CLUS_2          3           15
[1] 2 2
[1] FALSE
D33V2, binary
              cls
clus            0  1
  AR MUTATED    4  3
  AR WILD-TYPE 16 18
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      4    3
  AR WILD-TYPE   16   18
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          4           16
  CLUS_2          3           18
[1] 2 2
[1] FALSE
D33V3, binary
              cls
clus            0  1
  AR MUTATED    4  0
  AR WILD-TYPE 11 14
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      4    0
  AR WILD-TYPE   11   14
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          4           11
  CLUS_2          0           14
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        0      4      0
  AR WILD-TYPE      5      9     11
D33V4, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          0            5
  CLUS_2          4            9
  CLUS_3          0           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"
D33V5, binary
              cls
clus           0 1
  AR MUTATED   1 4
  AR WILD-TYPE 8 8
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      1    4
  AR WILD-TYPE    8    8
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1            8
  CLUS_2          4            8
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        1      3      1
  AR WILD-TYPE      6      6      4
D33V6, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1            6
  CLUS_2          3            6
  CLUS_3          1            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"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AR MUTATED        2      2      0      3
  AR WILD-TYPE      9      9     10      6
D33V7, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2            9
  CLUS_2          2            9
  CLUS_3          0           10
  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
  AR MUTATED        1      3      1      1      1
  AR WILD-TYPE      5      8      6     11      4
D33V8, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1            5
  CLUS_2          3            8
  CLUS_3          1            6
  CLUS_4          1           11
  CLUS_5          1            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"
D33V9, binary
              cls
clus            0  1
  AR MUTATED    2  4
  AR WILD-TYPE 15 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      2    4
  AR WILD-TYPE   15   15
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           15
  CLUS_2          4           15
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  AR MUTATED        0      0      2      0      1      1      1      1      0
  AR WILD-TYPE      4      5      3      6      6      0      3      0      3
D33V10, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          0            4
  CLUS_2          0            5
  CLUS_3          2            3
  CLUS_4          0            6
  CLUS_5          1            6
  CLUS_6          1            0
  CLUS_7          1            3
  CLUS_8          1            0
  CLUS_9          0            3
[1] 9 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 = ARHGEF5 MUTATION ANALYSIS
D34V1, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    2  1
  ARHGEF5 WILD-TYPE 21 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      2    1
  ARHGEF5 WILD-TYPE   21   17
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               2                21
  CLUS_2               1                17
[1] 2 2
[1] FALSE
D34V2, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    1  2
  ARHGEF5 WILD-TYPE 19 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      1    2
  ARHGEF5 WILD-TYPE   19   19
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                19
[1] 2 2
[1] FALSE
D34V3, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    1  0
  ARHGEF5 WILD-TYPE 14 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      1    0
  ARHGEF5 WILD-TYPE   14   14
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               1                14
  CLUS_2               0                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ARHGEF5 MUTATED        0      1      0
  ARHGEF5 WILD-TYPE      5     12     11
D34V4, multiclass
[1] "Remove cluster labels:" "ARHGEF5 MUTATED"       
clus
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1                28 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-GS-A9TT 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
D34V5, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    1  2
  ARHGEF5 WILD-TYPE  8 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      1    2
  ARHGEF5 WILD-TYPE    8   10
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ARHGEF5 MUTATED        0      2      1
  ARHGEF5 WILD-TYPE      7      7      4
D34V6, multiclass
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                 7
  CLUS_3               1                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARHGEF5 MUTATED        1      1      0      1
  ARHGEF5 WILD-TYPE     10     10     10      8
D34V7, multiclass
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                10
  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
  ARHGEF5 MUTATED        0      1      0      1      1
  ARHGEF5 WILD-TYPE      6     10      7     11      4
D34V8, multiclass
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               1                11
  CLUS_5               1                 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"
D34V9, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    0  2
  ARHGEF5 WILD-TYPE 17 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      0    2
  ARHGEF5 WILD-TYPE   17   17
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                17
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARHGEF5 MUTATED        0      0      0      0      0      0      1      1
  ARHGEF5 WILD-TYPE      4      5      5      6      7      1      3      0
                   vv
clus                CLUS_9
  ARHGEF5 MUTATED        0
  ARHGEF5 WILD-TYPE      3
D34V10, multiclass
[1] "Remove cluster labels:" "ARHGEF5 MUTATED"       
clus
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                2                34 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F        TCGA-FA-A86F 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-GR-7353        TCGA-GR-A4D4 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GS-A9TQ        TCGA-GS-A9TT 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-GS-A9TU        TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-GS-A9U3        TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-RQ-AAAT        TCGA-VB-A8QN 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 

Clustering(35) Variable = RNF39 MUTATION ANALYSIS
D35V1, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  2
  RNF39 WILD-TYPE 22 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    2
  RNF39 WILD-TYPE   22   16
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              22
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D35V2, binary
                 cls
clus               0  1
  RNF39 MUTATED    2  1
  RNF39 WILD-TYPE 18 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      2    1
  RNF39 WILD-TYPE   18   20
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             1              20
[1] 2 2
[1] FALSE
D35V3, binary
                 cls
clus               0  1
  RNF39 MUTATED    0  1
  RNF39 WILD-TYPE 15 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      0    1
  RNF39 WILD-TYPE   15   13
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF39 MUTATED        0      0      1
  RNF39 WILD-TYPE      5     13     10
D35V4, multiclass
[1] "Remove cluster labels:" "RNF39 MUTATED"         
clus
  RNF39 MUTATED RNF39 WILD-TYPE 
              1              28 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-FA-A86F      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-FM-8000 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-GS-A9TT      TCGA-GS-A9TV      TCGA-GS-A9TW      TCGA-GS-A9TX 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
     TCGA-GS-A9TZ      TCGA-GS-A9U4      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" "RNF39 WILD-TYPE" 
D35V5, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  2
  RNF39 WILD-TYPE  8 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    2
  RNF39 WILD-TYPE    8   10
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF39 MUTATED        1      2      0
  RNF39 WILD-TYPE      6      7      5
D35V6, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             2               7
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNF39 MUTATED        1      1      0      1
  RNF39 WILD-TYPE     10     10     10      8
D35V7, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              10
  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
  RNF39 MUTATED        0      1      1      0      1
  RNF39 WILD-TYPE      6     10      6     12      4
D35V8, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             1               6
  CLUS_4             0              12
  CLUS_5             1               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"
D35V9, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  2
  RNF39 WILD-TYPE 16 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    2
  RNF39 WILD-TYPE   16   17
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             2              17
[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        0      0      1      0      1      0      0      1
  RNF39 WILD-TYPE      4      5      4      6      6      1      4      0
                 vv
clus              CLUS_9
  RNF39 MUTATED        0
  RNF39 WILD-TYPE      3
D35V10, multiclass
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             0               6
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = ABCA1 MUTATION ANALYSIS
D36V1, binary
                 cls
clus               0  1
  ABCA1 MUTATED    2  3
  ABCA1 WILD-TYPE 21 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      2    3
  ABCA1 WILD-TYPE   21   15
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D36V2, binary
                 cls
clus               0  1
  ABCA1 MUTATED    3  2
  ABCA1 WILD-TYPE 17 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      3    2
  ABCA1 WILD-TYPE   17   19
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D36V3, binary
                 cls
clus               0  1
  ABCA1 MUTATED    1  1
  ABCA1 WILD-TYPE 14 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      1    1
  ABCA1 WILD-TYPE   14   13
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ABCA1 MUTATED        0      1      1
  ABCA1 WILD-TYPE      5     12     10
D36V4, multiclass
[1] "Remove cluster labels:" "ABCA1 MUTATED"         
clus
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              2              27 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A6HN      TCGA-FA-A6HO 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F      TCGA-FA-A86F 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FF-A7CR 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-FF-A7CX      TCGA-FM-8000      TCGA-GS-A9TT      TCGA-GS-A9TV 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" "ABCA1 WILD-TYPE" 
D36V5, binary
                 cls
clus               0  1
  ABCA1 MUTATED    2  2
  ABCA1 WILD-TYPE  7 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      2    2
  ABCA1 WILD-TYPE    7   10
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ABCA1 MUTATED        0      2      2
  ABCA1 WILD-TYPE      7      7      3
D36V6, multiclass
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             2               7
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ABCA1 MUTATED        2      1      1      1
  ABCA1 WILD-TYPE      9     10      9      8
D36V7, multiclass
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             2               9
  CLUS_2             1              10
  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
  ABCA1 MUTATED        0      1      1      2      1
  ABCA1 WILD-TYPE      6     10      6     10      4
D36V8, multiclass
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             1               6
  CLUS_4             2              10
  CLUS_5             1               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"
D36V9, binary
                 cls
clus               0  1
  ABCA1 MUTATED    2  2
  ABCA1 WILD-TYPE 15 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      2    2
  ABCA1 WILD-TYPE   15   17
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             2              17
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ABCA1 MUTATED        0      0      1      1      1      0      0      1
  ABCA1 WILD-TYPE      4      5      4      5      6      1      4      0
                 vv
clus              CLUS_9
  ABCA1 MUTATED        0
  ABCA1 WILD-TYPE      3
D36V10, multiclass
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = CS MUTATION ANALYSIS
D37V1, binary
              cls
clus            0  1
  CS MUTATED    2  1
  CS WILD-TYPE 21 17
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      2    1
  CS WILD-TYPE   21   17
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          2           21
  CLUS_2          1           17
[1] 2 2
[1] FALSE
D37V2, binary
              cls
clus            0  1
  CS MUTATED    3  0
  CS WILD-TYPE 17 21
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      3    0
  CS WILD-TYPE   17   21
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          3           17
  CLUS_2          0           21
[1] 2 2
[1] FALSE
D37V3, binary
              cls
clus            0  1
  CS MUTATED    0  1
  CS WILD-TYPE 15 13
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      0    1
  CS WILD-TYPE   15   13
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          0           15
  CLUS_2          1           13
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  CS MUTATED        0      0      1
  CS WILD-TYPE      5     13     10
D37V4, multiclass
[1] "Remove cluster labels:" "CS MUTATED"            
clus
  CS MUTATED CS WILD-TYPE 
           1           28 
  TCGA-FA-8693   TCGA-FA-A4BB   TCGA-FA-A4XK   TCGA-FA-A6HN   TCGA-FA-A6HO 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-FA-A7DS   TCGA-FA-A7Q1   TCGA-FA-A82F   TCGA-FA-A86F   TCGA-FF-8041 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-FF-8042   TCGA-FF-8043   TCGA-FF-8046   TCGA-FF-8047   TCGA-FF-8061 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-FF-8062   TCGA-FF-A7CR   TCGA-FF-A7CW   TCGA-FF-A7CX   TCGA-FM-8000 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-GS-A9TT   TCGA-GS-A9TW   TCGA-GS-A9TX   TCGA-GS-A9TZ   TCGA-GS-A9U4 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-RQ-A68N   TCGA-RQ-A6JB   TCGA-VB-A8QN 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
D37V5, binary
              cls
clus            0  1
  CS MUTATED    1  1
  CS WILD-TYPE  8 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      1    1
  CS WILD-TYPE    8   11
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          1            8
  CLUS_2          1           11
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  CS MUTATED        0      1      1
  CS WILD-TYPE      7      8      4
D37V6, multiclass
[1] "Remove cluster labels:" "CS MUTATED"            
clus
  CS MUTATED CS WILD-TYPE 
           2           19 
  TCGA-FA-8693   TCGA-FA-A4BB   TCGA-FA-A4XK   TCGA-FA-A6HN   TCGA-FA-A6HO 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-FF-8041   TCGA-FF-8042   TCGA-FF-8043   TCGA-FF-8046   TCGA-FF-8047 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-FF-8061   TCGA-FF-8062   TCGA-FM-8000   TCGA-GR-7353   TCGA-GR-A4D5 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
  TCGA-GR-A4D6   TCGA-GR-A4D9   TCGA-RQ-A68N   TCGA-RQ-A6JB 
"CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" "CS WILD-TYPE" 
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CS MUTATED        0      2      0      1
  CS WILD-TYPE     11      9     10      8
D37V7, multiclass
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          0           11
  CLUS_2          2            9
  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
  CS MUTATED        1      2      0      0      0
  CS WILD-TYPE      5      9      7     12      5
D37V8, multiclass
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          1            5
  CLUS_2          2            9
  CLUS_3          0            7
  CLUS_4          0           12
  CLUS_5          0            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"
D37V9, binary
              cls
clus            0  1
  CS MUTATED    0  3
  CS WILD-TYPE 17 16
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      0    3
  CS WILD-TYPE   17   16
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          0           17
  CLUS_2          3           16
[1] 2 2
[1] FALSE
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  CS MUTATED        0      1      0      0      0      0      1      1      0
  CS WILD-TYPE      4      4      5      6      7      1      3      0      3
D37V10, multiclass
        clus
vv       CS MUTATED CS WILD-TYPE
  CLUS_1          0            4
  CLUS_2          1            4
  CLUS_3          0            5
  CLUS_4          0            6
  CLUS_5          0            7
  CLUS_6          0            1
  CLUS_7          1            3
  CLUS_8          1            0
  CLUS_9          0            3
[1] 9 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 = IFITM3 MUTATION ANALYSIS
D38V1, binary
                  cls
clus                0  1
  IFITM3 MUTATED    3  1
  IFITM3 WILD-TYPE 20 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      3    1
  IFITM3 WILD-TYPE   20   17
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              3               20
  CLUS_2              1               17
[1] 2 2
[1] FALSE
D38V2, binary
                  cls
clus                0  1
  IFITM3 MUTATED    2  2
  IFITM3 WILD-TYPE 18 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      2    2
  IFITM3 WILD-TYPE   18   19
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D38V3, binary
                  cls
clus                0  1
  IFITM3 MUTATED    3  0
  IFITM3 WILD-TYPE 12 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      3    0
  IFITM3 WILD-TYPE   12   14
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              0               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFITM3 MUTATED        0      3      0
  IFITM3 WILD-TYPE      5     10     11
D38V4, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              3               10
  CLUS_3              0               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"
D38V5, binary
                  cls
clus               0 1
  IFITM3 MUTATED   1 3
  IFITM3 WILD-TYPE 8 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      1    3
  IFITM3 WILD-TYPE    8    9
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFITM3 MUTATED        2      2      0
  IFITM3 WILD-TYPE      5      7      5
D38V6, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              2                7
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFITM3 MUTATED        1      1      0      2
  IFITM3 WILD-TYPE     10     10     10      7
D38V7, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               10
  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
  IFITM3 MUTATED        1      1      0      0      2
  IFITM3 WILD-TYPE      5     10      7     12      3
D38V8, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              0               12
  CLUS_5              2                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"
D38V9, binary
                  cls
clus                0  1
  IFITM3 MUTATED    1  3
  IFITM3 WILD-TYPE 16 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      1    3
  IFITM3 WILD-TYPE   16   16
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              3               16
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IFITM3 MUTATED        0      0      0      0      2      1      0      1
  IFITM3 WILD-TYPE      4      5      5      6      5      0      4      0
                  vv
clus               CLUS_9
  IFITM3 MUTATED        0
  IFITM3 WILD-TYPE      3
D38V10, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              1                0
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = RANBP2 MUTATION ANALYSIS
D39V1, binary
                  cls
clus                0  1
  RANBP2 MUTATED    3  3
  RANBP2 WILD-TYPE 20 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      3    3
  RANBP2 WILD-TYPE   20   15
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              3               20
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D39V2, binary
                  cls
clus                0  1
  RANBP2 MUTATED    3  3
  RANBP2 WILD-TYPE 17 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      3    3
  RANBP2 WILD-TYPE   17   18
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              3               18
[1] 2 2
[1] FALSE
D39V3, binary
                  cls
clus                0  1
  RANBP2 MUTATED    2  3
  RANBP2 WILD-TYPE 13 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      2    3
  RANBP2 WILD-TYPE   13   11
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              3               11
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RANBP2 MUTATED        1      2      2
  RANBP2 WILD-TYPE      4     11      9
D39V4, multiclass
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              2               11
  CLUS_3              2                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                  cls
clus               0 1
  RANBP2 MUTATED   0 3
  RANBP2 WILD-TYPE 9 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      0    3
  RANBP2 WILD-TYPE    9    9
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  RANBP2 MUTATED        0      3      0
  RANBP2 WILD-TYPE      7      6      5
D39V6, multiclass
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              3                6
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RANBP2 MUTATED        1      2      1      2
  RANBP2 WILD-TYPE     10      9      9      7
D39V7, multiclass
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              2                9
  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
  RANBP2 MUTATED        0      2      1      1      2
  RANBP2 WILD-TYPE      6      9      6     11      3
D39V8, multiclass
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                9
  CLUS_3              1                6
  CLUS_4              1               11
  CLUS_5              2                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"
D39V9, binary
                  cls
clus                0  1
  RANBP2 MUTATED    2  4
  RANBP2 WILD-TYPE 15 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      2    4
  RANBP2 WILD-TYPE   15   15
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RANBP2 MUTATED        1      1      1      0      1      0      1      1
  RANBP2 WILD-TYPE      3      4      4      6      6      1      3      0
                  vv
clus               CLUS_9
  RANBP2 MUTATED        0
  RANBP2 WILD-TYPE      3
D39V10, multiclass
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              1                4
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = KLHL6 MUTATION ANALYSIS
D40V1, binary
                 cls
clus               0  1
  KLHL6 MUTATED    2  4
  KLHL6 WILD-TYPE 21 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      2    4
  KLHL6 WILD-TYPE   21   14
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             4              14
[1] 2 2
[1] FALSE
D40V2, binary
                 cls
clus               0  1
  KLHL6 MUTATED    3  3
  KLHL6 WILD-TYPE 17 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      3    3
  KLHL6 WILD-TYPE   17   18
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D40V3, binary
                 cls
clus               0  1
  KLHL6 MUTATED    1  3
  KLHL6 WILD-TYPE 14 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      1    3
  KLHL6 WILD-TYPE   14   11
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KLHL6 MUTATED        0      1      3
  KLHL6 WILD-TYPE      5     12      8
D40V4, multiclass
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1              12
  CLUS_3             3               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"
D40V5, binary
                 cls
clus              0 1
  KLHL6 MUTATED   1 4
  KLHL6 WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      1    4
  KLHL6 WILD-TYPE    8    8
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KLHL6 MUTATED        1      3      1
  KLHL6 WILD-TYPE      6      6      4
D40V6, multiclass
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             3               6
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLHL6 MUTATED        1      2      1      2
  KLHL6 WILD-TYPE     10      9      9      7
D40V7, multiclass
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2               9
  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
  KLHL6 MUTATED        0      2      0      2      2
  KLHL6 WILD-TYPE      6      9      7     10      3
D40V8, multiclass
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2               9
  CLUS_3             0               7
  CLUS_4             2              10
  CLUS_5             2               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"
D40V9, binary
                 cls
clus               0  1
  KLHL6 MUTATED    1  4
  KLHL6 WILD-TYPE 16 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      1    4
  KLHL6 WILD-TYPE   16   15
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KLHL6 MUTATED        1      0      0      1      1      0      2      0
  KLHL6 WILD-TYPE      3      5      5      5      6      1      2      1
                 vv
clus              CLUS_9
  KLHL6 MUTATED        0
  KLHL6 WILD-TYPE      3
D40V10, multiclass
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             2               2
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = ZNF814 MUTATION ANALYSIS
D41V1, binary
                  cls
clus                0  1
  ZNF814 MUTATED    8  2
  ZNF814 WILD-TYPE 15 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      8    2
  ZNF814 WILD-TYPE   15   16
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              8               15
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D41V2, binary
                  cls
clus                0  1
  ZNF814 MUTATED    6  4
  ZNF814 WILD-TYPE 14 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      6    4
  ZNF814 WILD-TYPE   14   17
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              6               14
  CLUS_2              4               17
[1] 2 2
[1] FALSE
D41V3, binary
                  cls
clus                0  1
  ZNF814 MUTATED    4  2
  ZNF814 WILD-TYPE 11 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      4    2
  ZNF814 WILD-TYPE   11   12
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              4               11
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      4      1
  ZNF814 WILD-TYPE      4      9     10
D41V4, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              4                9
  CLUS_3              1               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"
D41V5, binary
                  cls
clus               0 1
  ZNF814 MUTATED   0 3
  ZNF814 WILD-TYPE 9 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    3
  ZNF814 WILD-TYPE    9    9
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      2      0
  ZNF814 WILD-TYPE      6      7      5
D41V6, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              2                7
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      3      5      2
  ZNF814 WILD-TYPE     11      8      5      7
D41V7, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              3                8
  CLUS_3              5                5
  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
  ZNF814 MUTATED        0      2      0      7      1
  ZNF814 WILD-TYPE      6      9      7      5      4
D41V8, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                9
  CLUS_3              0                7
  CLUS_4              7                5
  CLUS_5              1                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"
D41V9, binary
                  cls
clus                0  1
  ZNF814 MUTATED    3  5
  ZNF814 WILD-TYPE 14 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3    5
  ZNF814 WILD-TYPE   14   14
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              5               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      0      2      2      0      1      0      1
  ZNF814 WILD-TYPE      4      5      3      4      7      0      4      0
                  vv
clus               CLUS_9
  ZNF814 MUTATED        2
  ZNF814 WILD-TYPE      1
D41V10, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              2                3
  CLUS_4              2                4
  CLUS_5              0                7
  CLUS_6              1                0
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              2                1
[1] 9 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 = CYP4A11 MUTATION ANALYSIS
D42V1, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    3  1
  CYP4A11 WILD-TYPE 20 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      3    1
  CYP4A11 WILD-TYPE   20   17
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               3                20
  CLUS_2               1                17
[1] 2 2
[1] FALSE
D42V2, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    2  2
  CYP4A11 WILD-TYPE 18 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      2    2
  CYP4A11 WILD-TYPE   18   19
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               2                18
  CLUS_2               2                19
[1] 2 2
[1] FALSE
D42V3, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    3  0
  CYP4A11 WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      3    0
  CYP4A11 WILD-TYPE   12   14
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               3                12
  CLUS_2               0                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP4A11 MUTATED        0      3      0
  CYP4A11 WILD-TYPE      5     10     11
D42V4, multiclass
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                10
  CLUS_3               0                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"
D42V5, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    2  2
  CYP4A11 WILD-TYPE  7 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      2    2
  CYP4A11 WILD-TYPE    7   10
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP4A11 MUTATED        1      2      1
  CYP4A11 WILD-TYPE      6      7      4
D42V6, multiclass
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                 7
  CLUS_3               1                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP4A11 MUTATED        2      1      0      1
  CYP4A11 WILD-TYPE      9     10     10      8
D42V7, multiclass
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                10
  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
  CYP4A11 MUTATED        2      1      1      0      0
  CYP4A11 WILD-TYPE      4     10      6     12      5
D42V8, multiclass
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               1                10
  CLUS_3               1                 6
  CLUS_4               0                12
  CLUS_5               0                 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"
D42V9, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    3  1
  CYP4A11 WILD-TYPE 14 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      3    1
  CYP4A11 WILD-TYPE   14   18
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               3                14
  CLUS_2               1                18
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CYP4A11 MUTATED        0      0      1      0      2      0      0      1
  CYP4A11 WILD-TYPE      4      5      4      6      5      1      4      0
                   vv
clus                CLUS_9
  CYP4A11 MUTATED        0
  CYP4A11 WILD-TYPE      3
D42V10, multiclass
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               1                 4
  CLUS_4               0                 6
  CLUS_5               2                 5
  CLUS_6               0                 1
  CLUS_7               0                 4
  CLUS_8               1                 0
  CLUS_9               0                 3
[1] 9 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 = PIM1 MUTATION ANALYSIS
D43V1, binary
                cls
clus              0  1
  PIM1 MUTATED    5  3
  PIM1 WILD-TYPE 18 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      5    3
  PIM1 WILD-TYPE   18   15
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            5             18
  CLUS_2            3             15
[1] 2 2
[1] FALSE
D43V2, binary
                cls
clus              0  1
  PIM1 MUTATED    0  8
  PIM1 WILD-TYPE 20 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      0    8
  PIM1 WILD-TYPE   20   13
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            8             13
[1] 2 2
[1] FALSE
D43V3, binary
                cls
clus              0  1
  PIM1 MUTATED    4  2
  PIM1 WILD-TYPE 11 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      4    2
  PIM1 WILD-TYPE   11   12
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            4             11
  CLUS_2            2             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PIM1 MUTATED        1      3      2
  PIM1 WILD-TYPE      4     10      9
D43V4, multiclass
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            3             10
  CLUS_3            2              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                cls
clus              0  1
  PIM1 MUTATED    2  0
  PIM1 WILD-TYPE  7 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      2    0
  PIM1 WILD-TYPE    7   12
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            0             12
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PIM1 MUTATED        2      0      0
  PIM1 WILD-TYPE      5      9      5
D43V6, multiclass
[1] "Remove cluster labels:" "PIM1 MUTATED"          
clus
  PIM1 MUTATED PIM1 WILD-TYPE 
             2             19 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8062     TCGA-FM-8000 
"PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" 
    TCGA-G8-6324     TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5 
"PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" 
    TCGA-GR-A4D6     TCGA-GR-A4D9     TCGA-RQ-A6JB 
"PIM1 WILD-TYPE" "PIM1 WILD-TYPE" "PIM1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIM1 MUTATED        3      0      4      1
  PIM1 WILD-TYPE      8     11      6      8
D43V7, multiclass
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            0             11
  CLUS_3            4              6
  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
  PIM1 MUTATED        1      0      3      4      0
  PIM1 WILD-TYPE      5     11      4      8      5
D43V8, multiclass
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            0             11
  CLUS_3            3              4
  CLUS_4            4              8
  CLUS_5            0              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"
D43V9, binary
                cls
clus              0  1
  PIM1 MUTATED    6  1
  PIM1 WILD-TYPE 11 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      6    1
  PIM1 WILD-TYPE   11   18
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            6             11
  CLUS_2            1             18
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PIM1 MUTATED        1      0      2      3      1      0      0      0      0
  PIM1 WILD-TYPE      3      5      3      3      6      1      4      1      3
D43V10, multiclass
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            0              5
  CLUS_3            2              3
  CLUS_4            3              3
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            0              4
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = POTEE MUTATION ANALYSIS
D44V1, binary
                 cls
clus               0  1
  POTEE MUTATED    4  3
  POTEE WILD-TYPE 19 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      4    3
  POTEE WILD-TYPE   19   15
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             4              19
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D44V2, binary
                 cls
clus               0  1
  POTEE MUTATED    3  4
  POTEE WILD-TYPE 17 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      3    4
  POTEE WILD-TYPE   17   17
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             3              17
  CLUS_2             4              17
[1] 2 2
[1] FALSE
D44V3, binary
                 cls
clus               0  1
  POTEE MUTATED    5  0
  POTEE WILD-TYPE 10 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      5    0
  POTEE WILD-TYPE   10   14
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             5              10
  CLUS_2             0              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  POTEE MUTATED        1      4      0
  POTEE WILD-TYPE      4      9     11
D44V4, multiclass
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             1               4
  CLUS_2             4               9
  CLUS_3             0              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"
D44V5, binary
                 cls
clus              0 1
  POTEE MUTATED   3 4
  POTEE WILD-TYPE 6 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      3    4
  POTEE WILD-TYPE    6    8
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             3               6
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  POTEE MUTATED        4      3      0
  POTEE WILD-TYPE      3      6      5
D44V6, multiclass
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             4               3
  CLUS_2             3               6
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POTEE MUTATED        2      1      0      4
  POTEE WILD-TYPE      9     10     10      5
D44V7, multiclass
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             2               9
  CLUS_2             1              10
  CLUS_3             0              10
  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
  POTEE MUTATED        3      1      0      0      3
  POTEE WILD-TYPE      3     10      7     12      2
D44V8, multiclass
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             3               3
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             0              12
  CLUS_5             3               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"
D44V9, binary
                 cls
clus               0  1
  POTEE MUTATED    3  4
  POTEE WILD-TYPE 14 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      3    4
  POTEE WILD-TYPE   14   15
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             3              14
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  POTEE MUTATED        1      0      0      0      3      1      1      1
  POTEE WILD-TYPE      3      5      5      6      4      0      3      0
                 vv
clus              CLUS_9
  POTEE MUTATED        0
  POTEE WILD-TYPE      3
D44V10, multiclass
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             3               4
  CLUS_6             1               0
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = OR52E6 MUTATION ANALYSIS
D45V1, binary
                  cls
clus                0  1
  OR52E6 MUTATED    1  2
  OR52E6 WILD-TYPE 22 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      1    2
  OR52E6 WILD-TYPE   22   16
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D45V2, binary
                  cls
clus                0  1
  OR52E6 MUTATED    2  1
  OR52E6 WILD-TYPE 18 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      2    1
  OR52E6 WILD-TYPE   18   20
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D45V3, binary
                  cls
clus                0  1
  OR52E6 MUTATED    1  0
  OR52E6 WILD-TYPE 14 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      1    0
  OR52E6 WILD-TYPE   14   14
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR52E6 MUTATED        0      1      0
  OR52E6 WILD-TYPE      5     12     11
D45V4, multiclass
[1] "Remove cluster labels:" "OR52E6 MUTATED"        
clus
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               1               28 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A6HN       TCGA-FA-A6HO 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F       TCGA-FA-A86F 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-GS-A9TV       TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
      TCGA-GS-A9U4       TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" "OR52E6 WILD-TYPE" 
D45V5, binary
                  cls
clus                0  1
  OR52E6 MUTATED    1  2
  OR52E6 WILD-TYPE  8 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      1    2
  OR52E6 WILD-TYPE    8   10
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR52E6 MUTATED        0      2      1
  OR52E6 WILD-TYPE      7      7      4
D45V6, multiclass
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR52E6 MUTATED        1      1      0      1
  OR52E6 WILD-TYPE     10     10     10      8
D45V7, multiclass
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               10
  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
  OR52E6 MUTATED        0      1      1      0      1
  OR52E6 WILD-TYPE      6     10      6     12      4
D45V8, multiclass
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              1               10
  CLUS_3              1                6
  CLUS_4              0               12
  CLUS_5              1                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"
D45V9, binary
                  cls
clus                0  1
  OR52E6 MUTATED    1  2
  OR52E6 WILD-TYPE 16 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      1    2
  OR52E6 WILD-TYPE   16   17
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              2               17
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OR52E6 MUTATED        0      0      1      0      1      0      0      1
  OR52E6 WILD-TYPE      4      5      4      6      6      1      4      0
                  vv
clus               CLUS_9
  OR52E6 MUTATED        0
  OR52E6 WILD-TYPE      3
D45V10, multiclass
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = NBPF10 MUTATION ANALYSIS
D46V1, binary
                  cls
clus                0  1
  NBPF10 MUTATED    4  5
  NBPF10 WILD-TYPE 19 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      4    5
  NBPF10 WILD-TYPE   19   13
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              4               19
  CLUS_2              5               13
[1] 2 2
[1] FALSE
D46V2, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  7
  NBPF10 WILD-TYPE 18 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    7
  NBPF10 WILD-TYPE   18   14
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              7               14
[1] 2 2
[1] FALSE
D46V3, binary
                  cls
clus                0  1
  NBPF10 MUTATED    4  2
  NBPF10 WILD-TYPE 11 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      4    2
  NBPF10 WILD-TYPE   11   12
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              4               11
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        2      3      1
  NBPF10 WILD-TYPE      3     10     10
D46V4, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2                3
  CLUS_2              3               10
  CLUS_3              1               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"
D46V5, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  2
  NBPF10 WILD-TYPE  7 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    2
  NBPF10 WILD-TYPE    7   10
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        0      2      2
  NBPF10 WILD-TYPE      7      7      3
D46V6, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              2                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NBPF10 MUTATED        4      1      3      1
  NBPF10 WILD-TYPE      7     10      7      8
D46V7, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              4                7
  CLUS_2              1               10
  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
  NBPF10 MUTATED        1      1      4      2      1
  NBPF10 WILD-TYPE      5     10      3     10      4
D46V8, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              1               10
  CLUS_3              4                3
  CLUS_4              2               10
  CLUS_5              1                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"
D46V9, binary
                  cls
clus                0  1
  NBPF10 MUTATED    5  3
  NBPF10 WILD-TYPE 12 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      5    3
  NBPF10 WILD-TYPE   12   16
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              5               12
  CLUS_2              3               16
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NBPF10 MUTATED        1      1      2      1      1      0      1      0
  NBPF10 WILD-TYPE      3      4      3      5      6      1      3      1
                  vv
clus               CLUS_9
  NBPF10 MUTATED        1
  NBPF10 WILD-TYPE      2
D46V10, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              1                4
  CLUS_3              2                3
  CLUS_4              1                5
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              0                1
  CLUS_9              1                2
[1] 9 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 = PRB2 MUTATION ANALYSIS
D47V1, binary
                cls
clus              0  1
  PRB2 MUTATED    4  5
  PRB2 WILD-TYPE 19 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      4    5
  PRB2 WILD-TYPE   19   13
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            4             19
  CLUS_2            5             13
[1] 2 2
[1] FALSE
D47V2, binary
                cls
clus              0  1
  PRB2 MUTATED    4  5
  PRB2 WILD-TYPE 16 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      4    5
  PRB2 WILD-TYPE   16   16
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            4             16
  CLUS_2            5             16
[1] 2 2
[1] FALSE
D47V3, binary
                cls
clus              0  1
  PRB2 MUTATED    2  4
  PRB2 WILD-TYPE 13 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      2    4
  PRB2 WILD-TYPE   13   10
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            4             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PRB2 MUTATED        0      3      3
  PRB2 WILD-TYPE      5     10      8
D47V4, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0              5
  CLUS_2            3             10
  CLUS_3            3              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"
D47V5, binary
                cls
clus             0 1
  PRB2 MUTATED   0 4
  PRB2 WILD-TYPE 9 8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      0    4
  PRB2 WILD-TYPE    9    8
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            4              8
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PRB2 MUTATED        0      4      0
  PRB2 WILD-TYPE      7      5      5
D47V6, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            4              5
  CLUS_3            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRB2 MUTATED        2      4      0      3
  PRB2 WILD-TYPE      9      7     10      6
D47V7, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            4              7
  CLUS_3            0             10
  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
  PRB2 MUTATED        0      5      2      0      2
  PRB2 WILD-TYPE      6      6      5     12      3
D47V8, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            5              6
  CLUS_3            2              5
  CLUS_4            0             12
  CLUS_5            2              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"
D47V9, binary
                cls
clus              0  1
  PRB2 MUTATED    2  5
  PRB2 WILD-TYPE 15 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      2    5
  PRB2 WILD-TYPE   15   14
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             15
  CLUS_2            5             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PRB2 MUTATED        1      2      1      0      1      0      1      1      0
  PRB2 WILD-TYPE      3      3      4      6      6      1      3      0      3
D47V10, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            2              3
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            1              3
  CLUS_8            1              0
  CLUS_9            0              3
[1] 9 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 = MUC6 MUTATION ANALYSIS
D48V1, binary
                cls
clus              0  1
  MUC6 MUTATED   13  8
  MUC6 WILD-TYPE 10 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     13    8
  MUC6 WILD-TYPE   10   10
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1           13             10
  CLUS_2            8             10
[1] 2 2
[1] FALSE
D48V2, binary
                cls
clus              0  1
  MUC6 MUTATED   11 10
  MUC6 WILD-TYPE  9 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     11   10
  MUC6 WILD-TYPE    9   11
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1           11              9
  CLUS_2           10             11
[1] 2 2
[1] FALSE
D48V3, binary
                cls
clus             0 1
  MUC6 MUTATED   7 6
  MUC6 WILD-TYPE 8 8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      7    6
  MUC6 WILD-TYPE    8    8
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            7              8
  CLUS_2            6              8
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC6 MUTATED        4      4      5
  MUC6 WILD-TYPE      1      9      6
D48V4, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            4              1
  CLUS_2            4              9
  CLUS_3            5              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"
D48V5, binary
                cls
clus             0 1
  MUC6 MUTATED   4 8
  MUC6 WILD-TYPE 5 4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      4    8
  MUC6 WILD-TYPE    5    4
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            4              5
  CLUS_2            8              4
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC6 MUTATED        2      7      3
  MUC6 WILD-TYPE      5      2      2
D48V6, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            2              5
  CLUS_2            7              2
  CLUS_3            3              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC6 MUTATED        7      6      4      4
  MUC6 WILD-TYPE      4      5      6      5
D48V7, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            7              4
  CLUS_2            6              5
  CLUS_3            4              6
  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
  MUC6 MUTATED        2      5      4      7      3
  MUC6 WILD-TYPE      4      6      3      5      2
D48V8, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            5              6
  CLUS_3            4              3
  CLUS_4            7              5
  CLUS_5            3              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"
D48V9, binary
                cls
clus              0  1
  MUC6 MUTATED    7 12
  MUC6 WILD-TYPE 10  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      7   12
  MUC6 WILD-TYPE   10    7
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            7             10
  CLUS_2           12              7
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  MUC6 MUTATED        2      3      2      2      4      0      3      1      2
  MUC6 WILD-TYPE      2      2      3      4      3      1      1      0      1
D48V10, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            2              2
  CLUS_2            3              2
  CLUS_3            2              3
  CLUS_4            2              4
  CLUS_5            4              3
  CLUS_6            0              1
  CLUS_7            3              1
  CLUS_8            1              0
  CLUS_9            2              1
[1] 9 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 = SALL1 MUTATION ANALYSIS
D49V1, binary
                 cls
clus               0  1
  SALL1 MUTATED    3  2
  SALL1 WILD-TYPE 20 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      3    2
  SALL1 WILD-TYPE   20   16
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D49V2, binary
                 cls
clus               0  1
  SALL1 MUTATED    3  2
  SALL1 WILD-TYPE 17 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      3    2
  SALL1 WILD-TYPE   17   19
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D49V3, binary
                 cls
clus               0  1
  SALL1 MUTATED    1  2
  SALL1 WILD-TYPE 14 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      1    2
  SALL1 WILD-TYPE   14   12
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SALL1 MUTATED        0      2      1
  SALL1 WILD-TYPE      5     11     10
D49V4, multiclass
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2              11
  CLUS_3             1              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"
D49V5, binary
                 cls
clus               0  1
  SALL1 MUTATED    1  1
  SALL1 WILD-TYPE  8 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      1    1
  SALL1 WILD-TYPE    8   11
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SALL1 MUTATED        0      1      1
  SALL1 WILD-TYPE      7      8      4
D49V6, multiclass
[1] "Remove cluster labels:" "SALL1 MUTATED"         
clus
  SALL1 MUTATED SALL1 WILD-TYPE 
              2              19 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" 
     TCGA-FM-8000      TCGA-GR-7353      TCGA-GR-A4D5      TCGA-GR-A4D6 
"SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" 
     TCGA-GR-A4D9      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"SALL1 WILD-TYPE" "SALL1 WILD-TYPE" "SALL1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SALL1 MUTATED        1      2      1      1
  SALL1 WILD-TYPE     10      9      9      8
D49V7, multiclass
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2               9
  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
  SALL1 MUTATED        2      2      1      0      0
  SALL1 WILD-TYPE      4      9      6     12      5
D49V8, multiclass
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             2               9
  CLUS_3             1               6
  CLUS_4             0              12
  CLUS_5             0               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"
D49V9, binary
                 cls
clus               0  1
  SALL1 MUTATED    2  2
  SALL1 WILD-TYPE 15 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      2    2
  SALL1 WILD-TYPE   15   17
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             2              17
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SALL1 MUTATED        0      0      0      1      1      0      1      1
  SALL1 WILD-TYPE      4      5      5      5      6      1      3      0
                 vv
clus              CLUS_9
  SALL1 MUTATED        0
  SALL1 WILD-TYPE      3
D49V10, multiclass
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = PAK2 MUTATION ANALYSIS
D50V1, binary
                cls
clus              0  1
  PAK2 MUTATED    6  1
  PAK2 WILD-TYPE 17 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      6    1
  PAK2 WILD-TYPE   17   17
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            6             17
  CLUS_2            1             17
[1] 2 2
[1] FALSE
D50V2, binary
                cls
clus              0  1
  PAK2 MUTATED    3  4
  PAK2 WILD-TYPE 17 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      3    4
  PAK2 WILD-TYPE   17   17
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            3             17
  CLUS_2            4             17
[1] 2 2
[1] FALSE
D50V3, binary
                cls
clus              0  1
  PAK2 MUTATED    3  1
  PAK2 WILD-TYPE 12 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      3    1
  PAK2 WILD-TYPE   12   13
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            3             12
  CLUS_2            1             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PAK2 MUTATED        1      2      1
  PAK2 WILD-TYPE      4     11     10
D50V4, multiclass
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            2             11
  CLUS_3            1             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"
D50V5, binary
                cls
clus             0 1
  PAK2 MUTATED   2 3
  PAK2 WILD-TYPE 7 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      2    3
  PAK2 WILD-TYPE    7    9
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            3              9
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PAK2 MUTATED        1      2      2
  PAK2 WILD-TYPE      6      7      3
D50V6, multiclass
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            1              6
  CLUS_2            2              7
  CLUS_3            2              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PAK2 MUTATED        2      2      0      3
  PAK2 WILD-TYPE      9      9     10      6
D50V7, multiclass
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            2              9
  CLUS_3            0             10
  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
  PAK2 MUTATED        0      1      1      3      2
  PAK2 WILD-TYPE      6     10      6      9      3
D50V8, multiclass
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             10
  CLUS_3            1              6
  CLUS_4            3              9
  CLUS_5            2              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"
D50V9, binary
                cls
clus              0  1
  PAK2 MUTATED    1  5
  PAK2 WILD-TYPE 16 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      1    5
  PAK2 WILD-TYPE   16   14
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            1             16
  CLUS_2            5             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PAK2 MUTATED        0      0      1      0      1      1      1      1      1
  PAK2 WILD-TYPE      4      5      4      6      6      0      3      0      2
D50V10, multiclass
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              5
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            1              6
  CLUS_6            1              0
  CLUS_7            1              3
  CLUS_8            1              0
  CLUS_9            1              2
[1] 9 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 = FLG MUTATION ANALYSIS
D51V1, binary
               cls
clus             0  1
  FLG MUTATED    9  8
  FLG WILD-TYPE 14 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      9    8
  FLG WILD-TYPE   14   10
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           9            14
  CLUS_2           8            10
[1] 2 2
[1] FALSE
D51V2, binary
               cls
clus             0  1
  FLG MUTATED    8  9
  FLG WILD-TYPE 12 12
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      8    9
  FLG WILD-TYPE   12   12
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           8            12
  CLUS_2           9            12
[1] 2 2
[1] FALSE
D51V3, binary
               cls
clus            0 1
  FLG MUTATED   7 5
  FLG WILD-TYPE 8 9
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      7    5
  FLG WILD-TYPE    8    9
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           7             8
  CLUS_2           5             9
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  FLG MUTATED        2      5      5
  FLG WILD-TYPE      3      8      6
D51V4, multiclass
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           2             3
  CLUS_2           5             8
  CLUS_3           5             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"
D51V5, binary
               cls
clus            0 1
  FLG MUTATED   4 5
  FLG WILD-TYPE 5 7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      4    5
  FLG WILD-TYPE    5    7
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           4             5
  CLUS_2           5             7
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  FLG MUTATED        5      4      0
  FLG WILD-TYPE      2      5      5
D51V6, multiclass
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           5             2
  CLUS_2           4             5
  CLUS_3           0             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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLG MUTATED        4      5      4      4
  FLG WILD-TYPE      7      6      6      5
D51V7, multiclass
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           4             7
  CLUS_2           5             6
  CLUS_3           4             6
  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
  FLG MUTATED        4      4      2      4      3
  FLG WILD-TYPE      2      7      5      8      2
D51V8, multiclass
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           4             2
  CLUS_2           4             7
  CLUS_3           2             5
  CLUS_4           4             8
  CLUS_5           3             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"
D51V9, binary
               cls
clus             0  1
  FLG MUTATED    8  9
  FLG WILD-TYPE  9 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      8    9
  FLG WILD-TYPE    9   10
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           8             9
  CLUS_2           9            10
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  FLG MUTATED        3      2      0      3      6      0      0      1      2
  FLG WILD-TYPE      1      3      5      3      1      1      4      0      1
D51V10, multiclass
        clus
vv       FLG MUTATED FLG WILD-TYPE
  CLUS_1           3             1
  CLUS_2           2             3
  CLUS_3           0             5
  CLUS_4           3             3
  CLUS_5           6             1
  CLUS_6           0             1
  CLUS_7           0             4
  CLUS_8           1             0
  CLUS_9           2             1
[1] 9 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 = MUC17 MUTATION ANALYSIS
D52V1, binary
                 cls
clus               0  1
  MUC17 MUTATED    5  8
  MUC17 WILD-TYPE 18 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      5    8
  MUC17 WILD-TYPE   18   10
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             5              18
  CLUS_2             8              10
[1] 2 2
[1] FALSE
D52V2, binary
                 cls
clus               0  1
  MUC17 MUTATED    4  9
  MUC17 WILD-TYPE 16 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      4    9
  MUC17 WILD-TYPE   16   12
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             9              12
[1] 2 2
[1] FALSE
D52V3, binary
                 cls
clus               0  1
  MUC17 MUTATED    5  3
  MUC17 WILD-TYPE 10 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      5    3
  MUC17 WILD-TYPE   10   11
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             5              10
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED        0      5      3
  MUC17 WILD-TYPE      5      8      8
D52V4, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             5               8
  CLUS_3             3               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"
D52V5, binary
                 cls
clus              0 1
  MUC17 MUTATED   3 5
  MUC17 WILD-TYPE 6 7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      3    5
  MUC17 WILD-TYPE    6    7
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             5               7
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED        2      4      2
  MUC17 WILD-TYPE      5      5      3
D52V6, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             4               5
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC17 MUTATED        5      2      3      3
  MUC17 WILD-TYPE      6      9      7      6
D52V7, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             5               6
  CLUS_2             2               9
  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
  MUC17 MUTATED        3      3      3      2      2
  MUC17 WILD-TYPE      3      8      4     10      3
D52V8, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             3               3
  CLUS_2             3               8
  CLUS_3             3               4
  CLUS_4             2              10
  CLUS_5             2               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"
D52V9, binary
                 cls
clus               0  1
  MUC17 MUTATED    7  5
  MUC17 WILD-TYPE 10 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      7    5
  MUC17 WILD-TYPE   10   14
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             7              10
  CLUS_2             5              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MUC17 MUTATED        1      1      2      3      4      0      0      1
  MUC17 WILD-TYPE      3      4      3      3      3      1      4      0
                 vv
clus              CLUS_9
  MUC17 MUTATED        0
  MUC17 WILD-TYPE      3
D52V10, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             1               4
  CLUS_3             2               3
  CLUS_4             3               3
  CLUS_5             4               3
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = OR2T4 MUTATION ANALYSIS
D53V1, binary
                 cls
clus               0  1
  OR2T4 MUTATED    7  1
  OR2T4 WILD-TYPE 16 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      7    1
  OR2T4 WILD-TYPE   16   17
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             7              16
  CLUS_2             1              17
[1] 2 2
[1] FALSE
D53V2, binary
                 cls
clus               0  1
  OR2T4 MUTATED    6  2
  OR2T4 WILD-TYPE 14 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      6    2
  OR2T4 WILD-TYPE   14   19
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             6              14
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D53V3, binary
                 cls
clus               0  1
  OR2T4 MUTATED    2  3
  OR2T4 WILD-TYPE 13 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      2    3
  OR2T4 WILD-TYPE   13   11
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR2T4 MUTATED        2      1      2
  OR2T4 WILD-TYPE      3     12      9
D53V4, multiclass
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1              12
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                 cls
clus              0 1
  OR2T4 MUTATED   0 4
  OR2T4 WILD-TYPE 9 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      0    4
  OR2T4 WILD-TYPE    9    8
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR2T4 MUTATED        0      3      1
  OR2T4 WILD-TYPE      7      6      4
D53V6, multiclass
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             3               6
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR2T4 MUTATED        1      6      1      0
  OR2T4 WILD-TYPE     10      5      9      9
D53V7, multiclass
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             6               5
  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
  OR2T4 MUTATED        1      5      1      1      0
  OR2T4 WILD-TYPE      5      6      6     11      5
D53V8, multiclass
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             5               6
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             0               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"
D53V9, binary
                 cls
clus               0  1
  OR2T4 MUTATED    2  6
  OR2T4 WILD-TYPE 15 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      2    6
  OR2T4 WILD-TYPE   15   13
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             6              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OR2T4 MUTATED        1      4      0      1      0      0      0      1
  OR2T4 WILD-TYPE      3      1      5      5      7      1      4      0
                 vv
clus              CLUS_9
  OR2T4 MUTATED        1
  OR2T4 WILD-TYPE      2
D53V10, multiclass
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             4               1
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             0               7
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             1               2
[1] 9 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 = AMAC1L3 MUTATION ANALYSIS
D54V1, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    3  2
  AMAC1L3 WILD-TYPE 20 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      3    2
  AMAC1L3 WILD-TYPE   20   16
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                20
  CLUS_2               2                16
[1] 2 2
[1] FALSE
D54V2, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    3  2
  AMAC1L3 WILD-TYPE 17 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      3    2
  AMAC1L3 WILD-TYPE   17   19
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               2                19
[1] 2 2
[1] FALSE
D54V3, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    4  0
  AMAC1L3 WILD-TYPE 11 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      4    0
  AMAC1L3 WILD-TYPE   11   14
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               4                11
  CLUS_2               0                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMAC1L3 MUTATED        1      3      0
  AMAC1L3 WILD-TYPE      4     10     11
D54V4, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               3                10
  CLUS_3               0                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"
D54V5, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    3  2
  AMAC1L3 WILD-TYPE  6 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      3    2
  AMAC1L3 WILD-TYPE    6   10
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMAC1L3 MUTATED        3      2      0
  AMAC1L3 WILD-TYPE      4      7      5
D54V6, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               2                 7
  CLUS_3               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMAC1L3 MUTATED        3      1      0      1
  AMAC1L3 WILD-TYPE      8     10     10      8
D54V7, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               1                10
  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
  AMAC1L3 MUTATED        3      1      0      0      1
  AMAC1L3 WILD-TYPE      3     10      7     12      4
D54V8, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               0                12
  CLUS_5               1                 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"
D54V9, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    3  2
  AMAC1L3 WILD-TYPE 14 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      3    2
  AMAC1L3 WILD-TYPE   14   17
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                14
  CLUS_2               2                17
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AMAC1L3 MUTATED        1      0      0      0      3      0      0      1
  AMAC1L3 WILD-TYPE      3      5      5      6      4      1      4      0
                   vv
clus                CLUS_9
  AMAC1L3 MUTATED        0
  AMAC1L3 WILD-TYPE      3
D54V10, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               0                 5
  CLUS_4               0                 6
  CLUS_5               3                 4
  CLUS_6               0                 1
  CLUS_7               0                 4
  CLUS_8               1                 0
  CLUS_9               0                 3
[1] 9 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 = APOB MUTATION ANALYSIS
D55V1, binary
                cls
clus              0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 21 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2    1
  APOB WILD-TYPE   21   17
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            2             21
  CLUS_2            1             17
[1] 2 2
[1] FALSE
D55V2, binary
                cls
clus              0  1
  APOB MUTATED    3  0
  APOB WILD-TYPE 17 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      3    0
  APOB WILD-TYPE   17   21
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            3             17
  CLUS_2            0             21
[1] 2 2
[1] FALSE
D55V3, binary
                cls
clus              0  1
  APOB MUTATED    1  0
  APOB WILD-TYPE 14 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      1    0
  APOB WILD-TYPE   14   14
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1             14
  CLUS_2            0             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        0      1      0
  APOB WILD-TYPE      5     12     11
D55V4, multiclass
[1] "Remove cluster labels:" "APOB MUTATED"          
clus
  APOB MUTATED APOB WILD-TYPE 
             1             28 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TV     TCGA-GS-A9TX     TCGA-GS-A9TZ 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
D55V5, binary
                cls
clus              0  1
  APOB MUTATED    0  2
  APOB WILD-TYPE  9 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      0    2
  APOB WILD-TYPE    9   10
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        0      2      0
  APOB WILD-TYPE      7      7      5
D55V6, multiclass
[1] "Remove cluster labels:" "APOB MUTATED"          
clus
  APOB MUTATED APOB WILD-TYPE 
             2             19 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FM-8000     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GR-A4D9     TCGA-RQ-A68N     TCGA-RQ-A6JB 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOB MUTATED        0      1      0      2
  APOB WILD-TYPE     11     10     10      7
D55V7, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0             11
  CLUS_2            1             10
  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
  APOB MUTATED        0      1      0      1      1
  APOB WILD-TYPE      6     10      7     11      4
D55V8, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             10
  CLUS_3            0              7
  CLUS_4            1             11
  CLUS_5            1              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"
D55V9, binary
                cls
clus              0  1
  APOB MUTATED    0  3
  APOB WILD-TYPE 17 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      0    3
  APOB WILD-TYPE   17   16
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0             17
  CLUS_2            3             16
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  APOB MUTATED        0      0      1      0      1      0      0      1      0
  APOB WILD-TYPE      4      5      4      6      6      1      4      0      3
D55V10, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              5
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            0              4
  CLUS_8            1              0
  CLUS_9            0              3
[1] 9 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 = KRTAP4-7 MUTATION ANALYSIS
D56V1, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    7  1
  KRTAP4-7 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      7    1
  KRTAP4-7 WILD-TYPE   16   17
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                7                 16
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
D56V2, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    4  4
  KRTAP4-7 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      4    4
  KRTAP4-7 WILD-TYPE   16   17
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                4                 17
[1] 2 2
[1] FALSE
D56V3, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    3  4
  KRTAP4-7 WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      3    4
  KRTAP4-7 WILD-TYPE   12   10
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                4                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-7 MUTATED        0      3      4
  KRTAP4-7 WILD-TYPE      5     10      7
D56V4, multiclass
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                3                 10
  CLUS_3                4                  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"
D56V5, binary
                    cls
clus                 0 1
  KRTAP4-7 MUTATED   0 5
  KRTAP4-7 WILD-TYPE 9 7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      0    5
  KRTAP4-7 WILD-TYPE    9    7
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                5                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-7 MUTATED        2      3      0
  KRTAP4-7 WILD-TYPE      5      6      5
D56V6, multiclass
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                3                  6
  CLUS_3                0                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-7 MUTATED        1      3      2      2
  KRTAP4-7 WILD-TYPE     10      8      8      7
D56V7, multiclass
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                3                  8
  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
  KRTAP4-7 MUTATED        2      3      0      1      2
  KRTAP4-7 WILD-TYPE      4      8      7     11      3
D56V8, multiclass
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                3                  8
  CLUS_3                0                  7
  CLUS_4                1                 11
  CLUS_5                2                  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"
D56V9, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    2  6
  KRTAP4-7 WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      2    6
  KRTAP4-7 WILD-TYPE   15   13
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRTAP4-7 MUTATED        1      1      0      2      2      1      0      1
  KRTAP4-7 WILD-TYPE      3      4      5      4      5      0      4      0
                    vv
clus                 CLUS_9
  KRTAP4-7 MUTATED        0
  KRTAP4-7 WILD-TYPE      3
D56V10, multiclass
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  4
  CLUS_3                0                  5
  CLUS_4                2                  4
  CLUS_5                2                  5
  CLUS_6                1                  0
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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 = MUC16 MUTATION ANALYSIS
D57V1, binary
                 cls
clus               0  1
  MUC16 MUTATED    9  4
  MUC16 WILD-TYPE 14 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      9    4
  MUC16 WILD-TYPE   14   14
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             9              14
  CLUS_2             4              14
[1] 2 2
[1] FALSE
D57V2, binary
                 cls
clus               0  1
  MUC16 MUTATED    4  9
  MUC16 WILD-TYPE 16 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      4    9
  MUC16 WILD-TYPE   16   12
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             9              12
[1] 2 2
[1] FALSE
D57V3, binary
                 cls
clus               0  1
  MUC16 MUTATED    6  3
  MUC16 WILD-TYPE  9 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      6    3
  MUC16 WILD-TYPE    9   11
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             6               9
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC16 MUTATED        0      6      3
  MUC16 WILD-TYPE      5      7      8
D57V4, multiclass
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             6               7
  CLUS_3             3               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"
D57V5, binary
                 cls
clus              0 1
  MUC16 MUTATED   4 4
  MUC16 WILD-TYPE 5 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      4    4
  MUC16 WILD-TYPE    5    8
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             4               5
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC16 MUTATED        3      3      2
  MUC16 WILD-TYPE      4      6      3
D57V6, multiclass
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             3               4
  CLUS_2             3               6
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC16 MUTATED        3      3      3      4
  MUC16 WILD-TYPE      8      8      7      5
D57V7, multiclass
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             3               8
  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
  MUC16 MUTATED        1      3      2      4      3
  MUC16 WILD-TYPE      5      8      5      8      2
D57V8, multiclass
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             3               8
  CLUS_3             2               5
  CLUS_4             4               8
  CLUS_5             3               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"
D57V9, binary
                 cls
clus               0  1
  MUC16 MUTATED    4  7
  MUC16 WILD-TYPE 13 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      4    7
  MUC16 WILD-TYPE   13   12
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             4              13
  CLUS_2             7              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MUC16 MUTATED        1      2      1      2      3      1      0      1
  MUC16 WILD-TYPE      3      3      4      4      4      0      4      0
                 vv
clus              CLUS_9
  MUC16 MUTATED        0
  MUC16 WILD-TYPE      3
D57V10, multiclass
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             2               3
  CLUS_3             1               4
  CLUS_4             2               4
  CLUS_5             3               4
  CLUS_6             1               0
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = NEFH MUTATION ANALYSIS
D58V1, binary
                cls
clus              0  1
  NEFH MUTATED    5  1
  NEFH WILD-TYPE 18 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      5    1
  NEFH WILD-TYPE   18   17
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            5             18
  CLUS_2            1             17
[1] 2 2
[1] FALSE
D58V2, binary
                cls
clus              0  1
  NEFH MUTATED    2  4
  NEFH WILD-TYPE 18 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    4
  NEFH WILD-TYPE   18   17
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             18
  CLUS_2            4             17
[1] 2 2
[1] FALSE
D58V3, binary
                cls
clus              0  1
  NEFH MUTATED    5  0
  NEFH WILD-TYPE 10 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      5    0
  NEFH WILD-TYPE   10   14
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            5             10
  CLUS_2            0             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        2      3      0
  NEFH WILD-TYPE      3     10     11
D58V4, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2              3
  CLUS_2            3             10
  CLUS_3            0             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"
D58V5, binary
                cls
clus              0  1
  NEFH MUTATED    1  2
  NEFH WILD-TYPE  8 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      1    2
  NEFH WILD-TYPE    8   10
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        2      0      1
  NEFH WILD-TYPE      5      9      4
D58V6, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2              5
  CLUS_2            0              9
  CLUS_3            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        2      1      2      1
  NEFH WILD-TYPE      9     10      8      8
D58V7, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             10
  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
  NEFH MUTATED        2      1      1      1      1
  NEFH WILD-TYPE      4     10      6     11      4
D58V8, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2              4
  CLUS_2            1             10
  CLUS_3            1              6
  CLUS_4            1             11
  CLUS_5            1              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"
D58V9, binary
                cls
clus              0  1
  NEFH MUTATED    4  2
  NEFH WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    2
  NEFH WILD-TYPE   13   17
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            4             13
  CLUS_2            2             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  NEFH MUTATED        2      1      0      2      0      1      0      0      0
  NEFH WILD-TYPE      2      4      5      4      7      0      4      1      3
D58V10, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2              2
  CLUS_2            1              4
  CLUS_3            0              5
  CLUS_4            2              4
  CLUS_5            0              7
  CLUS_6            1              0
  CLUS_7            0              4
  CLUS_8            0              1
  CLUS_9            0              3
[1] 9 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 = KCNN3 MUTATION ANALYSIS
D59V1, binary
                 cls
clus               0  1
  KCNN3 MUTATED    2  5
  KCNN3 WILD-TYPE 21 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      2    5
  KCNN3 WILD-TYPE   21   13
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             5              13
[1] 2 2
[1] FALSE
D59V2, binary
                 cls
clus               0  1
  KCNN3 MUTATED    3  4
  KCNN3 WILD-TYPE 17 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      3    4
  KCNN3 WILD-TYPE   17   17
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             4              17
[1] 2 2
[1] FALSE
D59V3, binary
                 cls
clus               0  1
  KCNN3 MUTATED    2  5
  KCNN3 WILD-TYPE 13  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      2    5
  KCNN3 WILD-TYPE   13    9
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             5               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KCNN3 MUTATED        1      2      4
  KCNN3 WILD-TYPE      4     11      7
D59V4, multiclass
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             2              11
  CLUS_3             4               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"
D59V5, binary
                 cls
clus              0 1
  KCNN3 MUTATED   2 3
  KCNN3 WILD-TYPE 7 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      2    3
  KCNN3 WILD-TYPE    7    9
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             3               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KCNN3 MUTATED        1      3      1
  KCNN3 WILD-TYPE      6      6      4
D59V6, multiclass
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             3               6
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KCNN3 MUTATED        2      2      1      2
  KCNN3 WILD-TYPE      9      9      9      7
D59V7, multiclass
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             2               9
  CLUS_2             2               9
  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
  KCNN3 MUTATED        0      2      2      1      2
  KCNN3 WILD-TYPE      6      9      5     11      3
D59V8, multiclass
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2               9
  CLUS_3             2               5
  CLUS_4             1              11
  CLUS_5             2               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"
D59V9, binary
                 cls
clus               0  1
  KCNN3 MUTATED    3  3
  KCNN3 WILD-TYPE 14 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      3    3
  KCNN3 WILD-TYPE   14   16
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KCNN3 MUTATED        0      1      2      0      3      0      0      0
  KCNN3 WILD-TYPE      4      4      3      6      4      1      4      1
                 vv
clus              CLUS_9
  KCNN3 MUTATED        0
  KCNN3 WILD-TYPE      3
D59V10, multiclass
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             2               3
  CLUS_4             0               6
  CLUS_5             3               4
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = RNASEH2B MUTATION ANALYSIS
D60V1, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    1  2
  RNASEH2B WILD-TYPE 22 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      1    2
  RNASEH2B WILD-TYPE   22   16
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D60V2, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    2  1
  RNASEH2B WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      2    1
  RNASEH2B WILD-TYPE   18   20
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D60V3, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    1  1
  RNASEH2B WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      1    1
  RNASEH2B WILD-TYPE   14   13
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  RNASEH2B MUTATED        0      1      1
  RNASEH2B WILD-TYPE      5     12     10
D60V4, multiclass
[1] "Remove cluster labels:" "RNASEH2B MUTATED"      
clus
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 2                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FM-8000 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TV         TCGA-GS-A9TW 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9TZ         TCGA-GS-A9U4 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB         TCGA-VB-A8QN 
"RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" "RNASEH2B WILD-TYPE" 
D60V5, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    0  0
  RNASEH2B WILD-TYPE  9 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      0    0
  RNASEH2B WILD-TYPE    9   12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  RNASEH2B MUTATED        0      0      0
  RNASEH2B WILD-TYPE      7      9      5
D60V6, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RNASEH2B MUTATED        0      0      3      0
  RNASEH2B WILD-TYPE     11     11      7      9
D60V7, multiclass
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                0                 11
  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
  RNASEH2B MUTATED        1      0      0      2      0
  RNASEH2B WILD-TYPE      5     11      7     10      5
D60V8, multiclass
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                 11
  CLUS_3                0                  7
  CLUS_4                2                 10
  CLUS_5                0                  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"
D60V9, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    2  1
  RNASEH2B WILD-TYPE 15 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      2    1
  RNASEH2B WILD-TYPE   15   18
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RNASEH2B MUTATED        0      0      0      2      0      0      0      0
  RNASEH2B WILD-TYPE      4      5      5      4      7      1      4      1
                    vv
clus                 CLUS_9
  RNASEH2B MUTATED        1
  RNASEH2B WILD-TYPE      2
D60V10, multiclass
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                2                  4
  CLUS_5                0                  7
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                0                  1
  CLUS_9                1                  2
[1] 9 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 = FAM153B MUTATION ANALYSIS
D61V1, binary
                   cls
clus                 0  1
  FAM153B MUTATED    2  1
  FAM153B WILD-TYPE 21 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM153B MUTATED      2    1
  FAM153B WILD-TYPE   21   17
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               2                21
  CLUS_2               1                17
[1] 2 2
[1] FALSE
D61V2, binary
                   cls
clus                 0  1
  FAM153B MUTATED    1  2
  FAM153B WILD-TYPE 19 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM153B MUTATED      1    2
  FAM153B WILD-TYPE   19   19
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                19
[1] 2 2
[1] FALSE
D61V3, binary
                   cls
clus                 0  1
  FAM153B MUTATED    2  1
  FAM153B WILD-TYPE 13 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM153B MUTATED      2    1
  FAM153B WILD-TYPE   13   13
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM153B MUTATED        1      2      0
  FAM153B WILD-TYPE      4     11     11
D61V4, multiclass
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               2                11
  CLUS_3               0                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"
D61V5, binary
                   cls
clus                 0  1
  FAM153B MUTATED    0  1
  FAM153B WILD-TYPE  9 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM153B MUTATED      0    1
  FAM153B WILD-TYPE    9   11
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM153B MUTATED        0      1      0
  FAM153B WILD-TYPE      7      8      5
D61V6, multiclass
[1] "Remove cluster labels:" "FAM153B MUTATED"       
clus
  FAM153B MUTATED FAM153B WILD-TYPE 
                1                20 
       TCGA-FA-8693        TCGA-FA-A4XK        TCGA-FA-A6HN        TCGA-FA-A6HO 
"FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" 
       TCGA-G8-6324        TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5 
"FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" 
       TCGA-GR-A4D6        TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" "FAM153B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM153B MUTATED        1      1      1      0
  FAM153B WILD-TYPE     10     10      9      9
D61V7, multiclass
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                10
  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
  FAM153B MUTATED        0      1      1      1      0
  FAM153B WILD-TYPE      6     10      6     11      5
D61V8, multiclass
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                10
  CLUS_3               1                 6
  CLUS_4               1                11
  CLUS_5               0                 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"
D61V9, binary
                   cls
clus                 0  1
  FAM153B MUTATED    2  1
  FAM153B WILD-TYPE 15 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM153B MUTATED      2    1
  FAM153B WILD-TYPE   15   18
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               2                15
  CLUS_2               1                18
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FAM153B MUTATED        1      1      0      1      0      0      0      0
  FAM153B WILD-TYPE      3      4      5      5      7      1      4      1
                   vv
clus                CLUS_9
  FAM153B MUTATED        0
  FAM153B WILD-TYPE      3
D61V10, multiclass
        clus
vv       FAM153B MUTATED FAM153B WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 4
  CLUS_3               0                 5
  CLUS_4               1                 5
  CLUS_5               0                 7
  CLUS_6               0                 1
  CLUS_7               0                 4
  CLUS_8               0                 1
  CLUS_9               0                 3
[1] 9 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 = OTOP1 MUTATION ANALYSIS
D62V1, binary
                 cls
clus               0  1
  OTOP1 MUTATED    1  3
  OTOP1 WILD-TYPE 22 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      1    3
  OTOP1 WILD-TYPE   22   15
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             1              22
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D62V2, binary
                 cls
clus               0  1
  OTOP1 MUTATED    2  2
  OTOP1 WILD-TYPE 18 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      2    2
  OTOP1 WILD-TYPE   18   19
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D62V3, binary
                 cls
clus               0  1
  OTOP1 MUTATED    1  2
  OTOP1 WILD-TYPE 14 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      1    2
  OTOP1 WILD-TYPE   14   12
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OTOP1 MUTATED        0      1      2
  OTOP1 WILD-TYPE      5     12      9
D62V4, multiclass
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1              12
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                 cls
clus               0  1
  OTOP1 MUTATED    1  2
  OTOP1 WILD-TYPE  8 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      1    2
  OTOP1 WILD-TYPE    8   10
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OTOP1 MUTATED        1      2      0
  OTOP1 WILD-TYPE      6      7      5
D62V6, multiclass
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             2               7
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OTOP1 MUTATED        2      2      0      0
  OTOP1 WILD-TYPE      9      9     10      9
D62V7, multiclass
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             2               9
  CLUS_2             2               9
  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
  OTOP1 MUTATED        1      2      1      0      0
  OTOP1 WILD-TYPE      5      9      6     12      5
D62V8, multiclass
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             2               9
  CLUS_3             1               6
  CLUS_4             0              12
  CLUS_5             0               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"
D62V9, binary
                 cls
clus               0  1
  OTOP1 MUTATED    2  2
  OTOP1 WILD-TYPE 15 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      2    2
  OTOP1 WILD-TYPE   15   17
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             2              17
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OTOP1 MUTATED        0      1      0      0      2      0      1      0
  OTOP1 WILD-TYPE      4      4      5      6      5      1      3      1
                 vv
clus              CLUS_9
  OTOP1 MUTATED        0
  OTOP1 WILD-TYPE      3
D62V10, multiclass
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             2               5
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = AATK MUTATION ANALYSIS
D63V1, binary
                cls
clus              0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE 22 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    2
  AATK WILD-TYPE   22   16
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1             22
  CLUS_2            2             16
[1] 2 2
[1] FALSE
D63V2, binary
                cls
clus              0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE 19 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    2
  AATK WILD-TYPE   19   19
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2             19
[1] 2 2
[1] FALSE
D63V3, binary
                cls
clus              0  1
  AATK MUTATED    2  0
  AATK WILD-TYPE 13 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      2    0
  AATK WILD-TYPE   13   14
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            2             13
  CLUS_2            0             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  AATK MUTATED        0      2      0
  AATK WILD-TYPE      5     11     11
D63V4, multiclass
[1] "Remove cluster labels:" "AATK MUTATED"          
clus
  AATK MUTATED AATK WILD-TYPE 
             2             27 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A6HN     TCGA-FA-A6HO 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-GS-A9TT     TCGA-GS-A9TV 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"AATK WILD-TYPE" "AATK WILD-TYPE" "AATK WILD-TYPE" 
D63V5, binary
                cls
clus              0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE  8 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    2
  AATK WILD-TYPE    8   10
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             10
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  AATK MUTATED        0      2      1
  AATK WILD-TYPE      7      7      4
D63V6, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2              7
  CLUS_3            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AATK MUTATED        1      1      0      1
  AATK WILD-TYPE     10     10     10      8
D63V7, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1             10
  CLUS_2            1             10
  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
  AATK MUTATED        0      1      1      0      1
  AATK WILD-TYPE      6     10      6     12      4
D63V8, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             10
  CLUS_3            1              6
  CLUS_4            0             12
  CLUS_5            1              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"
D63V9, binary
                cls
clus              0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE 16 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      1    2
  AATK WILD-TYPE   16   17
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            1             16
  CLUS_2            2             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  AATK MUTATED        0      0      1      0      0      0      1      1      0
  AATK WILD-TYPE      4      5      4      6      7      1      3      0      3
D63V10, multiclass
        clus
vv       AATK MUTATED AATK WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              5
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            0              7
  CLUS_6            0              1
  CLUS_7            1              3
  CLUS_8            1              0
  CLUS_9            0              3
[1] 9 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 = ARID1A MUTATION ANALYSIS
D64V1, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  2
  ARID1A WILD-TYPE 20 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    2
  ARID1A WILD-TYPE   20   16
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               20
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D64V2, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  2
  ARID1A WILD-TYPE 17 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    2
  ARID1A WILD-TYPE   17   19
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               17
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D64V3, binary
                  cls
clus                0  1
  ARID1A MUTATED    1  1
  ARID1A WILD-TYPE 14 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1    1
  ARID1A WILD-TYPE   14   13
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               14
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      1      1
  ARID1A WILD-TYPE      5     12     10
D64V4, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-GS-A9TT       TCGA-GS-A9TV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D64V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  2
  ARID1A WILD-TYPE  7 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    2
  ARID1A WILD-TYPE    7   10
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      2      2
  ARID1A WILD-TYPE      7      7      3
D64V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              2                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      2      0      2
  ARID1A WILD-TYPE     10      9     10      7
D64V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               10
  CLUS_2              2                9
  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
  ARID1A MUTATED        1      2      0      1      1
  ARID1A WILD-TYPE      5      9      7     11      4
D64V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1                5
  CLUS_2              2                9
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              1                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"
D64V9, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  4
  ARID1A WILD-TYPE 17 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    4
  ARID1A WILD-TYPE   17   15
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               17
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARID1A MUTATED        0      1      0      0      0      0      2      1
  ARID1A WILD-TYPE      4      4      5      6      7      1      2      0
                  vv
clus               CLUS_9
  ARID1A MUTATED        0
  ARID1A WILD-TYPE      3
D64V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              0                7
  CLUS_6              0                1
  CLUS_7              2                2
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = GUCA1C MUTATION ANALYSIS
D65V1, binary
                  cls
clus                0  1
  GUCA1C MUTATED    1  2
  GUCA1C WILD-TYPE 22 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      1    2
  GUCA1C WILD-TYPE   22   16
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              1               22
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D65V2, binary
                  cls
clus                0  1
  GUCA1C MUTATED    2  1
  GUCA1C WILD-TYPE 18 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      2    1
  GUCA1C WILD-TYPE   18   20
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              2               18
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D65V3, binary
                  cls
clus                0  1
  GUCA1C MUTATED    1  0
  GUCA1C WILD-TYPE 14 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      1    0
  GUCA1C WILD-TYPE   14   14
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GUCA1C MUTATED        0      1      0
  GUCA1C WILD-TYPE      5     12     11
D65V4, multiclass
[1] "Remove cluster labels:" "GUCA1C MUTATED"        
clus
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               1               28 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A6HN       TCGA-FA-A6HO 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F       TCGA-FA-A86F 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-GS-A9TV       TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
      TCGA-GS-A9U4       TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" "GUCA1C WILD-TYPE" 
D65V5, binary
                  cls
clus                0  1
  GUCA1C MUTATED    1  2
  GUCA1C WILD-TYPE  8 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      1    2
  GUCA1C WILD-TYPE    8   10
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GUCA1C MUTATED        0      2      1
  GUCA1C WILD-TYPE      7      7      4
D65V6, multiclass
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GUCA1C MUTATED        1      1      0      1
  GUCA1C WILD-TYPE     10     10     10      8
D65V7, multiclass
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               10
  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
  GUCA1C MUTATED        0      1      1      0      1
  GUCA1C WILD-TYPE      6     10      6     12      4
D65V8, multiclass
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              0                6
  CLUS_2              1               10
  CLUS_3              1                6
  CLUS_4              0               12
  CLUS_5              1                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"
D65V9, binary
                  cls
clus                0  1
  GUCA1C MUTATED    1  2
  GUCA1C WILD-TYPE 16 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      1    2
  GUCA1C WILD-TYPE   16   17
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              1               16
  CLUS_2              2               17
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GUCA1C MUTATED        0      0      1      0      1      0      0      1
  GUCA1C WILD-TYPE      4      5      4      6      6      1      4      0
                  vv
clus               CLUS_9
  GUCA1C MUTATED        0
  GUCA1C WILD-TYPE      3
D65V10, multiclass
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = TRIM48 MUTATION ANALYSIS
D66V1, binary
                  cls
clus                0  1
  TRIM48 MUTATED    5  3
  TRIM48 WILD-TYPE 18 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      5    3
  TRIM48 WILD-TYPE   18   15
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              5               18
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D66V2, binary
                  cls
clus                0  1
  TRIM48 MUTATED    4  4
  TRIM48 WILD-TYPE 16 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      4    4
  TRIM48 WILD-TYPE   16   17
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              4               16
  CLUS_2              4               17
[1] 2 2
[1] FALSE
D66V3, binary
                  cls
clus                0  1
  TRIM48 MUTATED    3  4
  TRIM48 WILD-TYPE 12 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      3    4
  TRIM48 WILD-TYPE   12   10
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              4               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIM48 MUTATED        0      3      4
  TRIM48 WILD-TYPE      5     10      7
D66V4, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              3               10
  CLUS_3              4                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"
D66V5, binary
                  cls
clus               0 1
  TRIM48 MUTATED   0 3
  TRIM48 WILD-TYPE 9 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      0    3
  TRIM48 WILD-TYPE    9    9
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIM48 MUTATED        0      3      0
  TRIM48 WILD-TYPE      7      6      5
D66V6, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              3                6
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIM48 MUTATED        2      2      3      1
  TRIM48 WILD-TYPE      9      9      7      8
D66V7, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              2                9
  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
  TRIM48 MUTATED        1      2      1      3      1
  TRIM48 WILD-TYPE      5      9      6      9      4
D66V8, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              2                9
  CLUS_3              1                6
  CLUS_4              3                9
  CLUS_5              1                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"
D66V9, binary
                  cls
clus                0  1
  TRIM48 MUTATED    4  4
  TRIM48 WILD-TYPE 13 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      4    4
  TRIM48 WILD-TYPE   13   15
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              4               13
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TRIM48 MUTATED        0      1      0      3      2      0      1      1
  TRIM48 WILD-TYPE      4      4      5      3      5      1      3      0
                  vv
clus               CLUS_9
  TRIM48 MUTATED        0
  TRIM48 WILD-TYPE      3
D66V10, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              3                3
  CLUS_5              2                5
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = CSGALNACT2 MUTATION ANALYSIS
D67V1, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  2
  CSGALNACT2 WILD-TYPE 20 16
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    2
  CSGALNACT2 WILD-TYPE   20   16
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  3                   20
  CLUS_2                  2                   16
[1] 2 2
[1] FALSE
D67V2, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    2  3
  CSGALNACT2 WILD-TYPE 18 18
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      2    3
  CSGALNACT2 WILD-TYPE   18   18
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  2                   18
  CLUS_2                  3                   18
[1] 2 2
[1] FALSE
D67V3, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 12 14
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   12   14
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  3                   12
  CLUS_2                  0                   14
[1] 2 2
[1] FALSE
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3
  CSGALNACT2 MUTATED        0      3      0
  CSGALNACT2 WILD-TYPE      5     10     11
D67V4, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                    5
  CLUS_2                  3                   10
  CLUS_3                  0                   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"
D67V5, binary
                      cls
clus                   0 1
  CSGALNACT2 MUTATED   2 3
  CSGALNACT2 WILD-TYPE 7 9
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      2    3
  CSGALNACT2 WILD-TYPE    7    9
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  2                    7
  CLUS_2                  3                    9
[1] 2 2
[1] FALSE
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3
  CSGALNACT2 MUTATED        2      1      2
  CSGALNACT2 WILD-TYPE      5      8      3
D67V6, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  2                    5
  CLUS_2                  1                    8
  CLUS_3                  2                    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"
                      vv
clus                   CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSGALNACT2 MUTATED        1      2      0      2
  CSGALNACT2 WILD-TYPE     10      9     10      7
D67V7, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   10
  CLUS_2                  2                    9
  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
  CSGALNACT2 MUTATED        0      2      1      0      2
  CSGALNACT2 WILD-TYPE      6      9      6     12      3
D67V8, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                    6
  CLUS_2                  2                    9
  CLUS_3                  1                    6
  CLUS_4                  0                   12
  CLUS_5                  2                    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"
D67V9, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    1  4
  CSGALNACT2 WILD-TYPE 16 15
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      1    4
  CSGALNACT2 WILD-TYPE   16   15
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  1                   16
  CLUS_2                  4                   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      1      1      0      1      1      0      1
  CSGALNACT2 WILD-TYPE      4      4      4      6      6      0      4      0
                      vv
clus                   CLUS_9
  CSGALNACT2 MUTATED        0
  CSGALNACT2 WILD-TYPE      3
D67V10, multiclass
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  CLUS_1                  0                    4
  CLUS_2                  1                    4
  CLUS_3                  1                    4
  CLUS_4                  0                    6
  CLUS_5                  1                    6
  CLUS_6                  1                    0
  CLUS_7                  0                    4
  CLUS_8                  1                    0
  CLUS_9                  0                    3
[1] 9 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 = CRIPAK MUTATION ANALYSIS
D68V1, binary
                  cls
clus                0  1
  CRIPAK MUTATED    4  2
  CRIPAK WILD-TYPE 19 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      4    2
  CRIPAK WILD-TYPE   19   16
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              4               19
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D68V2, binary
                  cls
clus                0  1
  CRIPAK MUTATED    6  0
  CRIPAK WILD-TYPE 14 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      6    0
  CRIPAK WILD-TYPE   14   21
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              6               14
  CLUS_2              0               21
[1] 2 2
[1] FALSE
D68V3, binary
                  cls
clus                0  1
  CRIPAK MUTATED    0  2
  CRIPAK WILD-TYPE 15 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      0    2
  CRIPAK WILD-TYPE   15   12
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              0               15
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        1      0      1
  CRIPAK WILD-TYPE      4     13     10
D68V4, multiclass
[1] "Remove cluster labels:" "CRIPAK MUTATED"        
clus
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4XK       TCGA-FA-A6HN       TCGA-FA-A6HO 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F       TCGA-FA-A86F 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-A7CR       TCGA-FF-A7CW 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT       TCGA-GS-A9TV 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" "CRIPAK WILD-TYPE" 
D68V5, binary
                  cls
clus               0 1
  CRIPAK MUTATED   1 5
  CRIPAK WILD-TYPE 8 7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      1    5
  CRIPAK WILD-TYPE    8    7
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1                8
  CLUS_2              5                7
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        1      3      2
  CRIPAK WILD-TYPE      6      6      3
D68V6, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1                6
  CLUS_2              3                6
  CLUS_3              2                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        0      4      0      2
  CRIPAK WILD-TYPE     11      7     10      7
D68V7, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              0               11
  CLUS_2              4                7
  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
  CRIPAK MUTATED        1      4      0      0      1
  CRIPAK WILD-TYPE      5      7      7     12      4
D68V8, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1                5
  CLUS_2              4                7
  CLUS_3              0                7
  CLUS_4              0               12
  CLUS_5              1                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"
D68V9, binary
                  cls
clus                0  1
  CRIPAK MUTATED    0  6
  CRIPAK WILD-TYPE 17 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      0    6
  CRIPAK WILD-TYPE   17   13
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              0               17
  CLUS_2              6               13
[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      0      0      1      0      1      1
  CRIPAK WILD-TYPE      3      3      5      6      6      1      3      0
                  vv
clus               CLUS_9
  CRIPAK MUTATED        0
  CRIPAK WILD-TYPE      3
D68V10, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              1                3
  CLUS_2              2                3
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = DHRS4 MUTATION ANALYSIS
D69V1, binary
                 cls
clus               0  1
  DHRS4 MUTATED    2  2
  DHRS4 WILD-TYPE 21 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      2    2
  DHRS4 WILD-TYPE   21   16
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D69V2, binary
                 cls
clus               0  1
  DHRS4 MUTATED    4  0
  DHRS4 WILD-TYPE 16 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      4    0
  DHRS4 WILD-TYPE   16   21
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             0              21
[1] 2 2
[1] FALSE
D69V3, binary
                 cls
clus               0  1
  DHRS4 MUTATED    0  2
  DHRS4 WILD-TYPE 15 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      0    2
  DHRS4 WILD-TYPE   15   12
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DHRS4 MUTATED        0      0      2
  DHRS4 WILD-TYPE      5     13      9
D69V4, multiclass
[1] "Remove cluster labels:" "DHRS4 MUTATED"         
clus
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              2              27 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A7DS 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-FA-A7Q1      TCGA-FA-A82F      TCGA-FA-A86F      TCGA-FF-8041 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046      TCGA-FF-8047 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-FF-8061      TCGA-FF-8062      TCGA-FF-A7CR      TCGA-FF-A7CW 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-FF-A7CX      TCGA-FM-8000      TCGA-GS-A9TT      TCGA-GS-A9TV 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" "DHRS4 WILD-TYPE" 
D69V5, binary
                 cls
clus              0 1
  DHRS4 MUTATED   0 4
  DHRS4 WILD-TYPE 9 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      0    4
  DHRS4 WILD-TYPE    9    8
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DHRS4 MUTATED        0      4      0
  DHRS4 WILD-TYPE      7      5      5
D69V6, multiclass
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             4               5
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DHRS4 MUTATED        0      3      0      1
  DHRS4 WILD-TYPE     11      8     10      8
D69V7, multiclass
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             3               8
  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
  DHRS4 MUTATED        0      3      0      0      1
  DHRS4 WILD-TYPE      6      8      7     12      4
D69V8, multiclass
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3               8
  CLUS_3             0               7
  CLUS_4             0              12
  CLUS_5             1               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"
D69V9, binary
                 cls
clus               0  1
  DHRS4 MUTATED    0  3
  DHRS4 WILD-TYPE 17 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      0    3
  DHRS4 WILD-TYPE   17   16
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  DHRS4 MUTATED        0      1      0      0      1      0      0      1
  DHRS4 WILD-TYPE      4      4      5      6      6      1      4      0
                 vv
clus              CLUS_9
  DHRS4 MUTATED        0
  DHRS4 WILD-TYPE      3
D69V10, multiclass
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = FAM21A MUTATION ANALYSIS
D70V1, binary
                  cls
clus                0  1
  FAM21A MUTATED    3  1
  FAM21A WILD-TYPE 20 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      3    1
  FAM21A WILD-TYPE   20   17
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              3               20
  CLUS_2              1               17
[1] 2 2
[1] FALSE
D70V2, binary
                  cls
clus                0  1
  FAM21A MUTATED    3  1
  FAM21A WILD-TYPE 17 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      3    1
  FAM21A WILD-TYPE   17   20
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              3               17
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D70V3, binary
                  cls
clus                0  1
  FAM21A MUTATED    0  1
  FAM21A WILD-TYPE 15 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      0    1
  FAM21A WILD-TYPE   15   13
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0               15
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM21A MUTATED        0      0      1
  FAM21A WILD-TYPE      5     13     10
D70V4, multiclass
[1] "Remove cluster labels:" "FAM21A MUTATED"        
clus
  FAM21A MUTATED FAM21A WILD-TYPE 
               1               28 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-FF-8046       TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-GS-A9TV       TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
      TCGA-GS-A9U4       TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" "FAM21A WILD-TYPE" 
D70V5, binary
                  cls
clus               0 1
  FAM21A MUTATED   0 3
  FAM21A WILD-TYPE 9 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      0    3
  FAM21A WILD-TYPE    9    9
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM21A MUTATED        0      2      1
  FAM21A WILD-TYPE      7      7      4
D70V6, multiclass
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM21A MUTATED        0      2      1      1
  FAM21A WILD-TYPE     11      9      9      8
D70V7, multiclass
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0               11
  CLUS_2              2                9
  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
  FAM21A MUTATED        0      2      0      1      1
  FAM21A WILD-TYPE      6      9      7     11      4
D70V8, multiclass
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                9
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              1                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"
D70V9, binary
                  cls
clus                0  1
  FAM21A MUTATED    0  4
  FAM21A WILD-TYPE 17 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      0    4
  FAM21A WILD-TYPE   17   15
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0               17
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FAM21A MUTATED        0      1      0      1      1      0      0      1
  FAM21A WILD-TYPE      4      4      5      5      6      1      4      0
                  vv
clus               CLUS_9
  FAM21A MUTATED        0
  FAM21A WILD-TYPE      3
D70V10, multiclass
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              1                5
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = KIAA1529 MUTATION ANALYSIS
D71V1, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    3  1
  KIAA1529 WILD-TYPE 20 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      3    1
  KIAA1529 WILD-TYPE   20   17
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                3                 20
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
D71V2, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    2  2
  KIAA1529 WILD-TYPE 18 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      2    2
  KIAA1529 WILD-TYPE   18   19
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D71V3, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    1  0
  KIAA1529 WILD-TYPE 14 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      1    0
  KIAA1529 WILD-TYPE   14   14
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1529 MUTATED        0      1      0
  KIAA1529 WILD-TYPE      5     12     11
D71V4, multiclass
[1] "Remove cluster labels:" "KIAA1529 MUTATED"      
clus
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 1                 28 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-FM-8000         TCGA-GS-A9TT         TCGA-GS-A9TV 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" "KIAA1529 WILD-TYPE" 
        TCGA-VB-A8QN 
"KIAA1529 WILD-TYPE" 
D71V5, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    1  2
  KIAA1529 WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      1    2
  KIAA1529 WILD-TYPE    8   10
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1529 MUTATED        0      2      1
  KIAA1529 WILD-TYPE      7      7      4
D71V6, multiclass
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                  7
  CLUS_3                1                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1529 MUTATED        1      1      1      1
  KIAA1529 WILD-TYPE     10     10      9      8
D71V7, multiclass
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 10
  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
  KIAA1529 MUTATED        1      1      0      1      1
  KIAA1529 WILD-TYPE      5     10      7     11      4
D71V8, multiclass
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 10
  CLUS_3                0                  7
  CLUS_4                1                 11
  CLUS_5                1                  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"
D71V9, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    1  2
  KIAA1529 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      1    2
  KIAA1529 WILD-TYPE   16   17
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KIAA1529 MUTATED        0      0      0      1      1      0      0      1
  KIAA1529 WILD-TYPE      4      5      5      5      6      1      4      0
                    vv
clus                 CLUS_9
  KIAA1529 MUTATED        0
  KIAA1529 WILD-TYPE      3
D71V10, multiclass
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                1                  5
  CLUS_5                1                  6
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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 = OR2M5 MUTATION ANALYSIS
D72V1, binary
                 cls
clus               0  1
  OR2M5 MUTATED    3  1
  OR2M5 WILD-TYPE 20 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      3    1
  OR2M5 WILD-TYPE   20   17
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             1              17
[1] 2 2
[1] FALSE
D72V2, binary
                 cls
clus               0  1
  OR2M5 MUTATED    1  3
  OR2M5 WILD-TYPE 19 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      1    3
  OR2M5 WILD-TYPE   19   18
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D72V3, binary
                 cls
clus               0  1
  OR2M5 MUTATED    3  0
  OR2M5 WILD-TYPE 12 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      3    0
  OR2M5 WILD-TYPE   12   14
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             0              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR2M5 MUTATED        2      1      0
  OR2M5 WILD-TYPE      3     12     11
D72V4, multiclass
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1              12
  CLUS_3             0              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"
D72V5, binary
                 cls
clus               0  1
  OR2M5 MUTATED    3  0
  OR2M5 WILD-TYPE  6 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      3    0
  OR2M5 WILD-TYPE    6   12
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             0              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  OR2M5 MUTATED        2      0      1
  OR2M5 WILD-TYPE      5      9      4
D72V6, multiclass
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             0               9
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR2M5 MUTATED        3      0      0      1
  OR2M5 WILD-TYPE      8     11     10      8
D72V7, multiclass
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             0              11
  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
  OR2M5 MUTATED        2      0      1      1      0
  OR2M5 WILD-TYPE      4     11      6     11      5
D72V8, multiclass
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             0              11
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             0               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"
D72V9, binary
                 cls
clus               0  1
  OR2M5 MUTATED    3  0
  OR2M5 WILD-TYPE 14 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      3    0
  OR2M5 WILD-TYPE   14   19
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              19
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OR2M5 MUTATED        2      0      0      0      1      0      0      0
  OR2M5 WILD-TYPE      2      5      5      6      6      1      4      1
                 vv
clus              CLUS_9
  OR2M5 MUTATED        0
  OR2M5 WILD-TYPE      3
D72V10, multiclass
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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(73) Variable = KRT6A MUTATION ANALYSIS
D73V1, binary
                 cls
clus               0  1
  KRT6A MUTATED    1  3
  KRT6A WILD-TYPE 22 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      1    3
  KRT6A WILD-TYPE   22   15
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             1              22
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D73V2, binary
                 cls
clus               0  1
  KRT6A MUTATED    1  3
  KRT6A WILD-TYPE 19 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      1    3
  KRT6A WILD-TYPE   19   18
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             1              19
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D73V3, binary
                 cls
clus               0  1
  KRT6A MUTATED    2  2
  KRT6A WILD-TYPE 13 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      2    2
  KRT6A WILD-TYPE   13   12
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KRT6A MUTATED        0      2      2
  KRT6A WILD-TYPE      5     11      9
D73V4, multiclass
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2              11
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                 cls
clus               0  1
  KRT6A MUTATED    1  2
  KRT6A WILD-TYPE  8 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      1    2
  KRT6A WILD-TYPE    8   10
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KRT6A MUTATED        0      2      1
  KRT6A WILD-TYPE      7      7      4
D73V6, multiclass
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             0               7
  CLUS_2             2               7
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRT6A MUTATED        1      1      1      1
  KRT6A WILD-TYPE     10     10      9      8
D73V7, multiclass
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              10
  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
  KRT6A MUTATED        0      1      1      1      1
  KRT6A WILD-TYPE      6     10      6     11      4
D73V8, multiclass
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             1               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"
D73V9, binary
                 cls
clus               0  1
  KRT6A MUTATED    2  1
  KRT6A WILD-TYPE 15 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      2    1
  KRT6A WILD-TYPE   15   18
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             2              15
  CLUS_2             1              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRT6A MUTATED        0      0      1      1      1      0      0      0
  KRT6A WILD-TYPE      4      5      4      5      6      1      4      1
                 vv
clus              CLUS_9
  KRT6A MUTATED        0
  KRT6A WILD-TYPE      3
D73V10, multiclass
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = CYP2F1 MUTATION ANALYSIS
D74V1, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    2  2
  CYP2F1 WILD-TYPE 21 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      2    2
  CYP2F1 WILD-TYPE   21   16
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              2               21
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D74V2, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    3  1
  CYP2F1 WILD-TYPE 17 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      3    1
  CYP2F1 WILD-TYPE   17   20
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D74V3, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    0  2
  CYP2F1 WILD-TYPE 15 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      0    2
  CYP2F1 WILD-TYPE   15   12
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0               15
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CYP2F1 MUTATED        0      0      2
  CYP2F1 WILD-TYPE      5     13      9
D74V4, multiclass
[1] "Remove cluster labels:" "CYP2F1 MUTATED"        
clus
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR       TCGA-FF-A7CW 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT       TCGA-GS-A9TV 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" "CYP2F1 WILD-TYPE" 
D74V5, binary
                  cls
clus               0 1
  CYP2F1 MUTATED   0 3
  CYP2F1 WILD-TYPE 9 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      0    3
  CYP2F1 WILD-TYPE    9    9
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CYP2F1 MUTATED        0      3      0
  CYP2F1 WILD-TYPE      7      6      5
D74V6, multiclass
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              3                6
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP2F1 MUTATED        0      2      0      2
  CYP2F1 WILD-TYPE     11      9     10      7
D74V7, multiclass
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              2                9
  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
  CYP2F1 MUTATED        0      2      0      0      2
  CYP2F1 WILD-TYPE      6      9      7     12      3
D74V8, multiclass
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                9
  CLUS_3              0                7
  CLUS_4              0               12
  CLUS_5              2                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"
D74V9, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    0  4
  CYP2F1 WILD-TYPE 17 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      0    4
  CYP2F1 WILD-TYPE   17   15
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0               17
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CYP2F1 MUTATED        0      1      0      0      2      0      0      1
  CYP2F1 WILD-TYPE      4      4      5      6      5      1      4      0
                  vv
clus               CLUS_9
  CYP2F1 MUTATED        0
  CYP2F1 WILD-TYPE      3
D74V10, multiclass
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = FCGBP MUTATION ANALYSIS
D75V1, binary
                 cls
clus               0  1
  FCGBP MUTATED    2  3
  FCGBP WILD-TYPE 21 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2    3
  FCGBP WILD-TYPE   21   15
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             2              21
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D75V2, binary
                 cls
clus               0  1
  FCGBP MUTATED    4  1
  FCGBP WILD-TYPE 16 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      4    1
  FCGBP WILD-TYPE   16   20
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             4              16
  CLUS_2             1              20
[1] 2 2
[1] FALSE
D75V3, binary
                 cls
clus               0  1
  FCGBP MUTATED    1  1
  FCGBP WILD-TYPE 14 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      1    1
  FCGBP WILD-TYPE   14   13
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FCGBP MUTATED        0      1      1
  FCGBP WILD-TYPE      5     12     10
D75V4, multiclass
[1] "Remove cluster labels:" "FCGBP MUTATED"         
clus
  FCGBP MUTATED FCGBP WILD-TYPE 
              2              27 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A6HN      TCGA-FA-A6HO 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F      TCGA-FA-A86F 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FF-A7CR 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-FF-A7CX      TCGA-FM-8000      TCGA-GS-A9TT      TCGA-GS-A9TV 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"FCGBP WILD-TYPE" "FCGBP WILD-TYPE" "FCGBP WILD-TYPE" 
D75V5, binary
                 cls
clus              0 1
  FCGBP MUTATED   1 3
  FCGBP WILD-TYPE 8 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      1    3
  FCGBP WILD-TYPE    8    9
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             1               8
  CLUS_2             3               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FCGBP MUTATED        0      2      2
  FCGBP WILD-TYPE      7      7      3
D75V6, multiclass
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             0               7
  CLUS_2             2               7
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FCGBP MUTATED        1      2      1      1
  FCGBP WILD-TYPE     10      9      9      8
D75V7, multiclass
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2               9
  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
  FCGBP MUTATED        0      2      1      1      1
  FCGBP WILD-TYPE      6      9      6     11      4
D75V8, multiclass
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2               9
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             1               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"
D75V9, binary
                 cls
clus               0  1
  FCGBP MUTATED    2  3
  FCGBP WILD-TYPE 15 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2    3
  FCGBP WILD-TYPE   15   16
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             2              15
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FCGBP MUTATED        0      1      1      1      1      0      0      1
  FCGBP WILD-TYPE      4      4      4      5      6      1      4      0
                 vv
clus              CLUS_9
  FCGBP MUTATED        0
  FCGBP WILD-TYPE      3
D75V10, multiclass
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  CLUS_1             0               4
  CLUS_2             1               4
  CLUS_3             1               4
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = ZNF493 MUTATION ANALYSIS
D76V1, binary
                  cls
clus                0  1
  ZNF493 MUTATED    3  1
  ZNF493 WILD-TYPE 20 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      3    1
  ZNF493 WILD-TYPE   20   17
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              3               20
  CLUS_2              1               17
[1] 2 2
[1] FALSE
D76V2, binary
                  cls
clus                0  1
  ZNF493 MUTATED    2  2
  ZNF493 WILD-TYPE 18 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      2    2
  ZNF493 WILD-TYPE   18   19
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D76V3, binary
                  cls
clus                0  1
  ZNF493 MUTATED    1  0
  ZNF493 WILD-TYPE 14 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      1    0
  ZNF493 WILD-TYPE   14   14
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF493 MUTATED        0      1      0
  ZNF493 WILD-TYPE      5     12     11
D76V4, multiclass
[1] "Remove cluster labels:" "ZNF493 MUTATED"        
clus
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               1               28 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-FF-8046       TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-FF-A7CR       TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-GS-A9TV       TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-GS-A9U4       TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
D76V5, binary
                  cls
clus                0  1
  ZNF493 MUTATED    1  2
  ZNF493 WILD-TYPE  8 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      1    2
  ZNF493 WILD-TYPE    8   10
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF493 MUTATED        0      2      1
  ZNF493 WILD-TYPE      7      7      4
D76V6, multiclass
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2                7
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF493 MUTATED        1      1      1      1
  ZNF493 WILD-TYPE     10     10      9      8
D76V7, multiclass
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               10
  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
  ZNF493 MUTATED        0      1      0      2      1
  ZNF493 WILD-TYPE      6     10      7     10      4
D76V8, multiclass
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              2               10
  CLUS_5              1                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"
D76V9, binary
                  cls
clus                0  1
  ZNF493 MUTATED    1  2
  ZNF493 WILD-TYPE 16 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      1    2
  ZNF493 WILD-TYPE   16   17
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              2               17
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF493 MUTATED        0      0      0      1      1      0      0      1
  ZNF493 WILD-TYPE      4      5      5      5      6      1      4      0
                  vv
clus               CLUS_9
  ZNF493 MUTATED        0
  ZNF493 WILD-TYPE      3
D76V10, multiclass
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              1                5
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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(77) Variable = HLA-B MUTATION ANALYSIS
D77V1, binary
                 cls
clus               0  1
  HLA-B MUTATED    5  2
  HLA-B WILD-TYPE 18 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      5    2
  HLA-B WILD-TYPE   18   16
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             5              18
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D77V2, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  3
  HLA-B WILD-TYPE 16 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    3
  HLA-B WILD-TYPE   16   18
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             4              16
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D77V3, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  1
  HLA-B WILD-TYPE 11 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    1
  HLA-B WILD-TYPE   11   13
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             4              11
  CLUS_2             1              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        1      4      0
  HLA-B WILD-TYPE      4      9     11
D77V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1               4
  CLUS_2             4               9
  CLUS_3             0              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"
D77V5, binary
                 cls
clus              0 1
  HLA-B MUTATED   1 3
  HLA-B WILD-TYPE 8 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      1    3
  HLA-B WILD-TYPE    8    9
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1               8
  CLUS_2             3               9
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        2      2      0
  HLA-B WILD-TYPE      5      7      5
D77V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2               5
  CLUS_2             2               7
  CLUS_3             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-B MUTATED        2      2      1      2
  HLA-B WILD-TYPE      9      9      9      7
D77V7, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2               9
  CLUS_2             2               9
  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
  HLA-B MUTATED        1      2      1      1      2
  HLA-B WILD-TYPE      5      9      6     11      3
D77V8, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1               5
  CLUS_2             2               9
  CLUS_3             1               6
  CLUS_4             1              11
  CLUS_5             2               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"
D77V9, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  3
  HLA-B WILD-TYPE 14 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    3
  HLA-B WILD-TYPE   14   16
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              14
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  HLA-B MUTATED        2      0      0      1      1      1      0      1
  HLA-B WILD-TYPE      2      5      5      5      6      0      4      0
                 vv
clus              CLUS_9
  HLA-B MUTATED        0
  HLA-B WILD-TYPE      3
D77V10, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2               2
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             1               0
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = FCRLA MUTATION ANALYSIS
D78V1, binary
                 cls
clus               0  1
  FCRLA MUTATED    2  1
  FCRLA WILD-TYPE 21 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      2    1
  FCRLA WILD-TYPE   21   17
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             2              21
  CLUS_2             1              17
[1] 2 2
[1] FALSE
D78V2, binary
                 cls
clus               0  1
  FCRLA MUTATED    2  1
  FCRLA WILD-TYPE 18 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      2    1
  FCRLA WILD-TYPE   18   20
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             2              18
  CLUS_2             1              20
[1] 2 2
[1] FALSE
D78V3, binary
                 cls
clus               0  1
  FCRLA MUTATED    0  0
  FCRLA WILD-TYPE 15 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0    0
  FCRLA WILD-TYPE   15   14
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FCRLA MUTATED        0      0      0
  FCRLA WILD-TYPE      5     13     11
D78V4, multiclass
D78V5, binary
                 cls
clus               0  1
  FCRLA MUTATED    1  2
  FCRLA WILD-TYPE  8 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      1    2
  FCRLA WILD-TYPE    8   10
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FCRLA MUTATED        0      2      1
  FCRLA WILD-TYPE      7      7      4
D78V6, multiclass
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             0               7
  CLUS_2             2               7
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FCRLA MUTATED        1      1      0      1
  FCRLA WILD-TYPE     10     10     10      8
D78V7, multiclass
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              10
  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
  FCRLA MUTATED        0      1      0      1      1
  FCRLA WILD-TYPE      6     10      7     11      4
D78V8, multiclass
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             1               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"
D78V9, binary
                 cls
clus               0  1
  FCRLA MUTATED    0  2
  FCRLA WILD-TYPE 17 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0    2
  FCRLA WILD-TYPE   17   17
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  CLUS_1             0              17
  CLUS_2             2              17
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FCRLA MUTATED        0      0      0      0      1      0      0      1
  FCRLA WILD-TYPE      4      5      5      6      6      1      4      0
                 vv
clus              CLUS_9
  FCRLA MUTATED        0
  FCRLA WILD-TYPE      3
D78V10, multiclass
[1] "Remove cluster labels:" "FCRLA MUTATED"         
clus
  FCRLA MUTATED FCRLA WILD-TYPE 
              2              34 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F      TCGA-FA-A86F 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FF-A7CR 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-FM-8000      TCGA-GR-A4D4 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-GR-A4D5      TCGA-GR-A4D6      TCGA-GS-A9TQ      TCGA-GS-A9TT 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-GS-A9TU      TCGA-GS-A9TV      TCGA-GS-A9TW      TCGA-GS-A9TX 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-GS-A9U3      TCGA-GS-A9U4      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 
     TCGA-RQ-AAAT      TCGA-VB-A8QN 
"FCRLA WILD-TYPE" "FCRLA WILD-TYPE" 

Clustering(79) Variable = KLRC2 MUTATION ANALYSIS
D79V1, binary
                 cls
clus               0  1
  KLRC2 MUTATED    3  2
  KLRC2 WILD-TYPE 20 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      3    2
  KLRC2 WILD-TYPE   20   16
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D79V2, binary
                 cls
clus               0  1
  KLRC2 MUTATED    3  2
  KLRC2 WILD-TYPE 17 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      3    2
  KLRC2 WILD-TYPE   17   19
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             2              19
[1] 2 2
[1] FALSE
D79V3, binary
                 cls
clus               0  1
  KLRC2 MUTATED    1  2
  KLRC2 WILD-TYPE 14 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      1    2
  KLRC2 WILD-TYPE   14   12
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KLRC2 MUTATED        1      1      1
  KLRC2 WILD-TYPE      4     12     10
D79V4, multiclass
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             1              12
  CLUS_3             1              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"
D79V5, binary
                 cls
clus              0 1
  KLRC2 MUTATED   1 4
  KLRC2 WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      1    4
  KLRC2 WILD-TYPE    8    8
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             4               8
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KLRC2 MUTATED        1      3      1
  KLRC2 WILD-TYPE      6      6      4
D79V6, multiclass
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             3               6
  CLUS_3             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLRC2 MUTATED        1      2      0      2
  KLRC2 WILD-TYPE     10      9     10      7
D79V7, multiclass
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2               9
  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
  KLRC2 MUTATED        0      2      0      1      2
  KLRC2 WILD-TYPE      6      9      7     11      3
D79V8, multiclass
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2               9
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             2               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"
D79V9, binary
                 cls
clus               0  1
  KLRC2 MUTATED    0  4
  KLRC2 WILD-TYPE 17 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      0    4
  KLRC2 WILD-TYPE   17   15
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             4              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KLRC2 MUTATED        1      1      0      0      1      0      1      0
  KLRC2 WILD-TYPE      3      4      5      6      6      1      3      1
                 vv
clus              CLUS_9
  KLRC2 MUTATED        0
  KLRC2 WILD-TYPE      3
D79V10, multiclass
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = CD79B MUTATION ANALYSIS
D80V1, binary
                 cls
clus               0  1
  CD79B MUTATED    2  3
  CD79B WILD-TYPE 21 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    3
  CD79B WILD-TYPE   21   15
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2              21
  CLUS_2             3              15
[1] 2 2
[1] FALSE
D80V2, binary
                 cls
clus               0  1
  CD79B MUTATED    1  4
  CD79B WILD-TYPE 19 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      1    4
  CD79B WILD-TYPE   19   17
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             1              19
  CLUS_2             4              17
[1] 2 2
[1] FALSE
D80V3, binary
                 cls
clus               0  1
  CD79B MUTATED    0  3
  CD79B WILD-TYPE 15 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      0    3
  CD79B WILD-TYPE   15   11
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0              15
  CLUS_2             3              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD79B MUTATED        0      0      3
  CD79B WILD-TYPE      5     13      8
D80V4, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               5
  CLUS_2             0              13
  CLUS_3             3               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"
D80V5, binary
                 cls
clus               0  1
  CD79B MUTATED    1  1
  CD79B WILD-TYPE  8 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      1    1
  CD79B WILD-TYPE    8   11
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD79B MUTATED        1      1      0
  CD79B WILD-TYPE      6      8      5
D80V6, multiclass
[1] "Remove cluster labels:" "CD79B MUTATED"         
clus
  CD79B MUTATED CD79B WILD-TYPE 
              2              19 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FM-8000 
"CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" 
     TCGA-G8-6324      TCGA-GR-7353      TCGA-GR-A4D4      TCGA-GR-A4D5 
"CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" 
     TCGA-GR-A4D6      TCGA-GR-A4D9      TCGA-RQ-A6JB 
"CD79B WILD-TYPE" "CD79B WILD-TYPE" "CD79B WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD79B MUTATED        2      1      2      0
  CD79B WILD-TYPE      9     10      8      9
D80V7, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2               9
  CLUS_2             1              10
  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
  CD79B MUTATED        0      1      2      2      0
  CD79B WILD-TYPE      6     10      5     10      5
D80V8, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             2               5
  CLUS_4             2              10
  CLUS_5             0               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"
D80V9, binary
                 cls
clus               0  1
  CD79B MUTATED    2  1
  CD79B WILD-TYPE 15 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    1
  CD79B WILD-TYPE   15   18
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2              15
  CLUS_2             1              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CD79B MUTATED        0      0      2      1      0      0      0      0
  CD79B WILD-TYPE      4      5      3      5      7      1      4      1
                 vv
clus              CLUS_9
  CD79B MUTATED        0
  CD79B WILD-TYPE      3
D80V10, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             2               3
  CLUS_4             1               5
  CLUS_5             0               7
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             0               1
  CLUS_9             0               3
[1] 9 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 = TMSB4X MUTATION ANALYSIS
D81V1, binary
                  cls
clus                0  1
  TMSB4X MUTATED    4  1
  TMSB4X WILD-TYPE 19 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      4    1
  TMSB4X WILD-TYPE   19   17
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              4               19
  CLUS_2              1               17
[1] 2 2
[1] FALSE
D81V2, binary
                  cls
clus                0  1
  TMSB4X MUTATED    4  1
  TMSB4X WILD-TYPE 16 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      4    1
  TMSB4X WILD-TYPE   16   20
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              4               16
  CLUS_2              1               20
[1] 2 2
[1] FALSE
D81V3, binary
                  cls
clus                0  1
  TMSB4X MUTATED    2  3
  TMSB4X WILD-TYPE 13 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      2    3
  TMSB4X WILD-TYPE   13   11
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              2               13
  CLUS_2              3               11
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TMSB4X MUTATED        0      2      3
  TMSB4X WILD-TYPE      5     11      8
D81V4, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2               11
  CLUS_3              3                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"
D81V5, binary
                  cls
clus                0  1
  TMSB4X MUTATED    1  2
  TMSB4X WILD-TYPE  8 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      1    2
  TMSB4X WILD-TYPE    8   10
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TMSB4X MUTATED        2      1      0
  TMSB4X WILD-TYPE      5      8      5
D81V6, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              2                5
  CLUS_2              1                8
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMSB4X MUTATED        1      3      0      1
  TMSB4X WILD-TYPE     10      8     10      8
D81V7, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1               10
  CLUS_2              3                8
  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
  TMSB4X MUTATED        1      3      0      1      0
  TMSB4X WILD-TYPE      5      8      7     11      5
D81V8, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1                5
  CLUS_2              3                8
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              0                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"
D81V9, binary
                  cls
clus                0  1
  TMSB4X MUTATED    1  4
  TMSB4X WILD-TYPE 16 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      1    4
  TMSB4X WILD-TYPE   16   15
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1               16
  CLUS_2              4               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TMSB4X MUTATED        1      2      1      0      1      0      0      0
  TMSB4X WILD-TYPE      3      3      4      6      6      1      4      1
                  vv
clus               CLUS_9
  TMSB4X MUTATED        0
  TMSB4X WILD-TYPE      3
D81V10, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1                3
  CLUS_2              2                3
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              0                1
  CLUS_9              0                3
[1] 9 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(82) Variable = PRB1 MUTATION ANALYSIS
D82V1, binary
                cls
clus              0  1
  PRB1 MUTATED    4  1
  PRB1 WILD-TYPE 19 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      4    1
  PRB1 WILD-TYPE   19   17
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            4             19
  CLUS_2            1             17
[1] 2 2
[1] FALSE
D82V2, binary
                cls
clus              0  1
  PRB1 MUTATED    5  0
  PRB1 WILD-TYPE 15 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      5    0
  PRB1 WILD-TYPE   15   21
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            5             15
  CLUS_2            0             21
[1] 2 2
[1] FALSE
D82V3, binary
                cls
clus              0  1
  PRB1 MUTATED    1  1
  PRB1 WILD-TYPE 14 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      1    1
  PRB1 WILD-TYPE   14   13
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            1             14
  CLUS_2            1             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PRB1 MUTATED        0      1      1
  PRB1 WILD-TYPE      5     12     10
D82V4, multiclass
[1] "Remove cluster labels:" "PRB1 MUTATED"          
clus
  PRB1 MUTATED PRB1 WILD-TYPE 
             2             27 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HO 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-GS-A9TT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-GS-A9TV     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
D82V5, binary
                cls
clus             0 1
  PRB1 MUTATED   0 3
  PRB1 WILD-TYPE 9 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      0    3
  PRB1 WILD-TYPE    9    9
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            3              9
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PRB1 MUTATED        0      3      0
  PRB1 WILD-TYPE      7      6      5
D82V6, multiclass
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            3              6
  CLUS_3            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRB1 MUTATED        0      3      0      2
  PRB1 WILD-TYPE     11      8     10      7
D82V7, multiclass
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            3              8
  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
  PRB1 MUTATED        0      2      0      2      1
  PRB1 WILD-TYPE      6      9      7     10      4
D82V8, multiclass
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            2              9
  CLUS_3            0              7
  CLUS_4            2             10
  CLUS_5            1              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"
D82V9, binary
                cls
clus              0  1
  PRB1 MUTATED    0  5
  PRB1 WILD-TYPE 17 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      0    5
  PRB1 WILD-TYPE   17   14
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0             17
  CLUS_2            5             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PRB1 MUTATED        0      1      1      0      1      0      0      1      1
  PRB1 WILD-TYPE      4      4      4      6      6      1      4      0      2
D82V10, multiclass
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            1              4
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            1              6
  CLUS_6            0              1
  CLUS_7            0              4
  CLUS_8            1              0
  CLUS_9            1              2
[1] 9 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 = PCDHA7 MUTATION ANALYSIS
D83V1, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    1  3
  PCDHA7 WILD-TYPE 22 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      1    3
  PCDHA7 WILD-TYPE   22   15
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D83V2, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    1  3
  PCDHA7 WILD-TYPE 19 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      1    3
  PCDHA7 WILD-TYPE   19   18
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              3               18
[1] 2 2
[1] FALSE
D83V3, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    3  1
  PCDHA7 WILD-TYPE 12 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      3    1
  PCDHA7 WILD-TYPE   12   13
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PCDHA7 MUTATED        1      2      1
  PCDHA7 WILD-TYPE      4     11     10
D83V4, multiclass
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              2               11
  CLUS_3              1               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"
D83V5, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    4  0
  PCDHA7 WILD-TYPE  5 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      4    0
  PCDHA7 WILD-TYPE    5   12
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              4                5
  CLUS_2              0               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PCDHA7 MUTATED        4      0      0
  PCDHA7 WILD-TYPE      3      9      5
D83V6, multiclass
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              4                3
  CLUS_2              0                9
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHA7 MUTATED        3      0      0      1
  PCDHA7 WILD-TYPE      8     11     10      8
D83V7, multiclass
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              3                8
  CLUS_2              0               11
  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
  PCDHA7 MUTATED        2      0      1      0      1
  PCDHA7 WILD-TYPE      4     11      6     12      4
D83V8, multiclass
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              2                4
  CLUS_2              0               11
  CLUS_3              1                6
  CLUS_4              0               12
  CLUS_5              1                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"
D83V9, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    3  1
  PCDHA7 WILD-TYPE 14 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      3    1
  PCDHA7 WILD-TYPE   14   18
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              1               18
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PCDHA7 MUTATED        1      0      1      0      2      0      0      0
  PCDHA7 WILD-TYPE      3      5      4      6      5      1      4      1
                  vv
clus               CLUS_9
  PCDHA7 MUTATED        0
  PCDHA7 WILD-TYPE      3
D83V10, multiclass
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              0                1
  CLUS_9              0                3
[1] 9 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 = OR5H14 MUTATION ANALYSIS
D84V1, binary
                  cls
clus                0  1
  OR5H14 MUTATED    1  2
  OR5H14 WILD-TYPE 22 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      1    2
  OR5H14 WILD-TYPE   22   16
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D84V2, binary
                  cls
clus                0  1
  OR5H14 MUTATED    1  2
  OR5H14 WILD-TYPE 19 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      1    2
  OR5H14 WILD-TYPE   19   19
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D84V3, binary
                  cls
clus                0  1
  OR5H14 MUTATED    2  1
  OR5H14 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      2    1
  OR5H14 WILD-TYPE   13   13
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR5H14 MUTATED        0      2      1
  OR5H14 WILD-TYPE      5     11     10
D84V4, multiclass
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2               11
  CLUS_3              1               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"
D84V5, binary
                  cls
clus                0  1
  OR5H14 MUTATED    1  0
  OR5H14 WILD-TYPE  8 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      1    0
  OR5H14 WILD-TYPE    8   12
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              0               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR5H14 MUTATED        1      0      0
  OR5H14 WILD-TYPE      6      9      5
D84V6, multiclass
[1] "Remove cluster labels:" "OR5H14 MUTATED"        
clus
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               1               20 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FF-8041       TCGA-FF-8043       TCGA-FF-8046 
"OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FM-8000 
"OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" 
      TCGA-G8-6324       TCGA-GR-7353       TCGA-GR-A4D4       TCGA-GR-A4D5 
"OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" 
      TCGA-GR-A4D6       TCGA-GR-A4D9       TCGA-RQ-A68N       TCGA-RQ-A6JB 
"OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" "OR5H14 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR5H14 MUTATED        2      0      0      1
  OR5H14 WILD-TYPE      9     11     10      8
D84V7, multiclass
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              0               11
  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
  OR5H14 MUTATED        1      0      1      1      0
  OR5H14 WILD-TYPE      5     11      6     11      5
D84V8, multiclass
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              0               11
  CLUS_3              1                6
  CLUS_4              1               11
  CLUS_5              0                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"
D84V9, binary
                  cls
clus                0  1
  OR5H14 MUTATED    2  1
  OR5H14 WILD-TYPE 15 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      2    1
  OR5H14 WILD-TYPE   15   18
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              1               18
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OR5H14 MUTATED        0      0      1      0      2      0      0      0
  OR5H14 WILD-TYPE      4      5      4      6      5      1      4      1
                  vv
clus               CLUS_9
  OR5H14 MUTATED        0
  OR5H14 WILD-TYPE      3
D84V10, multiclass
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              0                1
  CLUS_9              0                3
[1] 9 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 = PER3 MUTATION ANALYSIS
D85V1, binary
                cls
clus              0  1
  PER3 MUTATED    4  0
  PER3 WILD-TYPE 19 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      4    0
  PER3 WILD-TYPE   19   18
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            4             19
  CLUS_2            0             18
[1] 2 2
[1] FALSE
D85V2, binary
                cls
clus              0  1
  PER3 MUTATED    2  2
  PER3 WILD-TYPE 18 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      2    2
  PER3 WILD-TYPE   18   19
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            2             19
[1] 2 2
[1] FALSE
D85V3, binary
                cls
clus              0  1
  PER3 MUTATED    1  0
  PER3 WILD-TYPE 14 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      1    0
  PER3 WILD-TYPE   14   14
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            1             14
  CLUS_2            0             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PER3 MUTATED        0      1      0
  PER3 WILD-TYPE      5     12     11
D85V4, multiclass
[1] "Remove cluster labels:" "PER3 MUTATED"          
clus
  PER3 MUTATED PER3 WILD-TYPE 
             1             28 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TV     TCGA-GS-A9TX     TCGA-GS-A9TZ 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
D85V5, binary
                cls
clus              0  1
  PER3 MUTATED    1  1
  PER3 WILD-TYPE  8 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      1    1
  PER3 WILD-TYPE    8   11
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             11
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PER3 MUTATED        0      1      1
  PER3 WILD-TYPE      7      8      4
D85V6, multiclass
[1] "Remove cluster labels:" "PER3 MUTATED"          
clus
  PER3 MUTATED PER3 WILD-TYPE 
             2             19 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FM-8000     TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GR-A4D6     TCGA-RQ-A68N     TCGA-RQ-A6JB 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PER3 MUTATED        1      1      1      1
  PER3 WILD-TYPE     10     10      9      8
D85V7, multiclass
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            1             10
  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
  PER3 MUTATED        0      1      0      3      0
  PER3 WILD-TYPE      6     10      7      9      5
D85V8, multiclass
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             10
  CLUS_3            0              7
  CLUS_4            3              9
  CLUS_5            0              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"
D85V9, binary
                cls
clus              0  1
  PER3 MUTATED    0  2
  PER3 WILD-TYPE 17 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      0    2
  PER3 WILD-TYPE   17   17
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  CLUS_1            0             17
  CLUS_2            2             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PER3 MUTATED        0      0      1      0      0      0      0      1      0
  PER3 WILD-TYPE      4      5      4      6      7      1      4      0      3
D85V10, multiclass
[1] "Remove cluster labels:" "PER3 MUTATED"          
clus
  PER3 MUTATED PER3 WILD-TYPE 
             2             34 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-GR-7353 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6     TCGA-GS-A9TQ 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV     TCGA-GS-A9TX 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-GS-A9U3     TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" "PER3 WILD-TYPE" 
    TCGA-RQ-AAAT     TCGA-VB-A8QN 
"PER3 WILD-TYPE" "PER3 WILD-TYPE" 

Clustering(86) Variable = PABPC1 MUTATION ANALYSIS
D86V1, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  4
  PABPC1 WILD-TYPE 20 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    4
  PABPC1 WILD-TYPE   20   14
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              3               20
  CLUS_2              4               14
[1] 2 2
[1] FALSE
D86V2, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  4
  PABPC1 WILD-TYPE 17 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    4
  PABPC1 WILD-TYPE   17   17
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              4               17
[1] 2 2
[1] FALSE
D86V3, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  2
  PABPC1 WILD-TYPE 12 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    2
  PABPC1 WILD-TYPE   12   12
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        0      3      2
  PABPC1 WILD-TYPE      5     10      9
D86V4, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              3               10
  CLUS_3              2                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V5, binary
                  cls
clus               0 1
  PABPC1 MUTATED   1 4
  PABPC1 WILD-TYPE 8 8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    4
  PABPC1 WILD-TYPE    8    8
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              4                8
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        2      3      0
  PABPC1 WILD-TYPE      5      6      5
D86V6, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              3                6
  CLUS_3              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PABPC1 MUTATED        3      1      1      2
  PABPC1 WILD-TYPE      8     10      9      7
D86V7, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              3                8
  CLUS_2              1               10
  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
  PABPC1 MUTATED        2      1      1      1      2
  PABPC1 WILD-TYPE      4     10      6     11      3
D86V8, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2                4
  CLUS_2              1               10
  CLUS_3              1                6
  CLUS_4              1               11
  CLUS_5              2                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"
D86V9, binary
                  cls
clus                0  1
  PABPC1 MUTATED    4  3
  PABPC1 WILD-TYPE 13 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      4    3
  PABPC1 WILD-TYPE   13   16
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              4               13
  CLUS_2              3               16
[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      1      1      3      1      0      1
  PABPC1 WILD-TYPE      4      5      4      5      4      0      4      0
                  vv
clus               CLUS_9
  PABPC1 MUTATED        0
  PABPC1 WILD-TYPE      3
D86V10, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              1                5
  CLUS_5              3                4
  CLUS_6              1                0
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = ITGA6 MUTATION ANALYSIS
D87V1, binary
                 cls
clus               0  1
  ITGA6 MUTATED    2  1
  ITGA6 WILD-TYPE 21 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      2    1
  ITGA6 WILD-TYPE   21   17
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             1              17
[1] 2 2
[1] FALSE
D87V2, binary
                 cls
clus               0  1
  ITGA6 MUTATED    2  1
  ITGA6 WILD-TYPE 18 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      2    1
  ITGA6 WILD-TYPE   18   20
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             1              20
[1] 2 2
[1] FALSE
D87V3, binary
                 cls
clus               0  1
  ITGA6 MUTATED    1  0
  ITGA6 WILD-TYPE 14 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      1    0
  ITGA6 WILD-TYPE   14   14
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             0              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGA6 MUTATED        0      1      0
  ITGA6 WILD-TYPE      5     12     11
D87V4, multiclass
[1] "Remove cluster labels:" "ITGA6 MUTATED"         
clus
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              1              28 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FA-A7Q1      TCGA-FA-A82F      TCGA-FA-A86F 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043      TCGA-FF-8046 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062      TCGA-FF-A7CR 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-FM-8000      TCGA-GS-A9TT 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-GS-A9TV      TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-GS-A9U4      TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
D87V5, binary
                 cls
clus               0  1
  ITGA6 MUTATED    0  2
  ITGA6 WILD-TYPE  9 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    2
  ITGA6 WILD-TYPE    9   10
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGA6 MUTATED        0      2      0
  ITGA6 WILD-TYPE      7      7      5
D87V6, multiclass
[1] "Remove cluster labels:" "ITGA6 MUTATED"         
clus
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              2              19 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-FM-8000      TCGA-GR-A4D4      TCGA-GR-A4D5      TCGA-GR-A4D6 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
     TCGA-GR-A4D9      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" "ITGA6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ITGA6 MUTATED        0      1      1      1
  ITGA6 WILD-TYPE     11     10      9      8
D87V7, multiclass
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             1              10
  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
  ITGA6 MUTATED        0      1      0      1      1
  ITGA6 WILD-TYPE      6     10      7     11      4
D87V8, multiclass
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             1              11
  CLUS_5             1               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"
D87V9, binary
                 cls
clus               0  1
  ITGA6 MUTATED    1  2
  ITGA6 WILD-TYPE 16 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      1    2
  ITGA6 WILD-TYPE   16   17
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             2              17
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ITGA6 MUTATED        0      0      0      1      1      0      0      1
  ITGA6 WILD-TYPE      4      5      5      5      6      1      4      0
                 vv
clus              CLUS_9
  ITGA6 MUTATED        0
  ITGA6 WILD-TYPE      3
D87V10, multiclass
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             1               6
  CLUS_6             0               1
  CLUS_7             0               4
  CLUS_8             1               0
  CLUS_9             0               3
[1] 9 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 = IGSF3 MUTATION ANALYSIS
D88V1, binary
                 cls
clus               0  1
  IGSF3 MUTATED    4  2
  IGSF3 WILD-TYPE 19 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      4    2
  IGSF3 WILD-TYPE   19   16
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             2              16
[1] 2 2
[1] FALSE
D88V2, binary
                 cls
clus               0  1
  IGSF3 MUTATED    3  3
  IGSF3 WILD-TYPE 17 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      3    3
  IGSF3 WILD-TYPE   17   18
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             3              18
[1] 2 2
[1] FALSE
D88V3, binary
                 cls
clus               0  1
  IGSF3 MUTATED    3  2
  IGSF3 WILD-TYPE 12 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      3    2
  IGSF3 WILD-TYPE   12   12
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             2              12
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        2      1      2
  IGSF3 WILD-TYPE      3     12      9
D88V4, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             2               3
  CLUS_2             1              12
  CLUS_3             2               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V5, binary
                 cls
clus               0  1
  IGSF3 MUTATED    3  1
  IGSF3 WILD-TYPE  6 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      3    1
  IGSF3 WILD-TYPE    6   11
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             1              11
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        2      0      2
  IGSF3 WILD-TYPE      5      9      3
D88V6, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             0               9
  CLUS_3             2               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IGSF3 MUTATED        3      1      1      1
  IGSF3 WILD-TYPE      8     10      9      8
D88V7, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             1              10
  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
  IGSF3 MUTATED        1      1      2      1      1
  IGSF3 WILD-TYPE      5     10      5     11      4
D88V8, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              10
  CLUS_3             2               5
  CLUS_4             1              11
  CLUS_5             1               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"
D88V9, binary
                 cls
clus               0  1
  IGSF3 MUTATED    3  3
  IGSF3 WILD-TYPE 14 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      3    3
  IGSF3 WILD-TYPE   14   16
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             3              16
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IGSF3 MUTATED        1      1      0      0      2      0      1      0
  IGSF3 WILD-TYPE      3      4      5      6      5      1      3      1
                 vv
clus              CLUS_9
  IGSF3 MUTATED        1
  IGSF3 WILD-TYPE      2
D88V10, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             2               5
  CLUS_6             0               1
  CLUS_7             1               3
  CLUS_8             0               1
  CLUS_9             1               2
[1] 9 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 = KRTAP1-1 MUTATION ANALYSIS
D89V1, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    2  1
  KRTAP1-1 WILD-TYPE 21 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      2    1
  KRTAP1-1 WILD-TYPE   21   17
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
D89V2, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    2  1
  KRTAP1-1 WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      2    1
  KRTAP1-1 WILD-TYPE   18   20
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D89V3, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    1  0
  KRTAP1-1 WILD-TYPE 14 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      1    0
  KRTAP1-1 WILD-TYPE   14   14
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP1-1 MUTATED        0      1      0
  KRTAP1-1 WILD-TYPE      5     12     11
D89V4, multiclass
[1] "Remove cluster labels:" "KRTAP1-1 MUTATED"      
clus
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 1                 28 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8062 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-FM-8000         TCGA-GS-A9TT         TCGA-GS-A9TV 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VB-A8QN 
"KRTAP1-1 WILD-TYPE" 
D89V5, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    1  2
  KRTAP1-1 WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      1    2
  KRTAP1-1 WILD-TYPE    8   10
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP1-1 MUTATED        1      2      0
  KRTAP1-1 WILD-TYPE      6      7      5
D89V6, multiclass
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                  7
  CLUS_3                0                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP1-1 MUTATED        0      1      0      2
  KRTAP1-1 WILD-TYPE     11     10     10      7
D89V7, multiclass
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                1                 10
  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
  KRTAP1-1 MUTATED        1      1      0      0      1
  KRTAP1-1 WILD-TYPE      5     10      7     12      4
D89V8, multiclass
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 10
  CLUS_3                0                  7
  CLUS_4                0                 12
  CLUS_5                1                  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"
D89V9, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    1  2
  KRTAP1-1 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      1    2
  KRTAP1-1 WILD-TYPE   16   17
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRTAP1-1 MUTATED        0      0      0      0      2      0      0      1
  KRTAP1-1 WILD-TYPE      4      5      5      6      5      1      4      0
                    vv
clus                 CLUS_9
  KRTAP1-1 MUTATED        0
  KRTAP1-1 WILD-TYPE      3
D89V10, multiclass
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                0                  5
  CLUS_4                0                  6
  CLUS_5                2                  5
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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 = C15ORF39 MUTATION ANALYSIS
D90V1, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    1  2
  C15ORF39 WILD-TYPE 22 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      1    2
  C15ORF39 WILD-TYPE   22   16
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
D90V2, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    2  1
  C15ORF39 WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      2    1
  C15ORF39 WILD-TYPE   18   20
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D90V3, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    0  1
  C15ORF39 WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      0    1
  C15ORF39 WILD-TYPE   15   13
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C15ORF39 MUTATED        0      0      1
  C15ORF39 WILD-TYPE      5     13     10
D90V4, multiclass
[1] "Remove cluster labels:" "C15ORF39 MUTATED"      
clus
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 1                 28 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-GS-A9TT 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-GS-A9TV         TCGA-GS-A9TW         TCGA-GS-A9TX 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-GS-A9TZ         TCGA-GS-A9U4         TCGA-RQ-A6JB 
"C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" "C15ORF39 WILD-TYPE" 
        TCGA-VB-A8QN 
"C15ORF39 WILD-TYPE" 
D90V5, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    1  2
  C15ORF39 WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      1    2
  C15ORF39 WILD-TYPE    8   10
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C15ORF39 MUTATED        1      2      0
  C15ORF39 WILD-TYPE      6      7      5
D90V6, multiclass
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                  7
  CLUS_3                0                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C15ORF39 MUTATED        1      1      0      1
  C15ORF39 WILD-TYPE     10     10     10      8
D90V7, multiclass
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 10
  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
  C15ORF39 MUTATED        0      1      1      0      1
  C15ORF39 WILD-TYPE      6     10      6     12      4
D90V8, multiclass
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 10
  CLUS_3                1                  6
  CLUS_4                0                 12
  CLUS_5                1                  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"
D90V9, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    1  2
  C15ORF39 WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      1    2
  C15ORF39 WILD-TYPE   16   17
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  C15ORF39 MUTATED        0      0      1      0      1      0      0      1
  C15ORF39 WILD-TYPE      4      5      4      6      6      1      4      0
                    vv
clus                 CLUS_9
  C15ORF39 MUTATED        0
  C15ORF39 WILD-TYPE      3
D90V10, multiclass
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                1                  4
  CLUS_4                0                  6
  CLUS_5                1                  6
  CLUS_6                0                  1
  CLUS_7                0                  4
  CLUS_8                1                  0
  CLUS_9                0                  3
[1] 9 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(91) Variable = FBXO34 MUTATION ANALYSIS
D91V1, binary
                  cls
clus                0  1
  FBXO34 MUTATED    1  2
  FBXO34 WILD-TYPE 22 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      1    2
  FBXO34 WILD-TYPE   22   16
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D91V2, binary
                  cls
clus                0  1
  FBXO34 MUTATED    1  2
  FBXO34 WILD-TYPE 19 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      1    2
  FBXO34 WILD-TYPE   19   19
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D91V3, binary
                  cls
clus                0  1
  FBXO34 MUTATED    2  0
  FBXO34 WILD-TYPE 13 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      2    0
  FBXO34 WILD-TYPE   13   14
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              0               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FBXO34 MUTATED        0      2      0
  FBXO34 WILD-TYPE      5     11     11
D91V4, multiclass
[1] "Remove cluster labels:" "FBXO34 MUTATED"        
clus
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               2               27 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A6HN       TCGA-FA-A6HO 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F       TCGA-FA-A86F 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-GS-A9TT 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-GS-A9TV       TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-GS-A9U4       TCGA-RQ-A68N       TCGA-RQ-A6JB 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
D91V5, binary
                  cls
clus                0  1
  FBXO34 MUTATED    1  1
  FBXO34 WILD-TYPE  8 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      1    1
  FBXO34 WILD-TYPE    8   11
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               11
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FBXO34 MUTATED        0      1      1
  FBXO34 WILD-TYPE      7      8      4
D91V6, multiclass
[1] "Remove cluster labels:" "FBXO34 MUTATED"        
clus
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               2               19 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A6HN       TCGA-FA-A6HO 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FM-8000 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-GR-7353       TCGA-GR-A4D4       TCGA-GR-A4D5       TCGA-GR-A4D6 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-GR-A4D9       TCGA-RQ-A68N       TCGA-RQ-A6JB 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXO34 MUTATED        2      1      0      0
  FBXO34 WILD-TYPE      9     10     10      9
D91V7, multiclass
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              1               10
  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
  FBXO34 MUTATED        0      1      2      0      0
  FBXO34 WILD-TYPE      6     10      5     12      5
D91V8, multiclass
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              1               10
  CLUS_3              2                5
  CLUS_4              0               12
  CLUS_5              0                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"
D91V9, binary
                  cls
clus                0  1
  FBXO34 MUTATED    2  1
  FBXO34 WILD-TYPE 15 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      2    1
  FBXO34 WILD-TYPE   15   18
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              1               18
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FBXO34 MUTATED        1      0      1      0      0      0      0      1
  FBXO34 WILD-TYPE      3      5      4      6      7      1      4      0
                  vv
clus               CLUS_9
  FBXO34 MUTATED        0
  FBXO34 WILD-TYPE      3
D91V10, multiclass
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              0                6
  CLUS_5              0                7
  CLUS_6              0                1
  CLUS_7              0                4
  CLUS_8              1                0
  CLUS_9              0                3
[1] 9 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 = ZNF880 MUTATION ANALYSIS
D92V1, binary
                  cls
clus                0  1
  ZNF880 MUTATED    5  3
  ZNF880 WILD-TYPE 18 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      5    3
  ZNF880 WILD-TYPE   18   15
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              5               18
  CLUS_2              3               15
[1] 2 2
[1] FALSE
D92V2, binary
                  cls
clus                0  1
  ZNF880 MUTATED    6  2
  ZNF880 WILD-TYPE 14 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      6    2
  ZNF880 WILD-TYPE   14   19
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              6               14
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D92V3, binary
                  cls
clus                0  1
  ZNF880 MUTATED    3  2
  ZNF880 WILD-TYPE 12 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      3    2
  ZNF880 WILD-TYPE   12   12
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              2               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF880 MUTATED        0      3      2
  ZNF880 WILD-TYPE      5     10      9
D92V4, multiclass
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              3               10
  CLUS_3              2                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V5, binary
                  cls
clus               0 1
  ZNF880 MUTATED   2 4
  ZNF880 WILD-TYPE 7 8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      2    4
  ZNF880 WILD-TYPE    7    8
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              4                8
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF880 MUTATED        2      3      1
  ZNF880 WILD-TYPE      5      6      4
D92V6, multiclass
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              3                6
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF880 MUTATED        1      3      1      3
  ZNF880 WILD-TYPE     10      8      9      6
D92V7, multiclass
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              3                8
  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
  ZNF880 MUTATED        2      3      0      1      2
  ZNF880 WILD-TYPE      4      8      7     11      3
D92V8, multiclass
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              2                4
  CLUS_2              3                8
  CLUS_3              0                7
  CLUS_4              1               11
  CLUS_5              2                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"
D92V9, binary
                  cls
clus                0  1
  ZNF880 MUTATED    1  7
  ZNF880 WILD-TYPE 16 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      1    7
  ZNF880 WILD-TYPE   16   12
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              7               12
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF880 MUTATED        0      2      0      0      2      1      1      1
  ZNF880 WILD-TYPE      4      3      5      6      5      0      3      0
                  vv
clus               CLUS_9
  ZNF880 MUTATED        1
  ZNF880 WILD-TYPE      2
D92V10, multiclass
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              2                3
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              2                5
  CLUS_6              1                0
  CLUS_7              1                3
  CLUS_8              1                0
  CLUS_9              1                2
[1] 9 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 = NBPF15 MUTATION ANALYSIS
D93V1, binary
                  cls
clus                0  1
  NBPF15 MUTATED    2  2
  NBPF15 WILD-TYPE 21 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      2    2
  NBPF15 WILD-TYPE   21   16
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              2               21
  CLUS_2              2               16
[1] 2 2
[1] FALSE
D93V2, binary
                  cls
clus                0  1
  NBPF15 MUTATED    2  2
  NBPF15 WILD-TYPE 18 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      2    2
  NBPF15 WILD-TYPE   18   19
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              2               19
[1] 2 2
[1] FALSE
D93V3, binary
                  cls
clus                0  1
  NBPF15 MUTATED    2  1
  NBPF15 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      2    1
  NBPF15 WILD-TYPE   13   13
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              1               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF15 MUTATED        0      2      1
  NBPF15 WILD-TYPE      5     11     10
D93V4, multiclass
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              2               11
  CLUS_3              1               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"
D93V5, binary
                  cls
clus               0 1
  NBPF15 MUTATED   1 3
  NBPF15 WILD-TYPE 8 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      1    3
  NBPF15 WILD-TYPE    8    9
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              3                9
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF15 MUTATED        2      1      1
  NBPF15 WILD-TYPE      5      8      4
D93V6, multiclass
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              1                8
  CLUS_3              1                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NBPF15 MUTATED        1      2      0      1
  NBPF15 WILD-TYPE     10      9     10      8
D93V7, multiclass
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              2                9
  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
  NBPF15 MUTATED        1      2      0      0      1
  NBPF15 WILD-TYPE      5      9      7     12      4
D93V8, multiclass
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              2                9
  CLUS_3              0                7
  CLUS_4              0               12
  CLUS_5              1                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"
D93V9, binary
                  cls
clus                0  1
  NBPF15 MUTATED    1  3
  NBPF15 WILD-TYPE 16 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      1    3
  NBPF15 WILD-TYPE   16   16
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              3               16
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NBPF15 MUTATED        1      1      0      0      1      0      1      0
  NBPF15 WILD-TYPE      3      4      5      6      6      1      3      1
                  vv
clus               CLUS_9
  NBPF15 MUTATED        0
  NBPF15 WILD-TYPE      3
D93V10, multiclass
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              1                4
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              1                6
  CLUS_6              0                1
  CLUS_7              1                3
  CLUS_8              0                1
  CLUS_9              0                3
[1] 9 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 = SLC22A16 MUTATION ANALYSIS
D94V1, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    2  1
  SLC22A16 WILD-TYPE 21 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      2    1
  SLC22A16 WILD-TYPE   21   17
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
D94V2, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    2  1
  SLC22A16 WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      2    1
  SLC22A16 WILD-TYPE   18   20
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D94V3, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    0  0
  SLC22A16 WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0    0
  SLC22A16 WILD-TYPE   15   14
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  SLC22A16 MUTATED        0      0      0
  SLC22A16 WILD-TYPE      5     13     11
D94V4, multiclass
D94V5, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    1  2
  SLC22A16 WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      1    2
  SLC22A16 WILD-TYPE    8   10
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  SLC22A16 MUTATED        0      2      1
  SLC22A16 WILD-TYPE      7      7      4
D94V6, multiclass
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                  7
  CLUS_3                1                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC22A16 MUTATED        1      1      0      1
  SLC22A16 WILD-TYPE     10     10     10      8
D94V7, multiclass
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 10
  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
  SLC22A16 MUTATED        0      1      0      1      1
  SLC22A16 WILD-TYPE      6     10      7     11      4
D94V8, multiclass
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 10
  CLUS_3                0                  7
  CLUS_4                1                 11
  CLUS_5                1                  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"
D94V9, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    0  2
  SLC22A16 WILD-TYPE 17 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0    2
  SLC22A16 WILD-TYPE   17   17
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SLC22A16 MUTATED        0      0      0      0      1      0      0      1
  SLC22A16 WILD-TYPE      4      5      5      6      6      1      4      0
                    vv
clus                 CLUS_9
  SLC22A16 MUTATED        0
  SLC22A16 WILD-TYPE      3
D94V10, multiclass
[1] "Remove cluster labels:" "SLC22A16 MUTATED"      
clus
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 2                 34 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-FM-8000         TCGA-GR-A4D4         TCGA-GR-A4D5 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-GR-A4D6         TCGA-GS-A9TQ         TCGA-GS-A9TT 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-GS-A9TU         TCGA-GS-A9TV         TCGA-GS-A9TW 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9U3         TCGA-GS-A9U4 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB         TCGA-RQ-AAAT 
"SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" "SLC22A16 WILD-TYPE" 
        TCGA-VB-A8QN 
"SLC22A16 WILD-TYPE" 
