[1] "ofn"        "-oTREAD-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/READ-TP/20140629/READ-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/20018501/transformed.cor.cli.txt"

nPatients in clinical file=169, in cluster file=122, common to both=122
[1]  40 122
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          108            14 
  APC MUTATED APC WILD-TYPE 
          108            14 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              111 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              111 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            91             31 
  TP53 MUTATED TP53 WILD-TYPE 
            91             31 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            11            111 
  NRAS MUTATED NRAS WILD-TYPE 
            11            111 
[1] "FMN2 MUTATION ANALYSIS"
[1] 3
  FMN2 MUTATED FMN2 WILD-TYPE 
            14            108 
  FMN2 MUTATED FMN2 WILD-TYPE 
            14            108 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               115 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               115 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             5            117 
  RPTN MUTATED RPTN WILD-TYPE 
             5            117 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            110 
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            110 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              6             116 
  RBM10 MUTATED RBM10 WILD-TYPE 
              6             116 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              5             117 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              5             117 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
[1] "GABRP MUTATION ANALYSIS"
[1] 3
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
             4            118 
  RLIM MUTATED RLIM WILD-TYPE 
             4            118 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              6             116 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              6             116 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              12              110 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              12              110 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             117 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             117 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            63             59 
  KRAS MUTATED KRAS WILD-TYPE 
            63             59 
[1] "FLT1 MUTATION ANALYSIS"
[1] 3
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
[1] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
[1] "AKAP9 MUTATION ANALYSIS"
[1] 3
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              7             115 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              7             115 
[1] "VCX2 MUTATION ANALYSIS"
[1] 3
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            117 
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            117 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            118 
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            118 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              36               86 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              36               86 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            13            109 
  BRAF MUTATED BRAF WILD-TYPE 
            13            109 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             113 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             113 
[1] "CDKL5 MUTATION ANALYSIS"
[1] 3
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              4             118 
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              4             118 
[1] "ZNF354C MUTATION ANALYSIS"
[1] 3
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
[1] "IQCD MUTATION ANALYSIS"
[1] 3
  IQCD MUTATED IQCD WILD-TYPE 
             3            119 
  IQCD MUTATED IQCD WILD-TYPE 
             3            119 
[1] "ZBED4 MUTATION ANALYSIS"
[1] 3
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              4             118 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              4             118 
[1] "GMCL1 MUTATION ANALYSIS"
[1] 3
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              4             118 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              4             118 
[1] "CIR1 MUTATION ANALYSIS"
[1] 3
  CIR1 MUTATED CIR1 WILD-TYPE 
             3            119 
  CIR1 MUTATED CIR1 WILD-TYPE 
             3            119 
[1] "AGL MUTATION ANALYSIS"
[1] 3
  AGL MUTATED AGL WILD-TYPE 
            4           118 
  AGL MUTATED AGL WILD-TYPE 
            4           118 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               10               112 
  FAM123B MUTATED FAM123B WILD-TYPE 
               10               112 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              10              112 
  CREBBP MUTATED CREBBP WILD-TYPE 
              10              112 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 122 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=5,	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 122 columns, 0 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       20     16     17
  APC WILD-TYPE      5      5      2
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          20             5
  CLUS_2          16             5
  CLUS_3          17             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 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  APC MUTATED        4     11      9      8      5      7      7      2
  APC WILD-TYPE      2      2      3      1      1      2      1      0
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           4             2
  CLUS_2          11             2
  CLUS_3           9             3
  CLUS_4           8             1
  CLUS_5           5             1
  CLUS_6           7             2
  CLUS_7           7             1
  CLUS_8           2             0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APC MUTATED       45     18     17     26
  APC WILD-TYPE      6      2      2      4
D1V3, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          45             6
  CLUS_2          18             2
  CLUS_3          17             2
  CLUS_4          26             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
  APC MUTATED       16     22     17
  APC WILD-TYPE      0      1      1
D1V4, multiclass
[1] "Remove cluster labels:" "APC WILD-TYPE"         
clus
  APC MUTATED APC WILD-TYPE 
           55             2 
 TCGA-AF-2687  TCGA-AF-2693  TCGA-AF-4110  TCGA-AF-6136  TCGA-AF-6655 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AF-6672  TCGA-AG-3731  TCGA-AG-3732  TCGA-AG-3742  TCGA-AG-A01W 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AG-A01Y  TCGA-AG-A020  TCGA-AG-A026  TCGA-AG-A02N  TCGA-AG-A036 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AH-6544  TCGA-AH-6547  TCGA-AH-6549  TCGA-AH-6643  TCGA-AH-6644 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-CI-6619  TCGA-CI-6620  TCGA-CI-6621  TCGA-CI-6622  TCGA-CI-6624 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-CL-5917  TCGA-CL-5918  TCGA-DC-5337  TCGA-DC-5869  TCGA-DC-6155 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-6157  TCGA-DC-6158  TCGA-DC-6160  TCGA-DC-6681  TCGA-DC-6682 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-6683  TCGA-DY-A0XA  TCGA-DY-A1DC  TCGA-DY-A1DD  TCGA-DY-A1DF 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DY-A1DG  TCGA-DY-A1H8  TCGA-EF-5830  TCGA-EI-6506  TCGA-EI-6508 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-EI-6510  TCGA-F5-6464  TCGA-F5-6465  TCGA-F5-6571  TCGA-F5-6702 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-F5-6811  TCGA-F5-6812  TCGA-F5-6813  TCGA-G5-6235  TCGA-G5-6641 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED       27     17     17     21      3
  APC WILD-TYPE      3      2      5      2      0
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          27             3
  CLUS_2          17             2
  CLUS_3          17             5
  CLUS_4          21             2
  CLUS_5           3             0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APC MUTATED       15     15     11     12     21     11
  APC WILD-TYPE      4      1      3      2      2      0
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          15             4
  CLUS_2          15             1
  CLUS_3          11             3
  CLUS_4          12             2
  CLUS_5          21             2
  CLUS_6          11             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED       14     13     20     13     48
  APC WILD-TYPE      2      0      2      0      9
D1V7, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          14             2
  CLUS_2          13             0
  CLUS_3          20             2
  CLUS_4          13             0
  CLUS_5          48             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  APC MUTATED       11     23      6     12     27     15     14
  APC WILD-TYPE      0      0      2      0      5      3      3
D1V8, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             0
  CLUS_2          23             0
  CLUS_3           6             2
  CLUS_4          12             0
  CLUS_5          27             5
  CLUS_6          15             3
  CLUS_7          14             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED       11     28     14      7     46
  APC WILD-TYPE      2      0      0      1      9
D1V9, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             2
  CLUS_2          28             0
  CLUS_3          14             0
  CLUS_4           7             1
  CLUS_5          46             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       19     41     46
  APC WILD-TYPE      1      3      8
D1V10, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             1
  CLUS_2          41             3
  CLUS_3          46             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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APC MUTATED        8      7     13      7
  APC WILD-TYPE      0      0      0      1
D1V11, multiclass
[1] "Remove cluster labels:" "APC WILD-TYPE"         
clus
  APC MUTATED APC WILD-TYPE 
           35             1 
 TCGA-AF-2687  TCGA-AF-4110  TCGA-AF-6655  TCGA-AF-6672  TCGA-AG-3731 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AG-3732  TCGA-AH-6544  TCGA-AH-6547  TCGA-AH-6549  TCGA-AH-6643 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-CI-6619  TCGA-CI-6620  TCGA-CI-6621  TCGA-CI-6624  TCGA-CL-5918 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-5337  TCGA-DC-5869  TCGA-DC-6157  TCGA-DC-6158  TCGA-DC-6681 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-6682  TCGA-DC-6683  TCGA-DY-A1DC  TCGA-DY-A1DD  TCGA-DY-A1DG 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DY-A1H8  TCGA-EI-6506  TCGA-F5-6464  TCGA-F5-6465  TCGA-F5-6571 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-F5-6702  TCGA-F5-6811  TCGA-F5-6812  TCGA-G5-6235  TCGA-G5-6641 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED        8      9     11      5      2
  APC WILD-TYPE      0      0      1      0      0
D1V12, multiclass
[1] "Remove cluster labels:" "APC WILD-TYPE"         
clus
  APC MUTATED APC WILD-TYPE 
           35             1 
 TCGA-AF-2687  TCGA-AF-4110  TCGA-AF-6655  TCGA-AF-6672  TCGA-AG-3731 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AG-3732  TCGA-AH-6544  TCGA-AH-6547  TCGA-AH-6549  TCGA-AH-6643 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-CI-6619  TCGA-CI-6620  TCGA-CI-6621  TCGA-CI-6624  TCGA-CL-5918 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-5337  TCGA-DC-5869  TCGA-DC-6157  TCGA-DC-6158  TCGA-DC-6681 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DC-6682  TCGA-DC-6683  TCGA-DY-A1DC  TCGA-DY-A1DD  TCGA-DY-A1DG 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-DY-A1H8  TCGA-EI-6506  TCGA-F5-6464  TCGA-F5-6465  TCGA-F5-6571 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-F5-6702  TCGA-F5-6811  TCGA-F5-6812  TCGA-G5-6235  TCGA-G5-6641 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 

Clustering(2) Variable = CRIPAK MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        0      0      0
  CRIPAK WILD-TYPE     25     21     19
D2V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CRIPAK MUTATED        0      0      0      0      0      0      0      0
  CRIPAK WILD-TYPE      6     13     12      9      6      9      8      2
D2V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        7      1      1      2
  CRIPAK WILD-TYPE     44     19     18     28
D2V3, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              7               44
  CLUS_2              1               19
  CLUS_3              1               18
  CLUS_4              2               28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        5      4      2
  CRIPAK WILD-TYPE     11     19     16
D2V4, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              5               11
  CLUS_2              4               19
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CRIPAK MUTATED        5      1      0      2      0
  CRIPAK WILD-TYPE     25     18     22     21      3
D2V5, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              5               25
  CLUS_2              1               18
  CLUS_3              0               22
  CLUS_4              2               21
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CRIPAK MUTATED        0      3      2      0      1      2
  CRIPAK WILD-TYPE     19     13     12     14     22      9
D2V6, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              0               19
  CLUS_2              3               13
  CLUS_3              2               12
  CLUS_4              0               14
  CLUS_5              1               22
  CLUS_6              2                9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CRIPAK MUTATED        2      3      4      2      0
  CRIPAK WILD-TYPE     14     10     18     11     57
D2V7, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               14
  CLUS_2              3               10
  CLUS_3              4               18
  CLUS_4              2               11
  CLUS_5              0               57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CRIPAK MUTATED        2      6      1      2      0      0      0
  CRIPAK WILD-TYPE      9     17      7     10     32     18     17
D2V8, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2                9
  CLUS_2              6               17
  CLUS_3              1                7
  CLUS_4              2               10
  CLUS_5              0               32
  CLUS_6              0               18
  CLUS_7              0               17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CRIPAK MUTATED        2      5      3      1      0
  CRIPAK WILD-TYPE     11     23     11      7     55
D2V9, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2               11
  CLUS_2              5               23
  CLUS_3              3               11
  CLUS_4              1                7
  CLUS_5              0               55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CRIPAK MUTATED        4      7      0
  CRIPAK WILD-TYPE     16     37     54
D2V10, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              4               16
  CLUS_2              7               37
  CLUS_3              0               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CRIPAK MUTATED        3      1      1      3
  CRIPAK WILD-TYPE      5      6     12      5
D2V11, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              3                5
  CLUS_2              1                6
  CLUS_3              1               12
  CLUS_4              3                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
  CRIPAK MUTATED        2      1      3      1      1
  CRIPAK WILD-TYPE      6      8      9      4      1
D2V12, multiclass
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  CLUS_1              2                6
  CLUS_2              1                8
  CLUS_3              3                9
  CLUS_4              1                4
  CLUS_5              1                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        9     15     17
  TP53 WILD-TYPE     16      6      2
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             16
  CLUS_2           15              6
  CLUS_3           17              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 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TP53 MUTATED        2      9      5      9      5      6      5      0
  TP53 WILD-TYPE      4      4      7      0      1      3      3      2
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            9              4
  CLUS_3            5              7
  CLUS_4            9              0
  CLUS_5            5              1
  CLUS_6            6              3
  CLUS_7            5              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       32     17     18     22
  TP53 WILD-TYPE     19      3      1      8
D3V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           32             19
  CLUS_2           17              3
  CLUS_3           18              1
  CLUS_4           22              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
  TP53 MUTATED       14     20     17
  TP53 WILD-TYPE      2      3      1
D3V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           14              2
  CLUS_2           20              3
  CLUS_3           17              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       18     16     16     19      3
  TP53 WILD-TYPE     12      3      6      4      0
D3V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             12
  CLUS_2           16              3
  CLUS_3           16              6
  CLUS_4           19              4
  CLUS_5            3              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED       12     12     13     11     14     10
  TP53 WILD-TYPE      7      4      1      3      9      1
D3V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12              7
  CLUS_2           12              4
  CLUS_3           13              1
  CLUS_4           11              3
  CLUS_5           14              9
  CLUS_6           10              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       12     12     15     12     39
  TP53 WILD-TYPE      4      1      7      1     18
D3V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12              4
  CLUS_2           12              1
  CLUS_3           15              7
  CLUS_4           12              1
  CLUS_5           39             18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED       11     19      7     10     21     10     12
  TP53 WILD-TYPE      0      4      1      2     11      8      5
D3V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11              0
  CLUS_2           19              4
  CLUS_3            7              1
  CLUS_4           10              2
  CLUS_5           21             11
  CLUS_6           10              8
  CLUS_7           12              5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       10     25     11      7     35
  TP53 WILD-TYPE      3      3      3      1     20
D3V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              3
  CLUS_2           25              3
  CLUS_3           11              3
  CLUS_4            7              1
  CLUS_5           35             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       18     36     34
  TP53 WILD-TYPE      2      8     20
D3V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18              2
  CLUS_2           36              8
  CLUS_3           34             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        8      5     10      8
  TP53 WILD-TYPE      0      2      3      0
D3V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              0
  CLUS_2            5              2
  CLUS_3           10              3
  CLUS_4            8              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8      7     10      5      1
  TP53 WILD-TYPE      0      2      2      0      1
D3V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              0
  CLUS_2            7              2
  CLUS_3           10              2
  CLUS_4            5              0
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        2      2      1
  NRAS WILD-TYPE     23     19     18
D4V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             23
  CLUS_2            2             19
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NRAS MUTATED        1      2      1      1      0      0      0      0
  NRAS WILD-TYPE      5     11     11      8      6      9      8      2
D4V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2             11
  CLUS_3            1             11
  CLUS_4            1              8
  CLUS_5            0              6
  CLUS_6            0              9
  CLUS_7            0              8
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        7      2      1      1
  NRAS WILD-TYPE     44     18     18     29
D4V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            7             44
  CLUS_2            2             18
  CLUS_3            1             18
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        2      2      2
  NRAS WILD-TYPE     14     21     16
D4V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             21
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        2      0      2      3      0
  NRAS WILD-TYPE     28     19     20     20      3
D4V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             28
  CLUS_2            0             19
  CLUS_3            2             20
  CLUS_4            3             20
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NRAS MUTATED        0      1      0      4      0      2
  NRAS WILD-TYPE     19     15     14     10     23      9
D4V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             19
  CLUS_2            1             15
  CLUS_3            0             14
  CLUS_4            4             10
  CLUS_5            0             23
  CLUS_6            2              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        1      1      4      0      5
  NRAS WILD-TYPE     15     12     18     13     52
D4V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1             12
  CLUS_3            4             18
  CLUS_4            0             13
  CLUS_5            5             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NRAS MUTATED        1      5      0      1      2      1      1
  NRAS WILD-TYPE     10     18      8     11     30     17     16
D4V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             10
  CLUS_2            5             18
  CLUS_3            0              8
  CLUS_4            1             11
  CLUS_5            2             30
  CLUS_6            1             17
  CLUS_7            1             16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        1      4      2      1      3
  NRAS WILD-TYPE     12     24     12      7     52
D4V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             12
  CLUS_2            4             24
  CLUS_3            2             12
  CLUS_4            1              7
  CLUS_5            3             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        0      6      5
  NRAS WILD-TYPE     20     38     49
D4V10, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             20
  CLUS_2            6             38
  CLUS_3            5             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        1      1      1      0
  NRAS WILD-TYPE      7      6     12      8
D4V11, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              7
  CLUS_2            1              6
  CLUS_3            1             12
  CLUS_4            0              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
  NRAS MUTATED        1      0      0      1      1
  NRAS WILD-TYPE      7      9     12      4      1
D4V12, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              7
  CLUS_2            0              9
  CLUS_3            0             12
  CLUS_4            1              4
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = FMN2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FMN2 MUTATED        0      2      1
  FMN2 WILD-TYPE     25     19     18
D5V1, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            0             25
  CLUS_2            2             19
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FMN2 MUTATED        0      1      0      1      0      0      1      0
  FMN2 WILD-TYPE      6     12     12      8      6      9      7      2
D5V2, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             12
  CLUS_3            0             12
  CLUS_4            1              8
  CLUS_5            0              6
  CLUS_6            0              9
  CLUS_7            1              7
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FMN2 MUTATED        4      0      5      5
  FMN2 WILD-TYPE     47     20     14     25
D5V3, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            4             47
  CLUS_2            0             20
  CLUS_3            5             14
  CLUS_4            5             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FMN2 MUTATED        4      6      2
  FMN2 WILD-TYPE     12     17     16
D5V4, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            6             17
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FMN2 MUTATED        2      1      2      5      0
  FMN2 WILD-TYPE     28     18     20     18      3
D5V5, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            2             28
  CLUS_2            1             18
  CLUS_3            2             20
  CLUS_4            5             18
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FMN2 MUTATED        0      2      2      4      1      1
  FMN2 WILD-TYPE     19     14     12     10     22     10
D5V6, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            2             14
  CLUS_3            2             12
  CLUS_4            4             10
  CLUS_5            1             22
  CLUS_6            1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FMN2 MUTATED        1      3      2      5      3
  FMN2 WILD-TYPE     15     10     20      8     54
D5V7, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            3             10
  CLUS_3            2             20
  CLUS_4            5              8
  CLUS_5            3             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FMN2 MUTATED        3      4      1      3      2      1      0
  FMN2 WILD-TYPE      8     19      7      9     30     17     17
D5V8, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            4             19
  CLUS_3            1              7
  CLUS_4            3              9
  CLUS_5            2             30
  CLUS_6            1             17
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FMN2 MUTATED        1      8      2      0      3
  FMN2 WILD-TYPE     12     20     12      8     52
D5V9, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            8             20
  CLUS_3            2             12
  CLUS_4            0              8
  CLUS_5            3             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FMN2 MUTATED        1     10      3
  FMN2 WILD-TYPE     19     34     51
D5V10, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            1             19
  CLUS_2           10             34
  CLUS_3            3             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FMN2 MUTATED        1      0      4      2
  FMN2 WILD-TYPE      7      7      9      6
D5V11, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            0              7
  CLUS_3            4              9
  CLUS_4            2              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
  FMN2 MUTATED        2      2      2      1      0
  FMN2 WILD-TYPE      6      7     10      4      2
D5V12, multiclass
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            2              7
  CLUS_3            2             10
  CLUS_4            1              4
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = SHROOM4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        0      0      0
  SHROOM4 WILD-TYPE     25     21     19
D6V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SHROOM4 MUTATED        0      0      0      0      0      0      0      0
  SHROOM4 WILD-TYPE      6     13     12      9      6      9      8      2
D6V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        4      0      2      1
  SHROOM4 WILD-TYPE     47     20     17     29
D6V3, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               4                47
  CLUS_2               0                20
  CLUS_3               2                17
  CLUS_4               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        1      4      1
  SHROOM4 WILD-TYPE     15     19     17
D6V4, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               4                19
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHROOM4 MUTATED        3      1      0      3      0
  SHROOM4 WILD-TYPE     27     18     22     20      3
D6V5, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               3                27
  CLUS_2               1                18
  CLUS_3               0                22
  CLUS_4               3                20
  CLUS_5               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SHROOM4 MUTATED        0      2      1      1      2      1
  SHROOM4 WILD-TYPE     19     14     13     13     21     10
D6V6, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                14
  CLUS_3               1                13
  CLUS_4               1                13
  CLUS_5               2                21
  CLUS_6               1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHROOM4 MUTATED        1      1      3      2      0
  SHROOM4 WILD-TYPE     15     12     19     11     57
D6V7, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                12
  CLUS_3               3                19
  CLUS_4               2                11
  CLUS_5               0                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SHROOM4 MUTATED        1      2      0      4      0      0      0
  SHROOM4 WILD-TYPE     10     21      8      8     32     18     17
D6V8, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                10
  CLUS_2               2                21
  CLUS_3               0                 8
  CLUS_4               4                 8
  CLUS_5               0                32
  CLUS_6               0                18
  CLUS_7               0                17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHROOM4 MUTATED        1      4      2      0      0
  SHROOM4 WILD-TYPE     12     24     12      8     55
D6V9, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                12
  CLUS_2               4                24
  CLUS_3               2                12
  CLUS_4               0                 8
  CLUS_5               0                55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        0      7      0
  SHROOM4 WILD-TYPE     20     37     54
D6V10, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                20
  CLUS_2               7                37
  CLUS_3               0                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        1      0      0      2
  SHROOM4 WILD-TYPE      7      7     13      6
D6V11, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                 7
  CLUS_3               0                13
  CLUS_4               2                 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
  SHROOM4 MUTATED        0      0      1      2      0
  SHROOM4 WILD-TYPE      8      9     11      3      2
D6V12, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               0                 9
  CLUS_3               1                11
  CLUS_4               2                 3
  CLUS_5               0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = RPTN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        0      0      0
  RPTN WILD-TYPE     25     21     19
D7V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RPTN MUTATED        0      0      0      0      0      0      0      0
  RPTN WILD-TYPE      6     13     12      9      6      9      8      2
D7V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPTN MUTATED        1      1      1      1
  RPTN WILD-TYPE     50     19     18     29
D7V3, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             50
  CLUS_2            1             19
  CLUS_3            1             18
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        2      2      1
  RPTN WILD-TYPE     14     21     17
D7V4, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             21
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPTN MUTATED        1      2      0      0      1
  RPTN WILD-TYPE     29     17     22     23      2
D7V5, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             29
  CLUS_2            2             17
  CLUS_3            0             22
  CLUS_4            0             23
  CLUS_5            1              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RPTN MUTATED        0      2      1      0      1      0
  RPTN WILD-TYPE     19     14     13     14     22     11
D7V6, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            0             19
  CLUS_2            2             14
  CLUS_3            1             13
  CLUS_4            0             14
  CLUS_5            1             22
  CLUS_6            0             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPTN MUTATED        2      1      1      1      0
  RPTN WILD-TYPE     14     12     21     12     57
D7V7, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             12
  CLUS_3            1             21
  CLUS_4            1             12
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RPTN MUTATED        1      1      1      2      0      0      0
  RPTN WILD-TYPE     10     22      7     10     32     18     17
D7V8, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             10
  CLUS_2            1             22
  CLUS_3            1              7
  CLUS_4            2             10
  CLUS_5            0             32
  CLUS_6            0             18
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPTN MUTATED        1      2      1      1      0
  RPTN WILD-TYPE     12     26     13      7     55
D7V9, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             26
  CLUS_3            1             13
  CLUS_4            1              7
  CLUS_5            0             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        1      4      0
  RPTN WILD-TYPE     19     40     54
D7V10, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             19
  CLUS_2            4             40
  CLUS_3            0             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPTN MUTATED        1      1      1      1
  RPTN WILD-TYPE      7      6     12      7
D7V11, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1              7
  CLUS_2            1              6
  CLUS_3            1             12
  CLUS_4            1              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
  RPTN MUTATED        1      2      0      1      0
  RPTN WILD-TYPE      7      7     12      4      2
D7V12, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2              7
  CLUS_3            0             12
  CLUS_4            1              4
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      2      0
  ARID1A WILD-TYPE     22     19     19
D8V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               22
  CLUS_2              2               19
  CLUS_3              0               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARID1A MUTATED        1      1      1      0      0      1      0      1
  ARID1A WILD-TYPE      5     12     11      9      6      8      8      1
D8V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1                5
  CLUS_2              1               12
  CLUS_3              1               11
  CLUS_4              0                9
  CLUS_5              0                6
  CLUS_6              1                8
  CLUS_7              0                8
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        6      3      1      1
  ARID1A WILD-TYPE     45     17     18     29
D8V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               45
  CLUS_2              3               17
  CLUS_3              1               18
  CLUS_4              1               29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      1      2
  ARID1A WILD-TYPE     13     22     16
D8V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               13
  CLUS_2              1               22
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        1      1      2      1      0
  ARID1A WILD-TYPE     29     18     20     22      3
D8V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               29
  CLUS_2              1               18
  CLUS_3              2               20
  CLUS_4              1               22
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED        2      0      2      0      0      1
  ARID1A WILD-TYPE     17     16     12     14     23     10
D8V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               17
  CLUS_2              0               16
  CLUS_3              2               12
  CLUS_4              0               14
  CLUS_5              0               23
  CLUS_6              1               10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      2      1      1      5
  ARID1A WILD-TYPE     14     11     21     12     52
D8V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               11
  CLUS_3              1               21
  CLUS_4              1               12
  CLUS_5              5               52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ARID1A MUTATED        2      3      0      1      2      1      2
  ARID1A WILD-TYPE      9     20      8     11     30     17     15
D8V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2                9
  CLUS_2              3               20
  CLUS_3              0                8
  CLUS_4              1               11
  CLUS_5              2               30
  CLUS_6              1               17
  CLUS_7              2               15
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      2      0      3
  ARID1A WILD-TYPE     12     24     12      8     52
D8V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               24
  CLUS_3              2               12
  CLUS_4              0                8
  CLUS_5              3               52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        2      5      3
  ARID1A WILD-TYPE     18     39     51
D8V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               18
  CLUS_2              5               39
  CLUS_3              3               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        2      0      1      1
  ARID1A WILD-TYPE      6      7     12      7
D8V11, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2                6
  CLUS_2              0                7
  CLUS_3              1               12
  CLUS_4              1                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        3      0      1      0      0
  ARID1A WILD-TYPE      5      9     11      5      2
D8V12, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3                5
  CLUS_2              0                9
  CLUS_3              1               11
  CLUS_4              0                5
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = CDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CDH1 MUTATED        0      1      0
  CDH1 WILD-TYPE     25     20     19
D9V1, multiclass
[1] "Remove cluster labels:" "CDH1 MUTATED"          
clus
  CDH1 MUTATED CDH1 WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDH1 MUTATED        0      1      0      0      0      0      0      0
  CDH1 WILD-TYPE      6     12     12      9      6      9      8      2
D9V2, multiclass
[1] "Remove cluster labels:" "CDH1 MUTATED"          
clus
  CDH1 MUTATED CDH1 WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDH1 MUTATED        6      1      1      4
  CDH1 WILD-TYPE     45     19     18     26
D9V3, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            6             45
  CLUS_2            1             19
  CLUS_3            1             18
  CLUS_4            4             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CDH1 MUTATED        5      3      3
  CDH1 WILD-TYPE     11     20     15
D9V4, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            5             11
  CLUS_2            3             20
  CLUS_3            3             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDH1 MUTATED        3      2      2      2      0
  CDH1 WILD-TYPE     27     17     20     21      3
D9V5, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            3             27
  CLUS_2            2             17
  CLUS_3            2             20
  CLUS_4            2             21
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CDH1 MUTATED        1      2      0      2      1      3
  CDH1 WILD-TYPE     18     14     14     12     22      8
D9V6, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             14
  CLUS_3            0             14
  CLUS_4            2             12
  CLUS_5            1             22
  CLUS_6            3              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDH1 MUTATED        3      3      3      2      1
  CDH1 WILD-TYPE     13     10     19     11     56
D9V7, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            3             13
  CLUS_2            3             10
  CLUS_3            3             19
  CLUS_4            2             11
  CLUS_5            1             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CDH1 MUTATED        1      6      1      3      0      1      0
  CDH1 WILD-TYPE     10     17      7      9     32     17     17
D9V8, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            6             17
  CLUS_3            1              7
  CLUS_4            3              9
  CLUS_5            0             32
  CLUS_6            1             17
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDH1 MUTATED        1      6      4      0      1
  CDH1 WILD-TYPE     12     22     10      8     54
D9V9, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            6             22
  CLUS_3            4             10
  CLUS_4            0              8
  CLUS_5            1             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CDH1 MUTATED        4      7      1
  CDH1 WILD-TYPE     16     37     53
D9V10, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            4             16
  CLUS_2            7             37
  CLUS_3            1             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDH1 MUTATED        3      1      2      3
  CDH1 WILD-TYPE      5      6     11      5
D9V11, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            3              5
  CLUS_2            1              6
  CLUS_3            2             11
  CLUS_4            3              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
  CDH1 MUTATED        2      1      4      1      1
  CDH1 WILD-TYPE      6      8      8      4      1
D9V12, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            1              8
  CLUS_3            4              8
  CLUS_4            1              4
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = RBM10 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RBM10 MUTATED        3      1      1
  RBM10 WILD-TYPE     22     20     18
D10V1, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             3              22
  CLUS_2             1              20
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RBM10 MUTATED        1      1      1      1      0      1      0      0
  RBM10 WILD-TYPE      5     12     11      8      6      8      8      2
D10V2, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              12
  CLUS_3             1              11
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             1               8
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBM10 MUTATED        4      1      0      1
  RBM10 WILD-TYPE     47     19     19     29
D10V3, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             1              19
  CLUS_3             0              19
  CLUS_4             1              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RBM10 MUTATED        0      0      1
  RBM10 WILD-TYPE     16     23     17
D10V4, multiclass
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              1              56 
     TCGA-AF-2687      TCGA-AF-2693      TCGA-AF-4110      TCGA-AF-6136 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3731      TCGA-AG-3732 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02N      TCGA-AG-A036      TCGA-AH-6544 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643      TCGA-AH-6644 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621      TCGA-CI-6622 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918      TCGA-DC-5337 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EF-5830 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508      TCGA-F5-6464 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RBM10 MUTATED        3      0      0      2      0
  RBM10 WILD-TYPE     27     19     22     21      3
D10V5, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             0              19
  CLUS_3             0              22
  CLUS_4             2              21
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RBM10 MUTATED        1      0      0      1      2      1
  RBM10 WILD-TYPE     18     16     14     13     21     10
D10V6, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             0              16
  CLUS_3             0              14
  CLUS_4             1              13
  CLUS_5             2              21
  CLUS_6             1              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RBM10 MUTATED        0      1      2      0      2
  RBM10 WILD-TYPE     16     12     20     13     55
D10V7, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              12
  CLUS_3             2              20
  CLUS_4             0              13
  CLUS_5             2              55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RBM10 MUTATED        0      2      0      0      2      1      0
  RBM10 WILD-TYPE     11     21      8     12     30     17     17
D10V8, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             2              21
  CLUS_3             0               8
  CLUS_4             0              12
  CLUS_5             2              30
  CLUS_6             1              17
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RBM10 MUTATED        0      1      0      1      4
  RBM10 WILD-TYPE     13     27     14      7     51
D10V9, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              27
  CLUS_3             0              14
  CLUS_4             1               7
  CLUS_5             4              51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RBM10 MUTATED        1      1      4
  RBM10 WILD-TYPE     19     43     50
D10V10, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              43
  CLUS_3             4              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBM10 MUTATED        0      0      0      0
  RBM10 WILD-TYPE      8      7     13      8
D10V11, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RBM10 MUTATED        0      0      0      0      0
  RBM10 WILD-TYPE      8      9     12      5      2
D10V12, multiclass

Clustering(11) Variable = HAUS6 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HAUS6 MUTATED        0      1      0
  HAUS6 WILD-TYPE     25     20     19
D11V1, multiclass
[1] "Remove cluster labels:" "HAUS6 MUTATED"         
clus
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  HAUS6 MUTATED        0      1      0      0      0      0      0      0
  HAUS6 WILD-TYPE      6     12     12      9      6      9      8      2
D11V2, multiclass
[1] "Remove cluster labels:" "HAUS6 MUTATED"         
clus
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" "HAUS6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HAUS6 MUTATED        4      0      1      0
  HAUS6 WILD-TYPE     47     20     18     30
D11V3, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             0              20
  CLUS_3             1              18
  CLUS_4             0              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HAUS6 MUTATED        1      2      1
  HAUS6 WILD-TYPE     15     21     17
D11V4, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              21
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HAUS6 MUTATED        0      1      1      2      0
  HAUS6 WILD-TYPE     30     18     21     21      3
D11V5, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             1              18
  CLUS_3             1              21
  CLUS_4             2              21
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HAUS6 MUTATED        1      2      0      1      0      0
  HAUS6 WILD-TYPE     18     14     14     13     23     11
D11V6, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             2              14
  CLUS_3             0              14
  CLUS_4             1              13
  CLUS_5             0              23
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HAUS6 MUTATED        1      2      0      1      1
  HAUS6 WILD-TYPE     15     11     22     12     56
D11V7, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              11
  CLUS_3             0              22
  CLUS_4             1              12
  CLUS_5             1              56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  HAUS6 MUTATED        0      3      0      1      0      1      0
  HAUS6 WILD-TYPE     11     20      8     11     32     17     17
D11V8, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             3              20
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0              32
  CLUS_6             1              17
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HAUS6 MUTATED        0      2      2      0      1
  HAUS6 WILD-TYPE     13     26     12      8     54
D11V9, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              26
  CLUS_3             2              12
  CLUS_4             0               8
  CLUS_5             1              54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HAUS6 MUTATED        0      4      1
  HAUS6 WILD-TYPE     20     40     53
D11V10, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             4              40
  CLUS_3             1              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HAUS6 MUTATED        0      1      1      1
  HAUS6 WILD-TYPE      8      6     12      7
D11V11, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1               6
  CLUS_3             1              12
  CLUS_4             1               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
  HAUS6 MUTATED        0      0      2      0      1
  HAUS6 WILD-TYPE      8      9     10      5      1
D11V12, multiclass
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               9
  CLUS_3             2              10
  CLUS_4             0               5
  CLUS_5             1               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0      3      0
  CTNNB1 WILD-TYPE     25     18     19
D12V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               25
  CLUS_2              3               18
  CLUS_3              0               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CTNNB1 MUTATED        0      3      0      0      0      0      0      0
  CTNNB1 WILD-TYPE      6     10     12      9      6      9      8      2
D12V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              3               10
  CLUS_3              0               12
  CLUS_4              0                9
  CLUS_5              0                6
  CLUS_6              0                9
  CLUS_7              0                8
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        7      3      3      6
  CTNNB1 WILD-TYPE     44     17     16     24
D12V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              7               44
  CLUS_2              3               17
  CLUS_3              3               16
  CLUS_4              6               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        4      8      4
  CTNNB1 WILD-TYPE     12     15     14
D12V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               12
  CLUS_2              8               15
  CLUS_3              4               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        2      5      2      5      0
  CTNNB1 WILD-TYPE     28     14     20     18      3
D12V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               28
  CLUS_2              5               14
  CLUS_3              2               20
  CLUS_4              5               18
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CTNNB1 MUTATED        0      4      3      3      1      3
  CTNNB1 WILD-TYPE     19     12     11     11     22      8
D12V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              4               12
  CLUS_3              3               11
  CLUS_4              3               11
  CLUS_5              1               22
  CLUS_6              3                8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        6      3      3      3      4
  CTNNB1 WILD-TYPE     10     10     19     10     53
D12V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              6               10
  CLUS_2              3               10
  CLUS_3              3               19
  CLUS_4              3               10
  CLUS_5              4               53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CTNNB1 MUTATED        5      5      1      4      0      4      0
  CTNNB1 WILD-TYPE      6     18      7      8     32     14     17
D12V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              5                6
  CLUS_2              5               18
  CLUS_3              1                7
  CLUS_4              4                8
  CLUS_5              0               32
  CLUS_6              4               14
  CLUS_7              0               17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        2      9      4      0      4
  CTNNB1 WILD-TYPE     11     19     10      8     51
D12V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              9               19
  CLUS_3              4               10
  CLUS_4              0                8
  CLUS_5              4               51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0     15      4
  CTNNB1 WILD-TYPE     20     29     50
D12V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               20
  CLUS_2             15               29
  CLUS_3              4               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        2      2      3      2
  CTNNB1 WILD-TYPE      6      5     10      6
D12V11, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2                6
  CLUS_2              2                5
  CLUS_3              3               10
  CLUS_4              2                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
  CTNNB1 MUTATED        1      3      2      1      2
  CTNNB1 WILD-TYPE      7      6     10      4      0
D12V12, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              3                6
  CLUS_3              2               10
  CLUS_4              1                4
  CLUS_5              2                0
[1] 5 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 = GABRP MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GABRP MUTATED        0      1      0
  GABRP WILD-TYPE     25     20     19
D13V1, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GABRP MUTATED        0      1      0      0      0      0      0      0
  GABRP WILD-TYPE      6     12     12      9      6      9      8      2
D13V2, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GABRP MUTATED        2      0      0      2
  GABRP WILD-TYPE     49     20     19     28
D13V3, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             2              49
  CLUS_2             0              20
  CLUS_3             0              19
  CLUS_4             2              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GABRP MUTATED        1      1      1
  GABRP WILD-TYPE     15     22     17
D13V4, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              22
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GABRP MUTATED        1      0      0      1      0
  GABRP WILD-TYPE     29     19     22     22      3
D13V5, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              2              95 
     TCGA-AF-2689      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-5654 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3574 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3612      TCGA-AG-3727      TCGA-AG-3731 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-4001      TCGA-AG-4005 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A036      TCGA-AH-6544 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643      TCGA-AH-6644 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-CI-6621      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GABRP MUTATED        0      0      0      0      1      1
  GABRP WILD-TYPE     19     16     14     14     22     10
D13V6, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              2              95 
     TCGA-AF-2689      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-5654 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3574 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3612      TCGA-AG-3727      TCGA-AG-3731 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-4001      TCGA-AG-4005 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A036      TCGA-AH-6544 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643      TCGA-AH-6644 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-CI-6621      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GABRP MUTATED        0      1      1      1      1
  GABRP WILD-TYPE     16     12     21     12     56
D13V7, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              12
  CLUS_3             1              21
  CLUS_4             1              12
  CLUS_5             1              56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GABRP MUTATED        0      1      0      1      0      2      0
  GABRP WILD-TYPE     11     22      8     11     32     16     17
D13V8, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             0              11
  CLUS_2             1              22
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0              32
  CLUS_6             2              16
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GABRP MUTATED        0      0      2      0      2
  GABRP WILD-TYPE     13     28     12      8     53
D13V9, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             0              13
  CLUS_2             0              28
  CLUS_3             2              12
  CLUS_4             0               8
  CLUS_5             2              53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GABRP MUTATED        1      1      2
  GABRP WILD-TYPE     19     43     52
D13V10, multiclass
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              43
  CLUS_3             2              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GABRP MUTATED        0      0      0      1
  GABRP WILD-TYPE      8      7     13      7
D13V11, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              1              35 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3731      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6235      TCGA-G5-6641 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GABRP MUTATED        0      1      0      0      0
  GABRP WILD-TYPE      8      8     12      5      2
D13V12, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              1              35 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AG-3731      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6235      TCGA-G5-6641 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 

Clustering(14) Variable = PON3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PON3 MUTATED        0      0      0
  PON3 WILD-TYPE     25     21     19
D14V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PON3 MUTATED        0      0      0      0      0      0      0      0
  PON3 WILD-TYPE      6     13     12      9      6      9      8      2
D14V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PON3 MUTATED        1      1      2      0
  PON3 WILD-TYPE     50     19     17     30
D14V3, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            1             50
  CLUS_2            1             19
  CLUS_3            2             17
  CLUS_4            0             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PON3 MUTATED        1      1      2
  PON3 WILD-TYPE     15     22     16
D14V4, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1             22
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PON3 MUTATED        1      0      0      1      0
  PON3 WILD-TYPE     29     19     22     22      3
D14V5, multiclass
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-DC-5337     TCGA-DC-5869 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PON3 MUTATED        0      0      1      0      0      1
  PON3 WILD-TYPE     19     16     13     14     23     10
D14V6, multiclass
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-DC-5337     TCGA-DC-5869 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PON3 MUTATED        0      1      1      2      0
  PON3 WILD-TYPE     16     12     21     11     57
D14V7, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            1             21
  CLUS_4            2             11
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PON3 MUTATED        0      2      0      2      0      0      0
  PON3 WILD-TYPE     11     21      8     10     32     18     17
D14V8, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            2             21
  CLUS_3            0              8
  CLUS_4            2             10
  CLUS_5            0             32
  CLUS_6            0             18
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PON3 MUTATED        0      2      2      0      0
  PON3 WILD-TYPE     13     26     12      8     55
D14V9, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             26
  CLUS_3            2             12
  CLUS_4            0              8
  CLUS_5            0             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PON3 MUTATED        0      4      0
  PON3 WILD-TYPE     20     40     54
D14V10, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            4             40
  CLUS_3            0             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PON3 MUTATED        1      0      0      2
  PON3 WILD-TYPE      7      7     13      6
D14V11, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            0              7
  CLUS_3            0             13
  CLUS_4            2              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
  PON3 MUTATED        1      0      1      1      0
  PON3 WILD-TYPE      7      9     11      4      2
D14V12, multiclass
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            0              9
  CLUS_3            1             11
  CLUS_4            1              4
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = RLIM MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RLIM MUTATED        1      0      0
  RLIM WILD-TYPE     24     21     19
D15V1, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RLIM MUTATED        0      0      1      0      0      0      0      0
  RLIM WILD-TYPE      6     13     11      9      6      9      8      2
D15V2, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RLIM MUTATED        2      0      2      0
  RLIM WILD-TYPE     49     20     17     30
D15V3, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            2             49
  CLUS_2            0             20
  CLUS_3            2             17
  CLUS_4            0             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RLIM MUTATED        3      0      0
  RLIM WILD-TYPE     13     23     18
D15V4, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            3             13
  CLUS_2            0             23
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RLIM MUTATED        1      0      0      2      0
  RLIM WILD-TYPE     29     19     22     21      3
D15V5, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            1             29
  CLUS_2            0             19
  CLUS_3            0             22
  CLUS_4            2             21
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RLIM MUTATED        0      0      1      0      1      1
  RLIM WILD-TYPE     19     16     13     14     22     10
D15V6, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            0             19
  CLUS_2            0             16
  CLUS_3            1             13
  CLUS_4            0             14
  CLUS_5            1             22
  CLUS_6            1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RLIM MUTATED        1      0      1      2      0
  RLIM WILD-TYPE     15     13     21     11     57
D15V7, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0             13
  CLUS_3            1             21
  CLUS_4            2             11
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RLIM MUTATED        2      0      0      1      0      1      0
  RLIM WILD-TYPE      9     23      8     11     32     17     17
D15V8, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            2              9
  CLUS_2            0             23
  CLUS_3            0              8
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            1             17
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RLIM MUTATED        1      1      1      0      1
  RLIM WILD-TYPE     12     27     13      8     54
D15V9, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             27
  CLUS_3            1             13
  CLUS_4            0              8
  CLUS_5            1             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RLIM MUTATED        1      2      1
  RLIM WILD-TYPE     19     42     53
D15V10, multiclass
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2             42
  CLUS_3            1             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RLIM MUTATED        1      0      0      1
  RLIM WILD-TYPE      7      7     13      7
D15V11, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             2             34 
    TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3731 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1H8 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RLIM MUTATED        1      0      1      0      0
  RLIM WILD-TYPE      7      9     11      5      2
D15V12, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             2             34 
    TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3731 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1H8 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" 

Clustering(16) Variable = SMAD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD2 MUTATED        1      1      1
  SMAD2 WILD-TYPE     24     20     18
D16V1, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1              24
  CLUS_2             1              20
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SMAD2 MUTATED        0      0      1      0      0      1      1      0
  SMAD2 WILD-TYPE      6     13     11      9      6      8      7      2
D16V2, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0              13
  CLUS_3             1              11
  CLUS_4             0               9
  CLUS_5             0               6
  CLUS_6             1               8
  CLUS_7             1               7
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD2 MUTATED        5      0      1      0
  SMAD2 WILD-TYPE     46     20     18     30
D16V3, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             5              46
  CLUS_2             0              20
  CLUS_3             1              18
  CLUS_4             0              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD2 MUTATED        1      1      1
  SMAD2 WILD-TYPE     15     22     17
D16V4, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              22
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD2 MUTATED        0      1      0      3      0
  SMAD2 WILD-TYPE     30     18     22     20      3
D16V5, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             1              18
  CLUS_3             0              22
  CLUS_4             3              20
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SMAD2 MUTATED        0      2      0      0      2      0
  SMAD2 WILD-TYPE     19     14     14     14     21     11
D16V6, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             2              14
  CLUS_3             0              14
  CLUS_4             0              14
  CLUS_5             2              21
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD2 MUTATED        1      1      1      0      3
  SMAD2 WILD-TYPE     15     12     21     13     54
D16V7, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              12
  CLUS_3             1              21
  CLUS_4             0              13
  CLUS_5             3              54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SMAD2 MUTATED        0      2      0      0      2      1      1
  SMAD2 WILD-TYPE     11     21      8     12     30     17     16
D16V8, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             2              21
  CLUS_3             0               8
  CLUS_4             0              12
  CLUS_5             2              30
  CLUS_6             1              17
  CLUS_7             1              16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD2 MUTATED        0      1      1      0      4
  SMAD2 WILD-TYPE     13     27     13      8     51
D16V9, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             1              27
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             4              51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD2 MUTATED        0      2      4
  SMAD2 WILD-TYPE     20     42     50
D16V10, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             2              42
  CLUS_3             4              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD2 MUTATED        0      1      1      0
  SMAD2 WILD-TYPE      8      6     12      8
D16V11, multiclass
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-F5-6464      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6641 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD2 MUTATED        0      0      1      0      1
  SMAD2 WILD-TYPE      8      9     11      5      1
D16V12, multiclass
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-F5-6464      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6641 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 

Clustering(17) Variable = TCF7L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        2      2      2
  TCF7L2 WILD-TYPE     23     19     17
D17V1, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               23
  CLUS_2              2               19
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TCF7L2 MUTATED        1      0      1      1      1      0      2      0
  TCF7L2 WILD-TYPE      5     13     11      8      5      9      6      2
D17V2, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              0               13
  CLUS_3              1               11
  CLUS_4              1                8
  CLUS_5              1                5
  CLUS_6              0                9
  CLUS_7              2                6
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        4      2      3      3
  TCF7L2 WILD-TYPE     47     18     16     27
D17V3, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              4               47
  CLUS_2              2               18
  CLUS_3              3               16
  CLUS_4              3               27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        2      3      1
  TCF7L2 WILD-TYPE     14     20     17
D17V4, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              3               20
  CLUS_3              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCF7L2 MUTATED        1      3      1      2      0
  TCF7L2 WILD-TYPE     29     16     21     21      3
D17V5, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               29
  CLUS_2              3               16
  CLUS_3              1               21
  CLUS_4              2               21
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TCF7L2 MUTATED        0      2      0      3      1      1
  TCF7L2 WILD-TYPE     19     14     14     11     22     10
D17V6, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              2               14
  CLUS_3              0               14
  CLUS_4              3               11
  CLUS_5              1               22
  CLUS_6              1               10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCF7L2 MUTATED        1      1      2      2      6
  TCF7L2 WILD-TYPE     15     12     20     11     51
D17V7, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1               12
  CLUS_3              2               20
  CLUS_4              2               11
  CLUS_5              6               51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TCF7L2 MUTATED        1      3      1      1      5      0      1
  TCF7L2 WILD-TYPE     10     20      7     11     27     18     16
D17V8, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              3               20
  CLUS_3              1                7
  CLUS_4              1               11
  CLUS_5              5               27
  CLUS_6              0               18
  CLUS_7              1               16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCF7L2 MUTATED        1      5      0      0      5
  TCF7L2 WILD-TYPE     12     23     14      8     50
D17V9, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              5               23
  CLUS_3              0               14
  CLUS_4              0                8
  CLUS_5              5               50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        1      5      5
  TCF7L2 WILD-TYPE     19     39     49
D17V10, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              5               39
  CLUS_3              5               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        0      1      4      1
  TCF7L2 WILD-TYPE      8      6      9      7
D17V11, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              1                6
  CLUS_3              4                9
  CLUS_4              1                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
  TCF7L2 MUTATED        1      2      3      0      0
  TCF7L2 WILD-TYPE      7      7      9      5      2
D17V12, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              2                7
  CLUS_3              3                9
  CLUS_4              0                5
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = OXSM MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  OXSM MUTATED        0      1      0
  OXSM WILD-TYPE     25     20     19
D18V1, multiclass
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  OXSM MUTATED        0      1      0      0      0      0      0      0
  OXSM WILD-TYPE      6     12     12      9      6      9      8      2
D18V2, multiclass
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OXSM MUTATED        2      0      1      1
  OXSM WILD-TYPE     49     20     18     29
D18V3, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            2             49
  CLUS_2            0             20
  CLUS_3            1             18
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  OXSM MUTATED        0      1      2
  OXSM WILD-TYPE     16     22     16
D18V4, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             22
  CLUS_3            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OXSM MUTATED        0      0      1      2      0
  OXSM WILD-TYPE     30     19     21     21      3
D18V5, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            0             30
  CLUS_2            0             19
  CLUS_3            1             21
  CLUS_4            2             21
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  OXSM MUTATED        0      0      1      2      0      0
  OXSM WILD-TYPE     19     16     13     12     23     11
D18V6, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            0             19
  CLUS_2            0             16
  CLUS_3            1             13
  CLUS_4            2             12
  CLUS_5            0             23
  CLUS_6            0             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OXSM MUTATED        1      0      1      1      1
  OXSM WILD-TYPE     15     13     21     12     56
D18V7, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0             13
  CLUS_3            1             21
  CLUS_4            1             12
  CLUS_5            1             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  OXSM MUTATED        1      0      1      1      0      1      0
  OXSM WILD-TYPE     10     23      7     11     32     17     17
D18V8, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            1             10
  CLUS_2            0             23
  CLUS_3            1              7
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            1             17
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OXSM MUTATED        1      1      1      0      1
  OXSM WILD-TYPE     12     27     13      8     54
D18V9, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             27
  CLUS_3            1             13
  CLUS_4            0              8
  CLUS_5            1             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  OXSM MUTATED        0      3      1
  OXSM WILD-TYPE     20     41     53
D18V10, multiclass
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  CLUS_1            0             20
  CLUS_2            3             41
  CLUS_3            1             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OXSM MUTATED        0      0      1      1
  OXSM WILD-TYPE      8      7     12      7
D18V11, multiclass
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6624     TCGA-DC-5337     TCGA-DC-5869 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6683 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG     TCGA-DY-A1H8 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  OXSM MUTATED        1      0      0      1      0
  OXSM WILD-TYPE      7      9     12      4      2
D18V12, multiclass
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6624     TCGA-DC-5337     TCGA-DC-5869 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6683 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG     TCGA-DY-A1H8 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" 

Clustering(19) Variable = PCBP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCBP1 MUTATED        2      0      0
  PCBP1 WILD-TYPE     23     21     19
D19V1, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              63 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025      TCGA-AG-A026 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PCBP1 MUTATED        1      0      1      0      0      0      0      0
  PCBP1 WILD-TYPE      5     13     11      9      6      9      8      2
D19V2, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              63 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025      TCGA-AG-A026 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCBP1 MUTATED        4      0      0      1
  PCBP1 WILD-TYPE     47     20     19     29
D19V3, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             0              20
  CLUS_3             0              19
  CLUS_4             1              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCBP1 MUTATED        1      2      0
  PCBP1 WILD-TYPE     15     21     18
D19V4, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              21
  CLUS_3             0              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCBP1 MUTATED        0      1      0      2      0
  PCBP1 WILD-TYPE     30     18     22     21      3
D19V5, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             1              18
  CLUS_3             0              22
  CLUS_4             2              21
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCBP1 MUTATED        0      1      0      0      2      0
  PCBP1 WILD-TYPE     19     15     14     14     21     11
D19V6, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             1              15
  CLUS_3             0              14
  CLUS_4             0              14
  CLUS_5             2              21
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCBP1 MUTATED        1      1      2      0      1
  PCBP1 WILD-TYPE     15     12     20     13     56
D19V7, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              12
  CLUS_3             2              20
  CLUS_4             0              13
  CLUS_5             1              56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PCBP1 MUTATED        0      3      0      0      1      1      0
  PCBP1 WILD-TYPE     11     20      8     12     31     17     17
D19V8, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             3              20
  CLUS_3             0               8
  CLUS_4             0              12
  CLUS_5             1              31
  CLUS_6             1              17
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCBP1 MUTATED        0      2      1      0      2
  PCBP1 WILD-TYPE     13     26     13      8     53
D19V9, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              26
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             2              53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCBP1 MUTATED        0      3      2
  PCBP1 WILD-TYPE     20     41     52
D19V10, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             3              41
  CLUS_3             2              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCBP1 MUTATED        0      1      1      0
  PCBP1 WILD-TYPE      8      6     12      8
D19V11, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6547      TCGA-AH-6549 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCBP1 MUTATED        0      0      1      0      1
  PCBP1 WILD-TYPE      8      9     11      5      1
D19V12, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6547      TCGA-AH-6549 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 

Clustering(20) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       17     10      8
  KRAS WILD-TYPE      8     11     11
D20V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           17              8
  CLUS_2           10             11
  CLUS_3            8             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRAS MUTATED        3     10      9      3      3      5      0      2
  KRAS WILD-TYPE      3      3      3      6      3      4      8      0
D20V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3              3
  CLUS_2           10              3
  CLUS_3            9              3
  CLUS_4            3              6
  CLUS_5            3              3
  CLUS_6            5              4
  CLUS_7            0              8
  CLUS_8            2              0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED       31     14      4     13
  KRAS WILD-TYPE     20      6     15     17
D20V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           31             20
  CLUS_2           14              6
  CLUS_3            4             15
  CLUS_4           13             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        3     14     10
  KRAS WILD-TYPE     13      9      8
D20V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             13
  CLUS_2           14              9
  CLUS_3           10              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED       16     13      9      9      1
  KRAS WILD-TYPE     14      6     13     14      2
D20V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16             14
  CLUS_2           13              6
  CLUS_3            9             13
  CLUS_4            9             14
  CLUS_5            1              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED       10     10      3      4     16      5
  KRAS WILD-TYPE      9      6     11     10      7      6
D20V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10              9
  CLUS_2           10              6
  CLUS_3            3             11
  CLUS_4            4             10
  CLUS_5           16              7
  CLUS_6            5              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        8      6     15      5     28
  KRAS WILD-TYPE      8      7      7      8     29
D20V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8              8
  CLUS_2            6              7
  CLUS_3           15              7
  CLUS_4            5              8
  CLUS_5           28             29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KRAS MUTATED        4     12      4      7     11     13     11
  KRAS WILD-TYPE      7     11      4      5     21      5      6
D20V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4              7
  CLUS_2           12             11
  CLUS_3            4              4
  CLUS_4            7              5
  CLUS_5           11             21
  CLUS_6           13              5
  CLUS_7           11              6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        6     14      6      3     30
  KRAS WILD-TYPE      7     14      8      5     25
D20V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6              7
  CLUS_2           14             14
  CLUS_3            6              8
  CLUS_4            3              5
  CLUS_5           30             25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        5     24     30
  KRAS WILD-TYPE     15     20     24
D20V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5             15
  CLUS_2           24             20
  CLUS_3           30             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        2      4      6      3
  KRAS WILD-TYPE      6      3      7      5
D20V11, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2              6
  CLUS_2            4              3
  CLUS_3            6              7
  CLUS_4            3              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
  KRAS MUTATED        4      4      7      0      0
  KRAS WILD-TYPE      4      5      5      5      2
D20V12, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4              4
  CLUS_2            4              5
  CLUS_3            7              5
  CLUS_4            0              5
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = FLT1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT1 MUTATED        1      1      0
  FLT1 WILD-TYPE     24     20     19
D21V1, multiclass
[1] "Remove cluster labels:" "FLT1 MUTATED"          
clus
  FLT1 MUTATED FLT1 WILD-TYPE 
             2             63 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025     TCGA-AG-A026 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FLT1 MUTATED        0      0      1      0      0      1      0      0
  FLT1 WILD-TYPE      6     13     11      9      6      8      8      2
D21V2, multiclass
[1] "Remove cluster labels:" "FLT1 MUTATED"          
clus
  FLT1 MUTATED FLT1 WILD-TYPE 
             2             63 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025     TCGA-AG-A026 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"FLT1 WILD-TYPE" "FLT1 WILD-TYPE" "FLT1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT1 MUTATED        4      2      1      1
  FLT1 WILD-TYPE     47     18     18     29
D21V3, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            4             47
  CLUS_2            2             18
  CLUS_3            1             18
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT1 MUTATED        2      2      1
  FLT1 WILD-TYPE     14     21     17
D21V4, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             21
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FLT1 MUTATED        3      0      1      3      0
  FLT1 WILD-TYPE     27     19     21     20      3
D21V5, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            3             27
  CLUS_2            0             19
  CLUS_3            1             21
  CLUS_4            3             20
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FLT1 MUTATED        1      0      2      0      2      2
  FLT1 WILD-TYPE     18     16     12     14     21      9
D21V6, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            0             16
  CLUS_3            2             12
  CLUS_4            0             14
  CLUS_5            2             21
  CLUS_6            2              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FLT1 MUTATED        0      2      3      2      1
  FLT1 WILD-TYPE     16     11     19     11     56
D21V7, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            2             11
  CLUS_3            3             19
  CLUS_4            2             11
  CLUS_5            1             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FLT1 MUTATED        2      2      1      1      0      1      1
  FLT1 WILD-TYPE      9     21      7     11     32     17     16
D21V8, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            2             21
  CLUS_3            1              7
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            1             17
  CLUS_7            1             16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FLT1 MUTATED        2      1      2      1      2
  FLT1 WILD-TYPE     11     27     12      7     53
D21V9, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1             27
  CLUS_3            2             12
  CLUS_4            1              7
  CLUS_5            2             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT1 MUTATED        1      5      2
  FLT1 WILD-TYPE     19     39     52
D21V10, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            5             39
  CLUS_3            2             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT1 MUTATED        0      1      0      2
  FLT1 WILD-TYPE      8      6     13      6
D21V11, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1              6
  CLUS_3            0             13
  CLUS_4            2              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
  FLT1 MUTATED        0      2      1      0      0
  FLT1 WILD-TYPE      8      7     11      5      2
D21V12, multiclass
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            2              7
  CLUS_3            1             11
  CLUS_4            0              5
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = SLC12A6 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC12A6 MUTATED        1      1      0
  SLC12A6 WILD-TYPE     24     20     19
D22V1, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2                63 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A025        TCGA-AG-A026 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SLC12A6 MUTATED        0      1      1      0      0      0      0      0
  SLC12A6 WILD-TYPE      6     12     11      9      6      9      8      2
D22V2, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2                63 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A025        TCGA-AG-A026 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC12A6 MUTATED        4      1      1      0
  SLC12A6 WILD-TYPE     47     19     18     30
D22V3, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               4                47
  CLUS_2               1                19
  CLUS_3               1                18
  CLUS_4               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC12A6 MUTATED        0      3      1
  SLC12A6 WILD-TYPE     16     20     17
D22V4, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                20
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SLC12A6 MUTATED        0      2      0      1      0
  SLC12A6 WILD-TYPE     30     17     22     22      3
D22V5, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                30
  CLUS_2               2                17
  CLUS_3               0                22
  CLUS_4               1                22
  CLUS_5               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SLC12A6 MUTATED        0      1      1      0      1      0
  SLC12A6 WILD-TYPE     19     15     13     14     22     11
D22V6, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                19
  CLUS_2               1                15
  CLUS_3               1                13
  CLUS_4               0                14
  CLUS_5               1                22
  CLUS_6               0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SLC12A6 MUTATED        1      3      1      0      1
  SLC12A6 WILD-TYPE     15     10     21     13     56
D22V7, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               1                15
  CLUS_2               3                10
  CLUS_3               1                21
  CLUS_4               0                13
  CLUS_5               1                56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SLC12A6 MUTATED        0      3      0      1      0      2      0
  SLC12A6 WILD-TYPE     11     20      8     11     32     16     17
D22V8, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                11
  CLUS_2               3                20
  CLUS_3               0                 8
  CLUS_4               1                11
  CLUS_5               0                32
  CLUS_6               2                16
  CLUS_7               0                17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SLC12A6 MUTATED        0      4      0      0      2
  SLC12A6 WILD-TYPE     13     24     14      8     53
D22V9, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                13
  CLUS_2               4                24
  CLUS_3               0                14
  CLUS_4               0                 8
  CLUS_5               2                53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC12A6 MUTATED        0      4      2
  SLC12A6 WILD-TYPE     20     40     52
D22V10, multiclass
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  CLUS_1               0                20
  CLUS_2               4                40
  CLUS_3               2                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC12A6 MUTATED        1      0      1      0
  SLC12A6 WILD-TYPE      7      7     12      8
D22V11, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2                34 
       TCGA-AF-2687        TCGA-AF-4110        TCGA-AF-6655        TCGA-AF-6672 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AH-6544        TCGA-AH-6549 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AH-6643        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6681        TCGA-DC-6682 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DG 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EI-6506        TCGA-EI-6507        TCGA-F5-6464 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SLC12A6 MUTATED        0      1      0      0      1
  SLC12A6 WILD-TYPE      8      8     12      5      1
D22V12, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2                34 
       TCGA-AF-2687        TCGA-AF-4110        TCGA-AF-6655        TCGA-AF-6672 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AH-6544        TCGA-AH-6549 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AH-6643        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6681        TCGA-DC-6682 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DG 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EI-6506        TCGA-EI-6507        TCGA-F5-6464 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 

Clustering(23) Variable = AKAP9 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP9 MUTATED        2      1      0
  AKAP9 WILD-TYPE     23     20     19
D23V1, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             2              23
  CLUS_2             1              20
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AKAP9 MUTATED        0      1      2      0      0      0      0      0
  AKAP9 WILD-TYPE      6     12     10      9      6      9      8      2
D23V2, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              12
  CLUS_3             2              10
  CLUS_4             0               9
  CLUS_5             0               6
  CLUS_6             0               9
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AKAP9 MUTATED        4      2      1      0
  AKAP9 WILD-TYPE     47     18     18     30
D23V3, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             2              18
  CLUS_3             1              18
  CLUS_4             0              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP9 MUTATED        0      2      2
  AKAP9 WILD-TYPE     16     21     16
D23V4, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             2              21
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP9 MUTATED        1      0      0      3      0
  AKAP9 WILD-TYPE     29     19     22     20      3
D23V5, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             0              19
  CLUS_3             0              22
  CLUS_4             3              20
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AKAP9 MUTATED        0      0      1      0      3      0
  AKAP9 WILD-TYPE     19     16     13     14     20     11
D23V6, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             0              16
  CLUS_3             1              13
  CLUS_4             0              14
  CLUS_5             3              20
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP9 MUTATED        0      2      3      1      1
  AKAP9 WILD-TYPE     16     11     19     12     56
D23V7, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             2              11
  CLUS_3             3              19
  CLUS_4             1              12
  CLUS_5             1              56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AKAP9 MUTATED        0      2      0      1      0      4      0
  AKAP9 WILD-TYPE     11     21      8     11     32     14     17
D23V8, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             2              21
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0              32
  CLUS_6             4              14
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP9 MUTATED        1      1      1      0      4
  AKAP9 WILD-TYPE     12     27     13      8     51
D23V9, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              27
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             4              51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AKAP9 MUTATED        0      3      4
  AKAP9 WILD-TYPE     20     41     50
D23V10, multiclass
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             3              41
  CLUS_3             4              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AKAP9 MUTATED        0      1      0      1
  AKAP9 WILD-TYPE      8      6     13      7
D23V11, multiclass
[1] "Remove cluster labels:" "AKAP9 MUTATED"         
clus
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3731 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-CI-6624      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6157 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG      TCGA-DY-A1H8 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464      TCGA-F5-6465 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AKAP9 MUTATED        0      1      0      1      0
  AKAP9 WILD-TYPE      8      8     12      4      2
D23V12, multiclass
[1] "Remove cluster labels:" "AKAP9 MUTATED"         
clus
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3731 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-CI-6624      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6157 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DG      TCGA-DY-A1H8 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464      TCGA-F5-6465 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"AKAP9 WILD-TYPE" "AKAP9 WILD-TYPE" 

Clustering(24) Variable = VCX2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VCX2 MUTATED        0      0      0
  VCX2 WILD-TYPE     25     21     19
D24V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  VCX2 MUTATED        0      0      0      0      0      0      0      0
  VCX2 WILD-TYPE      6     13     12      9      6      9      8      2
D24V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VCX2 MUTATED        2      0      1      2
  VCX2 WILD-TYPE     49     20     18     28
D24V3, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            2             49
  CLUS_2            0             20
  CLUS_3            1             18
  CLUS_4            2             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VCX2 MUTATED        3      1      1
  VCX2 WILD-TYPE     13     22     17
D24V4, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            3             13
  CLUS_2            1             22
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VCX2 MUTATED        1      2      0      1      0
  VCX2 WILD-TYPE     29     17     22     22      3
D24V5, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            1             29
  CLUS_2            2             17
  CLUS_3            0             22
  CLUS_4            1             22
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  VCX2 MUTATED        0      2      1      0      0      1
  VCX2 WILD-TYPE     19     14     13     14     23     10
D24V6, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            2             14
  CLUS_3            1             13
  CLUS_4            0             14
  CLUS_5            0             23
  CLUS_6            1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VCX2 MUTATED        1      1      1      2      0
  VCX2 WILD-TYPE     15     12     21     11     57
D24V7, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            1             12
  CLUS_3            1             21
  CLUS_4            2             11
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  VCX2 MUTATED        1      2      1      1      0      0      0
  VCX2 WILD-TYPE     10     21      7     11     32     18     17
D24V8, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            2             21
  CLUS_3            1              7
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            0             18
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VCX2 MUTATED        2      2      1      0      0
  VCX2 WILD-TYPE     11     26     13      8     55
D24V9, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            2             26
  CLUS_3            1             13
  CLUS_4            0              8
  CLUS_5            0             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VCX2 MUTATED        3      2      0
  VCX2 WILD-TYPE     17     42     54
D24V10, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            3             17
  CLUS_2            2             42
  CLUS_3            0             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VCX2 MUTATED        0      1      2      2
  VCX2 WILD-TYPE      8      6     11      6
D24V11, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1              6
  CLUS_3            2             11
  CLUS_4            2              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
  VCX2 MUTATED        2      2      0      1      0
  VCX2 WILD-TYPE      6      7     12      4      2
D24V12, multiclass
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            2              7
  CLUS_3            0             12
  CLUS_4            1              4
  CLUS_5            0              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = ELF3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        1      2      0
  ELF3 WILD-TYPE     24     19     19
D25V1, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             24
  CLUS_2            2             19
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ELF3 MUTATED        0      2      1      0      0      0      0      0
  ELF3 WILD-TYPE      6     11     11      9      6      9      8      2
D25V2, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            2             11
  CLUS_3            1             11
  CLUS_4            0              9
  CLUS_5            0              6
  CLUS_6            0              9
  CLUS_7            0              8
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ELF3 MUTATED        2      0      0      2
  ELF3 WILD-TYPE     49     20     19     28
D25V3, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             49
  CLUS_2            0             20
  CLUS_3            0             19
  CLUS_4            2             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        0      0      1
  ELF3 WILD-TYPE     16     23     17
D25V4, multiclass
[1] "Remove cluster labels:" "ELF3 MUTATED"          
clus
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             56 
    TCGA-AF-2687     TCGA-AF-2693     TCGA-AF-4110     TCGA-AF-6136 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3731     TCGA-AG-3732 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02N     TCGA-AG-A036     TCGA-AH-6544 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6644     TCGA-CI-6619 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CI-6620     TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DY-A1DG     TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ELF3 MUTATED        0      0      1      2      0
  ELF3 WILD-TYPE     30     19     21     21      3
D25V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             30
  CLUS_2            0             19
  CLUS_3            1             21
  CLUS_4            2             21
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ELF3 MUTATED        1      0      0      2      0      0
  ELF3 WILD-TYPE     18     16     14     12     23     11
D25V6, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            0             16
  CLUS_3            0             14
  CLUS_4            2             12
  CLUS_5            0             23
  CLUS_6            0             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ELF3 MUTATED        0      1      2      0      1
  ELF3 WILD-TYPE     16     12     20     13     56
D25V7, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            2             20
  CLUS_4            0             13
  CLUS_5            1             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ELF3 MUTATED        0      1      1      0      0      2      0
  ELF3 WILD-TYPE     11     22      7     12     32     16     17
D25V8, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            1             22
  CLUS_3            1              7
  CLUS_4            0             12
  CLUS_5            0             32
  CLUS_6            2             16
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ELF3 MUTATED        0      1      0      0      3
  ELF3 WILD-TYPE     13     27     14      8     52
D25V9, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            1             27
  CLUS_3            0             14
  CLUS_4            0              8
  CLUS_5            3             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        1      0      3
  ELF3 WILD-TYPE     19     44     51
D25V10, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            0             44
  CLUS_3            3             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ELF3 MUTATED        0      0      0      1
  ELF3 WILD-TYPE      8      7     13      7
D25V11, multiclass
[1] "Remove cluster labels:" "ELF3 MUTATED"          
clus
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             35 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AH-6549     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6812     TCGA-G5-6235     TCGA-G5-6641 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ELF3 MUTATED        0      0      1      0      0
  ELF3 WILD-TYPE      8      9     11      5      2
D25V12, multiclass
[1] "Remove cluster labels:" "ELF3 MUTATED"          
clus
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             35 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-AH-6549     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-F5-6812     TCGA-G5-6235     TCGA-G5-6641 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 

Clustering(26) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        2      1      2
  PIK3CA WILD-TYPE     23     20     17
D26V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               23
  CLUS_2              1               20
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PIK3CA MUTATED        0      2      1      1      0      1      0      0
  PIK3CA WILD-TYPE      6     11     11      8      6      8      8      2
D26V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2               11
  CLUS_3              1               11
  CLUS_4              1                8
  CLUS_5              0                6
  CLUS_6              1                8
  CLUS_7              0                8
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED       12      4      9     11
  PIK3CA WILD-TYPE     39     16     10     19
D26V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             12               39
  CLUS_2              4               16
  CLUS_3              9               10
  CLUS_4             11               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        9     11     11
  PIK3CA WILD-TYPE      7     12      7
D26V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9                7
  CLUS_2             11               12
  CLUS_3             11                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        7      6      4     12      0
  PIK3CA WILD-TYPE     23     13     18     11      3
D26V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               23
  CLUS_2              6               13
  CLUS_3              4               18
  CLUS_4             12               11
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PIK3CA MUTATED        3      5      7      4      5      5
  PIK3CA WILD-TYPE     16     11      7     10     18      6
D26V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               16
  CLUS_2              5               11
  CLUS_3              7                7
  CLUS_4              4               10
  CLUS_5              5               18
  CLUS_6              5                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        9      5      8     10      4
  PIK3CA WILD-TYPE      7      8     14      3     53
D26V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9                7
  CLUS_2              5                8
  CLUS_3              8               14
  CLUS_4             10                3
  CLUS_5              4               53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PIK3CA MUTATED        8      9      5      7      2      4      1
  PIK3CA WILD-TYPE      3     14      3      5     30     14     16
D26V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8                3
  CLUS_2              9               14
  CLUS_3              5                3
  CLUS_4              7                5
  CLUS_5              2               30
  CLUS_6              4               14
  CLUS_7              1               16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        6     18      5      1      5
  PIK3CA WILD-TYPE      7     10      9      7     50
D26V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6                7
  CLUS_2             18               10
  CLUS_3              5                9
  CLUS_4              1                7
  CLUS_5              5               50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        7     24      4
  PIK3CA WILD-TYPE     13     20     50
D26V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               13
  CLUS_2             24               20
  CLUS_3              4               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        6      1      7      5
  PIK3CA WILD-TYPE      2      6      6      3
D26V11, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6                2
  CLUS_2              1                6
  CLUS_3              7                6
  CLUS_4              5                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        5      2      7      4      1
  PIK3CA WILD-TYPE      3      7      5      1      1
D26V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5                3
  CLUS_2              2                7
  CLUS_3              7                5
  CLUS_4              4                1
  CLUS_5              1                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        2      1      0
  BRAF WILD-TYPE     23     20     19
D27V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             23
  CLUS_2            1             20
  CLUS_3            0             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  BRAF MUTATED        0      1      1      0      1      0      0      0
  BRAF WILD-TYPE      6     12     11      9      5      9      8      2
D27V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             12
  CLUS_3            1             11
  CLUS_4            0              9
  CLUS_5            1              5
  CLUS_6            0              9
  CLUS_7            0              8
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        6      1      2      4
  BRAF WILD-TYPE     45     19     17     26
D27V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            6             45
  CLUS_2            1             19
  CLUS_3            2             17
  CLUS_4            4             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      2      5
  BRAF WILD-TYPE     13     21     13
D27V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             13
  CLUS_2            2             21
  CLUS_3            5             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        4      4      2      3      0
  BRAF WILD-TYPE     26     15     20     20      3
D27V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4             26
  CLUS_2            4             15
  CLUS_3            2             20
  CLUS_4            3             20
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BRAF MUTATED        0      2      4      2      1      4
  BRAF WILD-TYPE     19     14     10     12     22      7
D27V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             19
  CLUS_2            2             14
  CLUS_3            4             10
  CLUS_4            2             12
  CLUS_5            1             22
  CLUS_6            4              7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        4      1      4      3      1
  BRAF WILD-TYPE     12     12     18     10     56
D27V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4             12
  CLUS_2            1             12
  CLUS_3            4             18
  CLUS_4            3             10
  CLUS_5            1             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BRAF MUTATED        2      4      2      2      1      2      0
  BRAF WILD-TYPE      9     19      6     10     31     16     17
D27V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2              9
  CLUS_2            4             19
  CLUS_3            2              6
  CLUS_4            2             10
  CLUS_5            1             31
  CLUS_6            2             16
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        3      5      2      0      3
  BRAF WILD-TYPE     10     23     12      8     52
D27V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             10
  CLUS_2            5             23
  CLUS_3            2             12
  CLUS_4            0              8
  CLUS_5            3             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        4      7      2
  BRAF WILD-TYPE     16     37     52
D27V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4             16
  CLUS_2            7             37
  CLUS_3            2             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        2      1      1      1
  BRAF WILD-TYPE      6      6     12      7
D27V11, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2              6
  CLUS_2            1              6
  CLUS_3            1             12
  CLUS_4            1              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
  BRAF MUTATED        0      3      0      1      1
  BRAF WILD-TYPE      8      6     12      4      1
D27V12, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              8
  CLUS_2            3              6
  CLUS_3            0             12
  CLUS_4            1              4
  CLUS_5            1              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = KIAA1804 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1804 MUTATED        3      4      1
  KIAA1804 WILD-TYPE     22     17     18
D28V1, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 22
  CLUS_2                4                 17
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KIAA1804 MUTATED        0      1      3      1      0      2      1      0
  KIAA1804 WILD-TYPE      6     12      9      8      6      7      7      2
D28V2, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 12
  CLUS_3                3                  9
  CLUS_4                1                  8
  CLUS_5                0                  6
  CLUS_6                2                  7
  CLUS_7                1                  7
  CLUS_8                0                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1804 MUTATED        9      0      0      1
  KIAA1804 WILD-TYPE     42     20     19     29
D28V3, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                9                 42
  CLUS_2                0                 20
  CLUS_3                0                 19
  CLUS_4                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1804 MUTATED        0      0      2
  KIAA1804 WILD-TYPE     16     23     16
D28V4, multiclass
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 2                 55 
        TCGA-AF-2687         TCGA-AF-2693         TCGA-AF-4110 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3732         TCGA-AG-3742 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A036         TCGA-AH-6544 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6549         TCGA-AH-6643 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AH-6644         TCGA-CI-6619         TCGA-CI-6620 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-CI-6621         TCGA-CI-6622         TCGA-CI-6624 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-EI-6510         TCGA-F5-6464         TCGA-F5-6465 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6811 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-G5-6641 
"KIAA1804 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1804 MUTATED        4      0      2      3      0
  KIAA1804 WILD-TYPE     26     19     20     20      3
D28V5, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                0                 19
  CLUS_3                2                 20
  CLUS_4                3                 20
  CLUS_5                0                  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KIAA1804 MUTATED        2      0      1      2      4      0
  KIAA1804 WILD-TYPE     17     16     13     12     19     11
D28V6, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                0                 16
  CLUS_3                1                 13
  CLUS_4                2                 12
  CLUS_5                4                 19
  CLUS_6                0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1804 MUTATED        0      1      3      0      6
  KIAA1804 WILD-TYPE     16     12     19     13     51
D28V7, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
  CLUS_3                3                 19
  CLUS_4                0                 13
  CLUS_5                6                 51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KIAA1804 MUTATED        0      2      0      0      3      4      1
  KIAA1804 WILD-TYPE     11     21      8     12     29     14     16
D28V8, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                 21
  CLUS_3                0                  8
  CLUS_4                0                 12
  CLUS_5                3                 29
  CLUS_6                4                 14
  CLUS_7                1                 16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1804 MUTATED        0      0      1      0      9
  KIAA1804 WILD-TYPE     13     28     13      8     46
D28V9, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                0                 28
  CLUS_3                1                 13
  CLUS_4                0                  8
  CLUS_5                9                 46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1804 MUTATED        1      0      9
  KIAA1804 WILD-TYPE     19     44     45
D28V10, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                0                 44
  CLUS_3                9                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1804 MUTATED        0      0      0      0
  KIAA1804 WILD-TYPE      8      7     13      8
D28V11, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA1804 MUTATED        0      0      0      0      0
  KIAA1804 WILD-TYPE      8      9     12      5      2
D28V12, multiclass

Clustering(29) Variable = ERBB2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        2      1      1
  ERBB2 WILD-TYPE     23     20     18
D29V1, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              23
  CLUS_2             1              20
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ERBB2 MUTATED        0      1      2      1      0      0      0      0
  ERBB2 WILD-TYPE      6     12     10      8      6      9      8      2
D29V2, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              12
  CLUS_3             2              10
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             0               9
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        4      1      0      4
  ERBB2 WILD-TYPE     47     19     19     26
D29V3, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             1              19
  CLUS_3             0              19
  CLUS_4             4              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        0      4      1
  ERBB2 WILD-TYPE     16     19     17
D29V4, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             4              19
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        0      2      1      4      0
  ERBB2 WILD-TYPE     30     17     21     19      3
D29V5, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             2              17
  CLUS_3             1              21
  CLUS_4             4              19
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ERBB2 MUTATED        1      1      0      3      2      0
  ERBB2 WILD-TYPE     18     15     14     11     21     11
D29V6, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             1              15
  CLUS_3             0              14
  CLUS_4             3              11
  CLUS_5             2              21
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        2      3      3      0      1
  ERBB2 WILD-TYPE     14     10     19     13     56
D29V7, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             3              10
  CLUS_3             3              19
  CLUS_4             0              13
  CLUS_5             1              56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ERBB2 MUTATED        0      4      2      0      1      2      0
  ERBB2 WILD-TYPE     11     19      6     12     31     16     17
D29V8, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             4              19
  CLUS_3             2               6
  CLUS_4             0              12
  CLUS_5             1              31
  CLUS_6             2              16
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        2      2      1      0      4
  ERBB2 WILD-TYPE     11     26     13      8     51
D29V9, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2              26
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             4              51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        0      5      4
  ERBB2 WILD-TYPE     20     39     50
D29V10, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             5              39
  CLUS_3             4              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        0      1      1      1
  ERBB2 WILD-TYPE      8      6     12      7
D29V11, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1               6
  CLUS_3             1              12
  CLUS_4             1               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
  ERBB2 MUTATED        0      2      1      0      0
  ERBB2 WILD-TYPE      8      7     11      5      2
D29V12, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             2               7
  CLUS_3             1              11
  CLUS_4             0               5
  CLUS_5             0               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = CDKL5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDKL5 MUTATED        1      0      0
  CDKL5 WILD-TYPE     24     21     19
D30V1, multiclass
[1] "Remove cluster labels:" "CDKL5 MUTATED"         
clus
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDKL5 MUTATED        0      0      1      0      0      0      0      0
  CDKL5 WILD-TYPE      6     13     11      9      6      9      8      2
D30V2, multiclass
[1] "Remove cluster labels:" "CDKL5 MUTATED"         
clus
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKL5 MUTATED        1      1      1      1
  CDKL5 WILD-TYPE     50     19     18     29
D30V3, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             1              19
  CLUS_3             1              18
  CLUS_4             1              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDKL5 MUTATED        1      1      1
  CDKL5 WILD-TYPE     15     22     17
D30V4, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              22
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKL5 MUTATED        1      0      1      1      0
  CDKL5 WILD-TYPE     29     19     21     22      3
D30V5, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             0              19
  CLUS_3             1              21
  CLUS_4             1              22
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CDKL5 MUTATED        1      0      0      0      1      1
  CDKL5 WILD-TYPE     18     16     14     14     22     10
D30V6, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             0              16
  CLUS_3             0              14
  CLUS_4             0              14
  CLUS_5             1              22
  CLUS_6             1              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKL5 MUTATED        0      1      1      2      0
  CDKL5 WILD-TYPE     16     12     21     11     57
D30V7, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              12
  CLUS_3             1              21
  CLUS_4             2              11
  CLUS_5             0              57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CDKL5 MUTATED        1      1      0      1      0      1      0
  CDKL5 WILD-TYPE     10     22      8     11     32     17     17
D30V8, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              22
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0              32
  CLUS_6             1              17
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKL5 MUTATED        1      1      1      0      1
  CDKL5 WILD-TYPE     12     27     13      8     54
D30V9, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1              27
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             1              54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDKL5 MUTATED        1      2      1
  CDKL5 WILD-TYPE     19     42     53
D30V10, multiclass
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             2              42
  CLUS_3             1              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKL5 MUTATED        0      0      0      1
  CDKL5 WILD-TYPE      8      7     13      7
D30V11, multiclass
[1] "Remove cluster labels:" "CDKL5 MUTATED"         
clus
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              1              35 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DG 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6235      TCGA-G5-6641 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKL5 MUTATED        0      1      0      0      0
  CDKL5 WILD-TYPE      8      8     12      5      2
D30V12, multiclass
[1] "Remove cluster labels:" "CDKL5 MUTATED"         
clus
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              1              35 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DG 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EI-6506      TCGA-EI-6507      TCGA-F5-6464 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6812      TCGA-G5-6235      TCGA-G5-6641 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 

Clustering(31) Variable = ZNF354C MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ZNF354C MUTATED        1      0      0
  ZNF354C WILD-TYPE     24     21     19
D31V1, multiclass
[1] "Remove cluster labels:" "ZNF354C MUTATED"       
clus
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                1                64 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A008        TCGA-AG-A00C 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A025 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF354C MUTATED        0      0      1      0      0      0      0      0
  ZNF354C WILD-TYPE      6     13     11      9      6      9      8      2
D31V2, multiclass
[1] "Remove cluster labels:" "ZNF354C MUTATED"       
clus
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                1                64 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A008        TCGA-AG-A00C 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A025 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" "ZNF354C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF354C MUTATED        3      0      0      2
  ZNF354C WILD-TYPE     48     20     19     28
D31V3, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               3                48
  CLUS_2               0                20
  CLUS_3               0                19
  CLUS_4               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ZNF354C MUTATED        1      3      0
  ZNF354C WILD-TYPE     15     20     18
D31V4, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               1                15
  CLUS_2               3                20
  CLUS_3               0                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF354C MUTATED        0      1      0      4      0
  ZNF354C WILD-TYPE     30     18     22     19      3
D31V5, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               0                30
  CLUS_2               1                18
  CLUS_3               0                22
  CLUS_4               4                19
  CLUS_5               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZNF354C MUTATED        0      1      1      0      2      1
  ZNF354C WILD-TYPE     19     15     13     14     21     10
D31V6, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               0                19
  CLUS_2               1                15
  CLUS_3               1                13
  CLUS_4               0                14
  CLUS_5               2                21
  CLUS_6               1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF354C MUTATED        2      0      3      0      0
  ZNF354C WILD-TYPE     14     13     19     13     57
D31V7, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                13
  CLUS_3               3                19
  CLUS_4               0                13
  CLUS_5               0                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZNF354C MUTATED        1      2      1      0      0      1      0
  ZNF354C WILD-TYPE     10     21      7     12     32     17     17
D31V8, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               1                10
  CLUS_2               2                21
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               0                32
  CLUS_6               1                17
  CLUS_7               0                17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF354C MUTATED        1      1      1      1      1
  ZNF354C WILD-TYPE     12     27     13      7     54
D31V9, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                27
  CLUS_3               1                13
  CLUS_4               1                 7
  CLUS_5               1                54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ZNF354C MUTATED        0      4      1
  ZNF354C WILD-TYPE     20     40     53
D31V10, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               0                20
  CLUS_2               4                40
  CLUS_3               1                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF354C MUTATED        0      1      1      1
  ZNF354C WILD-TYPE      8      6     12      7
D31V11, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               1                 6
  CLUS_3               1                12
  CLUS_4               1                 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
  ZNF354C MUTATED        0      0      2      0      1
  ZNF354C WILD-TYPE      8      9     10      5      1
D31V12, multiclass
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               0                 9
  CLUS_3               2                10
  CLUS_4               0                 5
  CLUS_5               1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = LIG1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIG1 MUTATED        0      0      0
  LIG1 WILD-TYPE     25     21     19
D32V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LIG1 MUTATED        0      0      0      0      0      0      0      0
  LIG1 WILD-TYPE      6     13     12      9      6      9      8      2
D32V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LIG1 MUTATED        3      0      0      1
  LIG1 WILD-TYPE     48     20     19     29
D32V3, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            3             48
  CLUS_2            0             20
  CLUS_3            0             19
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIG1 MUTATED        0      3      1
  LIG1 WILD-TYPE     16     20     17
D32V4, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3             20
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LIG1 MUTATED        2      0      0      1      0
  LIG1 WILD-TYPE     28     19     22     22      3
D32V5, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            2             28
  CLUS_2            0             19
  CLUS_3            0             22
  CLUS_4            1             22
  CLUS_5            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LIG1 MUTATED        0      0      1      0      1      1
  LIG1 WILD-TYPE     19     16     13     14     22     10
D32V6, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            0             16
  CLUS_3            1             13
  CLUS_4            0             14
  CLUS_5            1             22
  CLUS_6            1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LIG1 MUTATED        0      1      3      0      0
  LIG1 WILD-TYPE     16     12     19     13     57
D32V7, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            3             19
  CLUS_4            0             13
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LIG1 MUTATED        0      2      1      1      0      0      0
  LIG1 WILD-TYPE     11     21      7     11     32     18     17
D32V8, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            2             21
  CLUS_3            1              7
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            0             18
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LIG1 MUTATED        0      2      1      1      0
  LIG1 WILD-TYPE     13     26     13      7     55
D32V9, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            2             26
  CLUS_3            1             13
  CLUS_4            1              7
  CLUS_5            0             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIG1 MUTATED        0      4      0
  LIG1 WILD-TYPE     20     40     54
D32V10, multiclass
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            4             40
  CLUS_3            0             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LIG1 MUTATED        0      0      0      2
  LIG1 WILD-TYPE      8      7     13      6
D32V11, multiclass
[1] "Remove cluster labels:" "LIG1 MUTATED"          
clus
  LIG1 MUTATED LIG1 WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-F5-6464     TCGA-F5-6465 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LIG1 MUTATED        0      1      1      0      0
  LIG1 WILD-TYPE      8      8     11      5      2
D32V12, multiclass
[1] "Remove cluster labels:" "LIG1 MUTATED"          
clus
  LIG1 MUTATED LIG1 WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-F5-6464     TCGA-F5-6465 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"LIG1 WILD-TYPE" "LIG1 WILD-TYPE" 

Clustering(33) Variable = IQCD MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IQCD MUTATED        1      0      0
  IQCD WILD-TYPE     24     21     19
D33V1, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  IQCD MUTATED        0      0      1      0      0      0      0      0
  IQCD WILD-TYPE      6     13     11      9      6      9      8      2
D33V2, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             1             64 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A025 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X     TCGA-AG-A032 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IQCD MUTATED        1      1      0      1
  IQCD WILD-TYPE     50     19     19     29
D33V3, multiclass
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  CLUS_1            1             50
  CLUS_2            1             19
  CLUS_3            0             19
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IQCD MUTATED        0      1      1
  IQCD WILD-TYPE     16     22     17
D33V4, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             2             55 
    TCGA-AF-2687     TCGA-AF-2693     TCGA-AF-6136     TCGA-AF-6655 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AF-6672     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A036     TCGA-AH-6544     TCGA-AH-6547 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IQCD MUTATED        0      0      0      2      0
  IQCD WILD-TYPE     30     19     22     21      3
D33V5, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01W 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026     TCGA-AG-A02G 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036     TCGA-AH-6544 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6644     TCGA-CI-6621 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IQCD MUTATED        0      0      0      1      1      0
  IQCD WILD-TYPE     19     16     14     13     22     11
D33V6, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A008 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01W 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026     TCGA-AG-A02G 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036     TCGA-AH-6544 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6644     TCGA-CI-6621 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IQCD MUTATED        0      1      2      0      0
  IQCD WILD-TYPE     16     12     20     13     57
D33V7, multiclass
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            2             20
  CLUS_4            0             13
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  IQCD MUTATED        0      1      1      0      0      1      0
  IQCD WILD-TYPE     11     22      7     12     32     17     17
D33V8, multiclass
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  CLUS_1            0             11
  CLUS_2            1             22
  CLUS_3            1              7
  CLUS_4            0             12
  CLUS_5            0             32
  CLUS_6            1             17
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IQCD MUTATED        1      1      0      0      1
  IQCD WILD-TYPE     12     27     14      8     54
D33V9, multiclass
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             27
  CLUS_3            0             14
  CLUS_4            0              8
  CLUS_5            1             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IQCD MUTATED        1      1      1
  IQCD WILD-TYPE     19     43     53
D33V10, multiclass
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  CLUS_1            1             19
  CLUS_2            1             43
  CLUS_3            1             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IQCD MUTATED        0      1      0      1
  IQCD WILD-TYPE      8      6     13      7
D33V11, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3731 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621     TCGA-CI-6624 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6157 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG     TCGA-DY-A1H8 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IQCD MUTATED        0      1      1      0      0
  IQCD WILD-TYPE      8      8     11      5      2
D33V12, multiclass
[1] "Remove cluster labels:" "IQCD MUTATED"          
clus
  IQCD MUTATED IQCD WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3731 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621     TCGA-CI-6624 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6157 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG     TCGA-DY-A1H8 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" "IQCD WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"IQCD WILD-TYPE" "IQCD WILD-TYPE" 

Clustering(34) Variable = ZBED4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZBED4 MUTATED        0      1      0
  ZBED4 WILD-TYPE     25     20     19
D34V1, multiclass
[1] "Remove cluster labels:" "ZBED4 MUTATED"         
clus
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZBED4 MUTATED        0      0      0      0      0      1      0      0
  ZBED4 WILD-TYPE      6     13     12      9      6      8      8      2
D34V2, multiclass
[1] "Remove cluster labels:" "ZBED4 MUTATED"         
clus
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZBED4 MUTATED        2      0      2      0
  ZBED4 WILD-TYPE     49     20     17     30
D34V3, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             0              20
  CLUS_3             2              17
  CLUS_4             0              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZBED4 MUTATED        0      1      2
  ZBED4 WILD-TYPE     16     22     16
D34V4, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              22
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZBED4 MUTATED        0      3      0      1      0
  ZBED4 WILD-TYPE     30     16     22     22      3
D34V5, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             3              16
  CLUS_3             0              22
  CLUS_4             1              22
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZBED4 MUTATED        0      2      1      0      1      0
  ZBED4 WILD-TYPE     19     14     13     14     22     11
D34V6, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             2              14
  CLUS_3             1              13
  CLUS_4             0              14
  CLUS_5             1              22
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZBED4 MUTATED        1      2      1      0      0
  ZBED4 WILD-TYPE     15     11     21     13     57
D34V7, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              11
  CLUS_3             1              21
  CLUS_4             0              13
  CLUS_5             0              57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZBED4 MUTATED        0      1      0      1      0      1      1
  ZBED4 WILD-TYPE     11     22      8     11     32     17     16
D34V8, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             1              22
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0              32
  CLUS_6             1              17
  CLUS_7             1              16
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZBED4 MUTATED        0      2      0      0      2
  ZBED4 WILD-TYPE     13     26     14      8     53
D34V9, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              26
  CLUS_3             0              14
  CLUS_4             0               8
  CLUS_5             2              53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZBED4 MUTATED        0      2      2
  ZBED4 WILD-TYPE     20     42     52
D34V10, multiclass
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             2              42
  CLUS_3             2              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZBED4 MUTATED        1      0      0      1
  ZBED4 WILD-TYPE      7      7     13      7
D34V11, multiclass
[1] "Remove cluster labels:" "ZBED4 MUTATED"         
clus
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6507      TCGA-F5-6464 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZBED4 MUTATED        0      0      1      0      1
  ZBED4 WILD-TYPE      8      9     11      5      1
D34V12, multiclass
[1] "Remove cluster labels:" "ZBED4 MUTATED"         
clus
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              2              34 
     TCGA-AF-2687      TCGA-AF-4110      TCGA-AF-6655      TCGA-AF-6672 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AH-6544      TCGA-AH-6547 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6624      TCGA-CL-5918      TCGA-DC-5337 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6681 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A1DC      TCGA-DY-A1DD 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6507      TCGA-F5-6464 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 

Clustering(35) Variable = GMCL1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GMCL1 MUTATED        1      0      0
  GMCL1 WILD-TYPE     24     21     19
D35V1, multiclass
[1] "Remove cluster labels:" "GMCL1 MUTATED"         
clus
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  GMCL1 MUTATED        0      0      1      0      0      0      0      0
  GMCL1 WILD-TYPE      6     13     11      9      6      9      8      2
D35V2, multiclass
[1] "Remove cluster labels:" "GMCL1 MUTATED"         
clus
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              1              64 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A025 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02X      TCGA-AG-A032 
"GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" "GMCL1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GMCL1 MUTATED        2      0      1      1
  GMCL1 WILD-TYPE     49     20     18     29
D35V3, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             0              20
  CLUS_3             1              18
  CLUS_4             1              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GMCL1 MUTATED        1      0      2
  GMCL1 WILD-TYPE     15     23     16
D35V4, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0              23
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GMCL1 MUTATED        0      1      0      3      0
  GMCL1 WILD-TYPE     30     18     22     20      3
D35V5, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             0              30
  CLUS_2             1              18
  CLUS_3             0              22
  CLUS_4             3              20
  CLUS_5             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GMCL1 MUTATED        0      2      0      1      1      0
  GMCL1 WILD-TYPE     19     14     14     13     22     11
D35V6, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             2              14
  CLUS_3             0              14
  CLUS_4             1              13
  CLUS_5             1              22
  CLUS_6             0              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GMCL1 MUTATED        1      0      2      1      0
  GMCL1 WILD-TYPE     15     13     20     12     57
D35V7, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0              13
  CLUS_3             2              20
  CLUS_4             1              12
  CLUS_5             0              57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GMCL1 MUTATED        1      1      1      0      0      1      0
  GMCL1 WILD-TYPE     10     22      7     12     32     17     17
D35V8, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              22
  CLUS_3             1               7
  CLUS_4             0              12
  CLUS_5             0              32
  CLUS_6             1              17
  CLUS_7             0              17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GMCL1 MUTATED        0      2      1      0      1
  GMCL1 WILD-TYPE     13     26     13      8     54
D35V9, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2              26
  CLUS_3             1              13
  CLUS_4             0               8
  CLUS_5             1              54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GMCL1 MUTATED        1      2      1
  GMCL1 WILD-TYPE     19     42     53
D35V10, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             2              42
  CLUS_3             1              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GMCL1 MUTATED        0      1      1      1
  GMCL1 WILD-TYPE      8      6     12      7
D35V11, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1               6
  CLUS_3             1              12
  CLUS_4             1               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
  GMCL1 MUTATED        0      1      1      0      1
  GMCL1 WILD-TYPE      8      8     11      5      1
D35V12, multiclass
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1               8
  CLUS_3             1              11
  CLUS_4             0               5
  CLUS_5             1               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = CIR1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CIR1 MUTATED        0      0      0
  CIR1 WILD-TYPE     25     21     19
D36V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CIR1 MUTATED        0      0      0      0      0      0      0      0
  CIR1 WILD-TYPE      6     13     12      9      6      9      8      2
D36V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CIR1 MUTATED        1      1      0      1
  CIR1 WILD-TYPE     50     19     19     29
D36V3, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            1             50
  CLUS_2            1             19
  CLUS_3            0             19
  CLUS_4            1             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CIR1 MUTATED        2      1      0
  CIR1 WILD-TYPE     14     22     18
D36V4, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             22
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CIR1 MUTATED        1      0      1      0      0
  CIR1 WILD-TYPE     29     19     21     23      3
D36V5, multiclass
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-CL-5918     TCGA-DC-5869 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DF     TCGA-DY-A1DG 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CIR1 MUTATED        0      0      0      1      0      1
  CIR1 WILD-TYPE     19     16     14     13     23     10
D36V6, multiclass
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             2             95 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3731 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-CL-5918     TCGA-DC-5869 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DF     TCGA-DY-A1DG 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CIR1 MUTATED        0      1      1      1      0
  CIR1 WILD-TYPE     16     12     21     12     57
D36V7, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            1             21
  CLUS_4            1             12
  CLUS_5            0             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CIR1 MUTATED        1      1      0      1      0      0      0
  CIR1 WILD-TYPE     10     22      8     11     32     18     17
D36V8, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            1             22
  CLUS_3            0              8
  CLUS_4            1             11
  CLUS_5            0             32
  CLUS_6            0             18
  CLUS_7            0             17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CIR1 MUTATED        1      1      1      0      0
  CIR1 WILD-TYPE     12     27     13      8     55
D36V9, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            1             27
  CLUS_3            1             13
  CLUS_4            0              8
  CLUS_5            0             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CIR1 MUTATED        1      2      0
  CIR1 WILD-TYPE     19     42     54
D36V10, multiclass
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2             42
  CLUS_3            0             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CIR1 MUTATED        1      0      0      1
  CIR1 WILD-TYPE      7      7     13      7
D36V11, multiclass
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5869 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DG     TCGA-DY-A1H8 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CIR1 MUTATED        0      1      0      1      0
  CIR1 WILD-TYPE      8      8     12      4      2
D36V12, multiclass
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             2             34 
    TCGA-AF-2687     TCGA-AF-4110     TCGA-AF-6655     TCGA-AF-6672 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AH-6544     TCGA-AH-6547 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6624     TCGA-CL-5918     TCGA-DC-5869 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6681     TCGA-DC-6682 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A1DC     TCGA-DY-A1DG     TCGA-DY-A1H8 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-F5-6464     TCGA-F5-6465 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 

Clustering(37) Variable = AGL MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  AGL MUTATED        2      0      0
  AGL WILD-TYPE     23     21     19
D37V1, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            2            63 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3574    TCGA-AG-3575    TCGA-AG-3578    TCGA-AG-3580    TCGA-AG-3581 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3584    TCGA-AG-3586    TCGA-AG-3587 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3593    TCGA-AG-3594    TCGA-AG-3598    TCGA-AG-3599    TCGA-AG-3600 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3601    TCGA-AG-3602    TCGA-AG-3605    TCGA-AG-3608    TCGA-AG-3609 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3611    TCGA-AG-3612    TCGA-AG-3726    TCGA-AG-3727    TCGA-AG-3878 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3881    TCGA-AG-3882    TCGA-AG-3883    TCGA-AG-3887    TCGA-AG-3890 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3892    TCGA-AG-3893    TCGA-AG-3894    TCGA-AG-3896    TCGA-AG-3898 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3901    TCGA-AG-3902    TCGA-AG-3909    TCGA-AG-3999    TCGA-AG-4001 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-4005    TCGA-AG-4007    TCGA-AG-4008    TCGA-AG-4015    TCGA-AG-A008 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A00C    TCGA-AG-A00H    TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A015    TCGA-AG-A016    TCGA-AG-A01L    TCGA-AG-A025    TCGA-AG-A026 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A02G    TCGA-AG-A02X    TCGA-AG-A032 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  AGL MUTATED        0      1      1      0      0      0      0      0
  AGL WILD-TYPE      6     12     11      9      6      9      8      2
D37V2, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            2            63 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3574    TCGA-AG-3575    TCGA-AG-3578    TCGA-AG-3580    TCGA-AG-3581 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3584    TCGA-AG-3586    TCGA-AG-3587 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3593    TCGA-AG-3594    TCGA-AG-3598    TCGA-AG-3599    TCGA-AG-3600 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3601    TCGA-AG-3602    TCGA-AG-3605    TCGA-AG-3608    TCGA-AG-3609 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3611    TCGA-AG-3612    TCGA-AG-3726    TCGA-AG-3727    TCGA-AG-3878 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3881    TCGA-AG-3882    TCGA-AG-3883    TCGA-AG-3887    TCGA-AG-3890 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3892    TCGA-AG-3893    TCGA-AG-3894    TCGA-AG-3896    TCGA-AG-3898 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-3901    TCGA-AG-3902    TCGA-AG-3909    TCGA-AG-3999    TCGA-AG-4001 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-4005    TCGA-AG-4007    TCGA-AG-4008    TCGA-AG-4015    TCGA-AG-A008 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A00C    TCGA-AG-A00H    TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A015    TCGA-AG-A016    TCGA-AG-A01L    TCGA-AG-A025    TCGA-AG-A026 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A02G    TCGA-AG-A02X    TCGA-AG-A032 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AGL MUTATED        3      1      0      0
  AGL WILD-TYPE     48     19     19     30
D37V3, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           3            48
  CLUS_2           1            19
  CLUS_3           0            19
  CLUS_4           0            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  AGL MUTATED        0      1      1
  AGL WILD-TYPE     16     22     17
D37V4, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            2            55 
   TCGA-AF-2687    TCGA-AF-2693    TCGA-AF-4110    TCGA-AF-6136    TCGA-AF-6655 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AF-6672    TCGA-AG-3732    TCGA-AG-3742    TCGA-AG-A01W    TCGA-AG-A01Y 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AG-A020    TCGA-AG-A026    TCGA-AG-A02N    TCGA-AG-A036    TCGA-AH-6544 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AH-6547    TCGA-AH-6549    TCGA-AH-6643    TCGA-AH-6644    TCGA-CI-6619 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-CI-6620    TCGA-CI-6621    TCGA-CI-6622    TCGA-CI-6624    TCGA-CL-5917 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-CL-5918    TCGA-DC-5337    TCGA-DC-5869    TCGA-DC-6155    TCGA-DC-6157 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-6158    TCGA-DC-6160    TCGA-DC-6681    TCGA-DC-6682    TCGA-DC-6683 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DT-5265    TCGA-DY-A0XA    TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DF 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DY-A1DG    TCGA-DY-A1H8    TCGA-EF-5830    TCGA-EI-6506    TCGA-EI-6508 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-EI-6510    TCGA-F5-6464    TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-F5-6811    TCGA-F5-6812    TCGA-F5-6813    TCGA-G5-6235    TCGA-G5-6641 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AGL MUTATED        0      0      2      2      0
  AGL WILD-TYPE     30     19     20     21      3
D37V5, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           0            30
  CLUS_2           0            19
  CLUS_3           2            20
  CLUS_4           2            21
  CLUS_5           0             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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AGL MUTATED        1      0      1      0      1      1
  AGL WILD-TYPE     18     16     13     14     22     10
D37V6, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           1            18
  CLUS_2           0            16
  CLUS_3           1            13
  CLUS_4           0            14
  CLUS_5           1            22
  CLUS_6           1            10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AGL MUTATED        1      0      2      0      1
  AGL WILD-TYPE     15     13     20     13     56
D37V7, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           1            15
  CLUS_2           0            13
  CLUS_3           2            20
  CLUS_4           0            13
  CLUS_5           1            56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AGL MUTATED        0      1      1      0      1      1      0
  AGL WILD-TYPE     11     22      7     12     31     17     17
D37V8, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           0            11
  CLUS_2           1            22
  CLUS_3           1             7
  CLUS_4           0            12
  CLUS_5           1            31
  CLUS_6           1            17
  CLUS_7           0            17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AGL MUTATED        0      1      0      1      2
  AGL WILD-TYPE     13     27     14      7     53
D37V9, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           0            13
  CLUS_2           1            27
  CLUS_3           0            14
  CLUS_4           1             7
  CLUS_5           2            53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  AGL MUTATED        1      1      2
  AGL WILD-TYPE     19     43     52
D37V10, multiclass
        clus
vv       AGL MUTATED AGL WILD-TYPE
  CLUS_1           1            19
  CLUS_2           1            43
  CLUS_3           2            52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AGL MUTATED        1      0      0      1
  AGL WILD-TYPE      7      7     13      7
D37V11, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            2            34 
   TCGA-AF-2687    TCGA-AF-4110    TCGA-AF-6655    TCGA-AF-6672    TCGA-AG-3732 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549    TCGA-AH-6643    TCGA-CI-6619 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-CI-6620    TCGA-CI-6621    TCGA-CI-6624    TCGA-CL-5918    TCGA-DC-5337 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-5869    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6681    TCGA-DC-6682 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-6683    TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DG    TCGA-DY-A1H8 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-EI-6506    TCGA-F5-6464    TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-F5-6811    TCGA-F5-6812    TCGA-G5-6235    TCGA-G5-6641 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AGL MUTATED        1      0      1      0      0
  AGL WILD-TYPE      7      9     11      5      2
D37V12, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            2            34 
   TCGA-AF-2687    TCGA-AF-4110    TCGA-AF-6655    TCGA-AF-6672    TCGA-AG-3732 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549    TCGA-AH-6643    TCGA-CI-6619 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-CI-6620    TCGA-CI-6621    TCGA-CI-6624    TCGA-CL-5918    TCGA-DC-5337 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-5869    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6681    TCGA-DC-6682 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-6683    TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DG    TCGA-DY-A1H8 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-EI-6506    TCGA-F5-6464    TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-F5-6811    TCGA-F5-6812    TCGA-G5-6235    TCGA-G5-6641 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 

Clustering(38) Variable = FAM123B MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM123B MUTATED        2      1      2
  FAM123B WILD-TYPE     23     20     17
D38V1, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                23
  CLUS_2               1                20
  CLUS_3               2                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FAM123B MUTATED        0      1      1      0      2      0      1      0
  FAM123B WILD-TYPE      6     12     11      9      4      9      7      2
D38V2, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                12
  CLUS_3               1                11
  CLUS_4               0                 9
  CLUS_5               2                 4
  CLUS_6               0                 9
  CLUS_7               1                 7
  CLUS_8               0                 2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM123B MUTATED        3      3      0      4
  FAM123B WILD-TYPE     48     17     19     26
D38V3, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               3                48
  CLUS_2               3                17
  CLUS_3               0                19
  CLUS_4               4                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM123B MUTATED        1      1      3
  FAM123B WILD-TYPE     15     22     15
D38V4, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                22
  CLUS_3               3                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM123B MUTATED        4      2      0      3      0
  FAM123B WILD-TYPE     26     17     22     20      3
D38V5, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               4                26
  CLUS_2               2                17
  CLUS_3               0                22
  CLUS_4               3                20
  CLUS_5               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAM123B MUTATED        1      0      1      1      4      2
  FAM123B WILD-TYPE     18     16     13     13     19      9
D38V6, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                16
  CLUS_3               1                13
  CLUS_4               1                13
  CLUS_5               4                19
  CLUS_6               2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM123B MUTATED        2      0      3      1      4
  FAM123B WILD-TYPE     14     13     19     12     53
D38V7, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                13
  CLUS_3               3                19
  CLUS_4               1                12
  CLUS_5               4                53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FAM123B MUTATED        2      1      1      0      1      3      2
  FAM123B WILD-TYPE      9     22      7     12     31     15     15
D38V8, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                22
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               1                31
  CLUS_6               3                15
  CLUS_7               2                15
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM123B MUTATED        2      2      0      0      6
  FAM123B WILD-TYPE     11     26     14      8     49
D38V9, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                26
  CLUS_3               0                14
  CLUS_4               0                 8
  CLUS_5               6                49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM123B MUTATED        1      3      6
  FAM123B WILD-TYPE     19     41     48
D38V10, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                19
  CLUS_2               3                41
  CLUS_3               6                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM123B MUTATED        0      0      1      1
  FAM123B WILD-TYPE      8      7     12      7
D38V11, multiclass
[1] "Remove cluster labels:" "FAM123B MUTATED"       
clus
  FAM123B MUTATED FAM123B WILD-TYPE 
                2                34 
       TCGA-AF-2687        TCGA-AF-4110        TCGA-AF-6655        TCGA-AF-6672 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AH-6547        TCGA-AH-6549 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AH-6643        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6681        TCGA-DC-6682 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A1DC        TCGA-DY-A1DG        TCGA-DY-A1H8 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-EI-6506        TCGA-EI-6507        TCGA-F5-6464        TCGA-F5-6465 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM123B MUTATED        0      1      1      0      0
  FAM123B WILD-TYPE      8      8     11      5      2
D38V12, multiclass
[1] "Remove cluster labels:" "FAM123B MUTATED"       
clus
  FAM123B MUTATED FAM123B WILD-TYPE 
                2                34 
       TCGA-AF-2687        TCGA-AF-4110        TCGA-AF-6655        TCGA-AF-6672 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AH-6547        TCGA-AH-6549 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AH-6643        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6681        TCGA-DC-6682 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A1DC        TCGA-DY-A1DG        TCGA-DY-A1H8 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-EI-6506        TCGA-EI-6507        TCGA-F5-6464        TCGA-F5-6465 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 

Clustering(39) Variable = VANGL1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  VANGL1 MUTATED        0      0      0
  VANGL1 WILD-TYPE     25     21     19
D39V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  VANGL1 MUTATED        0      0      0      0      0      0      0      0
  VANGL1 WILD-TYPE      6     13     12      9      6      9      8      2
D39V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VANGL1 MUTATED        3      0      0      0
  VANGL1 WILD-TYPE     48     20     19     30
D39V3, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              3               48
  CLUS_2              0               20
  CLUS_3              0               19
  CLUS_4              0               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  VANGL1 MUTATED        1      0      1
  VANGL1 WILD-TYPE     15     23     17
D39V4, multiclass
[1] "Remove cluster labels:" "VANGL1 MUTATED"        
clus
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               2               55 
      TCGA-AF-2687       TCGA-AF-2693       TCGA-AF-4110       TCGA-AF-6136 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3732       TCGA-AG-3742 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A026 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A036       TCGA-AH-6544       TCGA-AH-6547 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CI-6620       TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CL-5917       TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6155       TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6681       TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VANGL1 MUTATED        1      0      1      1      0
  VANGL1 WILD-TYPE     29     19     21     22      3
D39V5, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              1               29
  CLUS_2              0               19
  CLUS_3              1               21
  CLUS_4              1               22
  CLUS_5              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  VANGL1 MUTATED        1      1      0      0      1      0
  VANGL1 WILD-TYPE     18     15     14     14     22     11
D39V6, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              1               18
  CLUS_2              1               15
  CLUS_3              0               14
  CLUS_4              0               14
  CLUS_5              1               22
  CLUS_6              0               11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VANGL1 MUTATED        2      0      1      0      0
  VANGL1 WILD-TYPE     14     13     21     13     57
D39V7, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              0               13
  CLUS_3              1               21
  CLUS_4              0               13
  CLUS_5              0               57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  VANGL1 MUTATED        0      2      0      1      0      0      0
  VANGL1 WILD-TYPE     11     21      8     11     32     18     17
D39V8, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              2               21
  CLUS_3              0                8
  CLUS_4              1               11
  CLUS_5              0               32
  CLUS_6              0               18
  CLUS_7              0               17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VANGL1 MUTATED        0      1      2      0      0
  VANGL1 WILD-TYPE     13     27     12      8     55
D39V9, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              1               27
  CLUS_3              2               12
  CLUS_4              0                8
  CLUS_5              0               55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  VANGL1 MUTATED        1      2      0
  VANGL1 WILD-TYPE     19     42     54
D39V10, multiclass
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              2               42
  CLUS_3              0               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VANGL1 MUTATED        1      1      0      0
  VANGL1 WILD-TYPE      7      6     13      8
D39V11, multiclass
[1] "Remove cluster labels:" "VANGL1 MUTATED"        
clus
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               2               34 
      TCGA-AF-2687       TCGA-AF-4110       TCGA-AF-6655       TCGA-AF-6672 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AH-6643       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CI-6624       TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6681       TCGA-DC-6682 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DG 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EI-6506       TCGA-EI-6507       TCGA-F5-6464 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  VANGL1 MUTATED        1      0      0      0      1
  VANGL1 WILD-TYPE      7      9     12      5      1
D39V12, multiclass
[1] "Remove cluster labels:" "VANGL1 MUTATED"        
clus
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               2               34 
      TCGA-AF-2687       TCGA-AF-4110       TCGA-AF-6655       TCGA-AF-6672 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AH-6643       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CI-6624       TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6681       TCGA-DC-6682 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DG 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EI-6506       TCGA-EI-6507       TCGA-F5-6464 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 

Clustering(40) Variable = CREBBP MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CREBBP MUTATED        1      0      0
  CREBBP WILD-TYPE     24     21     19
D40V1, multiclass
[1] "Remove cluster labels:" "CREBBP MUTATED"        
clus
  CREBBP MUTATED CREBBP WILD-TYPE 
               1               64 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3878       TCGA-AG-3881       TCGA-AG-3882 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887       TCGA-AG-3890 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3909 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005       TCGA-AG-4007 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A008       TCGA-AG-A00C 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A025 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02X       TCGA-AG-A032 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CREBBP MUTATED        0      0      1      0      0      0      0      0
  CREBBP WILD-TYPE      6     13     11      9      6      9      8      2
D40V2, multiclass
[1] "Remove cluster labels:" "CREBBP MUTATED"        
clus
  CREBBP MUTATED CREBBP WILD-TYPE 
               1               64 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3878       TCGA-AG-3881       TCGA-AG-3882 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887       TCGA-AG-3890 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3909 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005       TCGA-AG-4007 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A008       TCGA-AG-A00C 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A025 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02X       TCGA-AG-A032 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CREBBP MUTATED        6      1      0      2
  CREBBP WILD-TYPE     45     19     19     28
D40V3, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              6               45
  CLUS_2              1               19
  CLUS_3              0               19
  CLUS_4              2               28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CREBBP MUTATED        1      3      5
  CREBBP WILD-TYPE     15     20     13
D40V4, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              1               15
  CLUS_2              3               20
  CLUS_3              5               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CREBBP MUTATED        1      2      1      4      1
  CREBBP WILD-TYPE     29     17     21     19      2
D40V5, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              1               29
  CLUS_2              2               17
  CLUS_3              1               21
  CLUS_4              4               19
  CLUS_5              1                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CREBBP MUTATED        1      0      1      1      4      2
  CREBBP WILD-TYPE     18     16     13     13     19      9
D40V6, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              1               18
  CLUS_2              0               16
  CLUS_3              1               13
  CLUS_4              1               13
  CLUS_5              4               19
  CLUS_6              2                9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CREBBP MUTATED        2      0      8      0      0
  CREBBP WILD-TYPE     14     13     14     13     57
D40V7, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              2               14
  CLUS_2              0               13
  CLUS_3              8               14
  CLUS_4              0               13
  CLUS_5              0               57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CREBBP MUTATED        1      4      2      1      0      2      0
  CREBBP WILD-TYPE     10     19      6     11     32     16     17
D40V8, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              1               10
  CLUS_2              4               19
  CLUS_3              2                6
  CLUS_4              1               11
  CLUS_5              0               32
  CLUS_6              2               16
  CLUS_7              0               17
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CREBBP MUTATED        1      4      1      2      2
  CREBBP WILD-TYPE     12     24     13      6     53
D40V9, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              1               12
  CLUS_2              4               24
  CLUS_3              1               13
  CLUS_4              2                6
  CLUS_5              2               53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CREBBP MUTATED        3      5      2
  CREBBP WILD-TYPE     17     39     52
D40V10, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              3               17
  CLUS_2              5               39
  CLUS_3              2               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CREBBP MUTATED        2      1      2      2
  CREBBP WILD-TYPE      6      6     11      6
D40V11, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              2                6
  CLUS_2              1                6
  CLUS_3              2               11
  CLUS_4              2                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
  CREBBP MUTATED        3      1      3      0      0
  CREBBP WILD-TYPE      5      8      9      5      2
D40V12, multiclass
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  CLUS_1              3                5
  CLUS_2              1                8
  CLUS_3              3                9
  CLUS_4              0                5
  CLUS_5              0                2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
