[1] "ofn"        "-oTCESC-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/CESC-TP/22541064/CESC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/22574677/transformed.cor.cli.txt"

nPatients in clinical file=307, in cluster file=194, common to both=194
[1]  20 194
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            22            172 
  MLL2 MUTATED MLL2 WILD-TYPE 
            22            172 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            165 
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            165 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
[1] "FAT2 MUTATION ANALYSIS"
[1] 3
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              185 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              185 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
[1] "C3ORF70 MUTATION ANALYSIS"
[1] 3
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                4               190 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                4               190 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
[1] "IFNGR1 MUTATION ANALYSIS"
[1] 3
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 194 columns.

Variable 1:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=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 194 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        0      2      4      7      2
  PTEN WILD-TYPE      6     70     27     37     36
D1V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              6
  CLUS_2            2             70
  CLUS_3            4             27
  CLUS_4            7             37
  CLUS_5            2             36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      5      7
  PTEN WILD-TYPE     47     68     64
D1V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             47
  CLUS_2            5             68
  CLUS_3            7             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        2      2      5
  PTEN WILD-TYPE     43     31     50
D1V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             43
  CLUS_2            2             31
  CLUS_3            5             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 CLUS_5
  PTEN MUTATED        2      2      4      0      1
  PTEN WILD-TYPE     25     38     28     18     15
D1V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             25
  CLUS_2            2             38
  CLUS_3            4             28
  CLUS_4            0             18
  CLUS_5            1             15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        5      8      2      0
  PTEN WILD-TYPE     34     56     47     41
D1V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             34
  CLUS_2            8             56
  CLUS_3            2             47
  CLUS_4            0             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        6      9      0
  PTEN WILD-TYPE     43    111     24
D1V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             43
  CLUS_2            9            111
  CLUS_3            0             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
  PTEN MUTATED        8      3      4
  PTEN WILD-TYPE     53     52     74
D1V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             53
  CLUS_2            3             52
  CLUS_3            4             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        4      6      3      2      0
  PTEN WILD-TYPE     37     44     55     13     30
D1V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             37
  CLUS_2            6             44
  CLUS_3            3             55
  CLUS_4            2             13
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      4      4
  PTEN WILD-TYPE     49     56     64
D1V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             49
  CLUS_2            4             56
  CLUS_3            4             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        4      6      5      0      0
  PTEN WILD-TYPE     15     56     54     22     22
D1V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             15
  CLUS_2            6             56
  CLUS_3            5             54
  CLUS_4            0             22
  CLUS_5            0             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = HLA-B MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-B MUTATED        1      5      2      2      1
  HLA-B WILD-TYPE      5     67     29     42     37
D2V1, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1               5
  CLUS_2             5              67
  CLUS_3             2              29
  CLUS_4             2              42
  CLUS_5             1              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        1      6      4
  HLA-B WILD-TYPE     49     67     67
D2V2, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              49
  CLUS_2             6              67
  CLUS_3             4              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        4      2      3
  HLA-B WILD-TYPE     41     31     52
D2V3, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             4              41
  CLUS_2             2              31
  CLUS_3             3              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 CLUS_5
  HLA-B MUTATED        3      1      4      1      0
  HLA-B WILD-TYPE     24     39     28     17     16
D2V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              24
  CLUS_2             1              39
  CLUS_3             4              28
  CLUS_4             1              17
  CLUS_5             0              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-B MUTATED        2      4      1      4
  HLA-B WILD-TYPE     37     60     48     37
D2V5, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2              37
  CLUS_2             4              60
  CLUS_3             1              48
  CLUS_4             4              37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        0     10      1
  HLA-B WILD-TYPE     49    110     23
D2V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              49
  CLUS_2            10             110
  CLUS_3             1              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        1      1      9
  HLA-B WILD-TYPE     60     54     69
D2V7, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              60
  CLUS_2             1              54
  CLUS_3             9              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-B MUTATED        0      5      2      1      3
  HLA-B WILD-TYPE     41     45     56     14     27
D2V8, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              41
  CLUS_2             5              45
  CLUS_3             2              56
  CLUS_4             1              14
  CLUS_5             3              27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        2      0      8
  HLA-B WILD-TYPE     54     60     60
D2V9, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2              54
  CLUS_2             0              60
  CLUS_3             8              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-B MUTATED        0      1      8      1      0
  HLA-B WILD-TYPE     19     61     51     21     22
D2V10, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              19
  CLUS_2             1              61
  CLUS_3             8              51
  CLUS_4             1              21
  CLUS_5             0              22
[1] 5 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 = HLA-A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-A MUTATED        0      4      2      6      3
  HLA-A WILD-TYPE      6     68     29     38     35
D3V1, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             0               6
  CLUS_2             4              68
  CLUS_3             2              29
  CLUS_4             6              38
  CLUS_5             3              35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        0      6     10
  HLA-A WILD-TYPE     50     67     61
D3V2, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             0              50
  CLUS_2             6              67
  CLUS_3            10              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        5      3      2
  HLA-A WILD-TYPE     40     30     53
D3V3, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             5              40
  CLUS_2             3              30
  CLUS_3             2              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 CLUS_5
  HLA-A MUTATED        5      0      4      1      0
  HLA-A WILD-TYPE     22     40     28     17     16
D3V4, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             5              22
  CLUS_2             0              40
  CLUS_3             4              28
  CLUS_4             1              17
  CLUS_5             0              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-A MUTATED        2      6      0      8
  HLA-A WILD-TYPE     37     58     49     33
D3V5, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              37
  CLUS_2             6              58
  CLUS_3             0              49
  CLUS_4             8              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        1     11      4
  HLA-A WILD-TYPE     48    109     20
D3V6, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              48
  CLUS_2            11             109
  CLUS_3             4              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
  HLA-A MUTATED        2      4     10
  HLA-A WILD-TYPE     59     51     68
D3V7, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              59
  CLUS_2             4              51
  CLUS_3            10              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-A MUTATED        0      4      3      3      6
  HLA-A WILD-TYPE     41     46     55     12     24
D3V8, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             0              41
  CLUS_2             4              46
  CLUS_3             3              55
  CLUS_4             3              12
  CLUS_5             6              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        2      4      8
  HLA-A WILD-TYPE     54     56     60
D3V9, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             2              54
  CLUS_2             4              56
  CLUS_3             8              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-A MUTATED        1      4      6      3      0
  HLA-A WILD-TYPE     18     58     53     19     22
D3V10, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              18
  CLUS_2             4              58
  CLUS_3             6              53
  CLUS_4             3              19
  CLUS_5             0              22
[1] 5 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 = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        1      1      1      7      1
  KRAS WILD-TYPE      5     71     30     37     37
D4V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              5
  CLUS_2            1             71
  CLUS_3            1             30
  CLUS_4            7             37
  CLUS_5            1             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        8      0      3
  KRAS WILD-TYPE     42     73     68
D4V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8             42
  CLUS_2            0             73
  CLUS_3            3             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      2      3
  KRAS WILD-TYPE     42     31     52
D4V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             42
  CLUS_2            2             31
  CLUS_3            3             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 CLUS_5
  KRAS MUTATED        2      2      1      0      3
  KRAS WILD-TYPE     25     38     31     18     13
D4V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2             25
  CLUS_2            2             38
  CLUS_3            1             31
  CLUS_4            0             18
  CLUS_5            3             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      0      6      1
  KRAS WILD-TYPE     35     64     43     40
D4V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             35
  CLUS_2            0             64
  CLUS_3            6             43
  CLUS_4            1             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8      2      1
  KRAS WILD-TYPE     41    118     23
D4V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8             41
  CLUS_2            2            118
  CLUS_3            1             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        7      4      0
  KRAS WILD-TYPE     54     51     78
D4V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7             54
  CLUS_2            4             51
  CLUS_3            0             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      0      2      1      0
  KRAS WILD-TYPE     33     50     56     14     30
D4V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8             33
  CLUS_2            0             50
  CLUS_3            2             56
  CLUS_4            1             14
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        6      5      0
  KRAS WILD-TYPE     50     55     68
D4V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             50
  CLUS_2            5             55
  CLUS_3            0             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      2      0      0      5
  KRAS WILD-TYPE     15     60     59     22     17
D4V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             15
  CLUS_2            2             60
  CLUS_3            0             59
  CLUS_4            0             22
  CLUS_5            5             17
[1] 5 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 = MLL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED        0      5      5      7      5
  MLL2 WILD-TYPE      6     67     26     37     33
D5V1, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            5             67
  CLUS_3            5             26
  CLUS_4            7             37
  CLUS_5            5             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6     10      6
  MLL2 WILD-TYPE     44     63     65
D5V2, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             44
  CLUS_2           10             63
  CLUS_3            6             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        4      6      5
  MLL2 WILD-TYPE     41     27     50
D5V3, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             41
  CLUS_2            6             27
  CLUS_3            5             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 CLUS_5
  MLL2 MUTATED        2      2      7      2      2
  MLL2 WILD-TYPE     25     38     25     16     14
D5V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2             25
  CLUS_2            2             38
  CLUS_3            7             25
  CLUS_4            2             16
  CLUS_5            2             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        5     10      4      3
  MLL2 WILD-TYPE     34     54     45     38
D5V5, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             34
  CLUS_2           10             54
  CLUS_3            4             45
  CLUS_4            3             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        4     18      0
  MLL2 WILD-TYPE     45    102     24
D5V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             45
  CLUS_2           18            102
  CLUS_3            0             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
  MLL2 MUTATED        8      7      7
  MLL2 WILD-TYPE     53     48     71
D5V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            8             53
  CLUS_2            7             48
  CLUS_3            7             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED        3      8      9      0      2
  MLL2 WILD-TYPE     38     42     49     15     28
D5V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            3             38
  CLUS_2            8             42
  CLUS_3            9             49
  CLUS_4            0             15
  CLUS_5            2             28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6      9      7
  MLL2 WILD-TYPE     50     51     61
D5V9, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             50
  CLUS_2            9             51
  CLUS_3            7             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED        1      7      9      2      3
  MLL2 WILD-TYPE     18     55     50     20     19
D5V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            7             55
  CLUS_3            9             50
  CLUS_4            2             20
  CLUS_5            3             19
[1] 5 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 = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        0      5      2      5      6
  FBXW7 WILD-TYPE      6     67     29     39     32
D6V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             5              67
  CLUS_3             2              29
  CLUS_4             5              39
  CLUS_5             6              32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        5      8      6
  FBXW7 WILD-TYPE     45     65     65
D6V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5              45
  CLUS_2             8              65
  CLUS_3             6              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        6      5      6
  FBXW7 WILD-TYPE     39     28     49
D6V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              39
  CLUS_2             5              28
  CLUS_3             6              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 CLUS_5
  FBXW7 MUTATED        3      5      4      2      3
  FBXW7 WILD-TYPE     24     35     28     16     13
D6V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3              24
  CLUS_2             5              35
  CLUS_3             4              28
  CLUS_4             2              16
  CLUS_5             3              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        1      9      5      4
  FBXW7 WILD-TYPE     38     55     44     37
D6V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1              38
  CLUS_2             9              55
  CLUS_3             5              44
  CLUS_4             4              37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        6     12      1
  FBXW7 WILD-TYPE     43    108     23
D6V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              43
  CLUS_2            12             108
  CLUS_3             1              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        7      2     10
  FBXW7 WILD-TYPE     54     53     68
D6V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             7              54
  CLUS_2             2              53
  CLUS_3            10              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        4      8      3      1      3
  FBXW7 WILD-TYPE     37     42     55     14     27
D6V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              37
  CLUS_2             8              42
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             3              27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        8      4      7
  FBXW7 WILD-TYPE     48     56     61
D6V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             8              48
  CLUS_2             4              56
  CLUS_3             7              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        4      5      7      2      1
  FBXW7 WILD-TYPE     15     57     52     20     21
D6V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              15
  CLUS_2             5              57
  CLUS_3             7              52
  CLUS_4             2              20
  CLUS_5             1              21
[1] 5 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 = EP300 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        1      6      7      2      4
  EP300 WILD-TYPE      5     66     24     42     34
D7V1, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             6              66
  CLUS_3             7              24
  CLUS_4             2              42
  CLUS_5             4              34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        4     12      5
  EP300 WILD-TYPE     46     61     66
D7V2, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             4              46
  CLUS_2            12              61
  CLUS_3             5              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        2      4      9
  EP300 WILD-TYPE     43     29     46
D7V3, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              43
  CLUS_2             4              29
  CLUS_3             9              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        2      5      8      0      0
  EP300 WILD-TYPE     25     35     24     18     16
D7V4, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              25
  CLUS_2             5              35
  CLUS_3             8              24
  CLUS_4             0              18
  CLUS_5             0              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        6     10      2      3
  EP300 WILD-TYPE     33     54     47     38
D7V5, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             6              33
  CLUS_2            10              54
  CLUS_3             2              47
  CLUS_4             3              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        2     18      1
  EP300 WILD-TYPE     47    102     23
D7V6, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              47
  CLUS_2            18             102
  CLUS_3             1              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        7      3     11
  EP300 WILD-TYPE     54     52     67
D7V7, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             7              54
  CLUS_2             3              52
  CLUS_3            11              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        1      9     10      1      0
  EP300 WILD-TYPE     40     41     48     14     30
D7V8, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             9              41
  CLUS_3            10              48
  CLUS_4             1              14
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        5      6      7
  EP300 WILD-TYPE     51     54     61
D7V9, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              51
  CLUS_2             6              54
  CLUS_3             7              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        2      6      9      1      0
  EP300 WILD-TYPE     17     56     50     21     22
D7V10, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             6              56
  CLUS_3             9              50
  CLUS_4             1              21
  CLUS_5             0              22
[1] 5 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 = MAPK1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAPK1 MUTATED        1      1      4      1      2
  MAPK1 WILD-TYPE      5     71     27     43     36
D8V1, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              71
  CLUS_3             4              27
  CLUS_4             1              43
  CLUS_5             2              36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        0      4      5
  MAPK1 WILD-TYPE     50     69     66
D8V2, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              50
  CLUS_2             4              69
  CLUS_3             5              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        3      0      4
  MAPK1 WILD-TYPE     42     33     51
D8V3, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              42
  CLUS_2             0              33
  CLUS_3             4              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 CLUS_5
  MAPK1 MUTATED        2      2      1      1      1
  MAPK1 WILD-TYPE     25     38     31     17     15
D8V4, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             2              25
  CLUS_2             2              38
  CLUS_3             1              31
  CLUS_4             1              17
  CLUS_5             1              15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAPK1 MUTATED        2      6      0      1
  MAPK1 WILD-TYPE     37     58     49     40
D8V5, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             2              37
  CLUS_2             6              58
  CLUS_3             0              49
  CLUS_4             1              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        0      9      0
  MAPK1 WILD-TYPE     49    111     24
D8V6, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              49
  CLUS_2             9             111
  CLUS_3             0              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
  MAPK1 MUTATED        0      5      4
  MAPK1 WILD-TYPE     61     50     74
D8V7, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              61
  CLUS_2             5              50
  CLUS_3             4              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAPK1 MUTATED        0      2      6      1      0
  MAPK1 WILD-TYPE     41     48     52     14     30
D8V8, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              48
  CLUS_3             6              52
  CLUS_4             1              14
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        0      6      3
  MAPK1 WILD-TYPE     56     54     65
D8V9, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             6              54
  CLUS_3             3              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAPK1 MUTATED        0      6      3      0      0
  MAPK1 WILD-TYPE     19     56     56     22     22
D8V10, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             6              56
  CLUS_3             3              56
  CLUS_4             0              22
  CLUS_5             0              22
[1] 5 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 = MLL3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL3 MUTATED        0      7      9      7      6
  MLL3 WILD-TYPE      6     65     22     37     32
D9V1, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            7             65
  CLUS_3            9             22
  CLUS_4            7             37
  CLUS_5            6             32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL3 MUTATED        5     17      7
  MLL3 WILD-TYPE     45     56     64
D9V2, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            5             45
  CLUS_2           17             56
  CLUS_3            7             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL3 MUTATED        4      6      8
  MLL3 WILD-TYPE     41     27     47
D9V3, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            4             41
  CLUS_2            6             27
  CLUS_3            8             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL3 MUTATED        3      4     10      0      1
  MLL3 WILD-TYPE     24     36     22     18     15
D9V4, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            3             24
  CLUS_2            4             36
  CLUS_3           10             22
  CLUS_4            0             18
  CLUS_5            1             15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL3 MUTATED        1     14      6      7
  MLL3 WILD-TYPE     38     50     43     34
D9V5, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            1             38
  CLUS_2           14             50
  CLUS_3            6             43
  CLUS_4            7             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL3 MUTATED        5     23      0
  MLL3 WILD-TYPE     44     97     24
D9V6, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            5             44
  CLUS_2           23             97
  CLUS_3            0             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
  MLL3 MUTATED        4     10     15
  MLL3 WILD-TYPE     57     45     63
D9V7, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            4             57
  CLUS_2           10             45
  CLUS_3           15             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL3 MUTATED        5      8     10      3      3
  MLL3 WILD-TYPE     36     42     48     12     27
D9V8, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            5             36
  CLUS_2            8             42
  CLUS_3           10             48
  CLUS_4            3             12
  CLUS_5            3             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL3 MUTATED        5     10     12
  MLL3 WILD-TYPE     51     50     56
D9V9, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            5             51
  CLUS_2           10             50
  CLUS_3           12             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL3 MUTATED        2      9     10      3      3
  MLL3 WILD-TYPE     17     53     49     19     19
D9V10, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            2             17
  CLUS_2            9             53
  CLUS_3           10             49
  CLUS_4            3             19
  CLUS_5            3             19
[1] 5 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 = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        0      2      2      9      1
  ARID1A WILD-TYPE      6     70     29     35     37
D10V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2               70
  CLUS_3              2               29
  CLUS_4              9               35
  CLUS_5              1               37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        7      2      5
  ARID1A WILD-TYPE     43     71     66
D10V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               43
  CLUS_2              2               71
  CLUS_3              5               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      3      5
  ARID1A WILD-TYPE     42     30     50
D10V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               42
  CLUS_2              3               30
  CLUS_3              5               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 CLUS_5
  ARID1A MUTATED        2      2      3      0      4
  ARID1A WILD-TYPE     25     38     29     18     12
D10V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               25
  CLUS_2              2               38
  CLUS_3              3               29
  CLUS_4              0               18
  CLUS_5              4               12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      2      5      2
  ARID1A WILD-TYPE     34     62     44     39
D10V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               34
  CLUS_2              2               62
  CLUS_3              5               44
  CLUS_4              2               39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       10      4      0
  ARID1A WILD-TYPE     39    116     24
D10V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               39
  CLUS_2              4              116
  CLUS_3              0               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
  ARID1A MUTATED        8      2      4
  ARID1A WILD-TYPE     53     53     74
D10V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              8               53
  CLUS_2              2               53
  CLUS_3              4               74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7      1      1      3      2
  ARID1A WILD-TYPE     34     49     57     12     28
D10V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               34
  CLUS_2              1               49
  CLUS_3              1               57
  CLUS_4              3               12
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        6      4      2
  ARID1A WILD-TYPE     50     56     66
D10V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               50
  CLUS_2              4               56
  CLUS_3              2               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5      1      3      1      2
  ARID1A WILD-TYPE     14     61     56     21     20
D10V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               14
  CLUS_2              1               61
  CLUS_3              3               56
  CLUS_4              1               21
  CLUS_5              2               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"

Clustering(11) Variable = NFE2L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED        0      4      2      2      4
  NFE2L2 WILD-TYPE      6     68     29     42     34
D11V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              4               68
  CLUS_3              2               29
  CLUS_4              2               42
  CLUS_5              4               34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0      8      4
  NFE2L2 WILD-TYPE     50     65     67
D11V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               50
  CLUS_2              8               65
  CLUS_3              4               67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        4      3      2
  NFE2L2 WILD-TYPE     41     30     53
D11V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               41
  CLUS_2              3               30
  CLUS_3              2               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 CLUS_5
  NFE2L2 MUTATED        1      0      4      3      1
  NFE2L2 WILD-TYPE     26     40     28     15     15
D11V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               26
  CLUS_2              0               40
  CLUS_3              4               28
  CLUS_4              3               15
  CLUS_5              1               15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED        3      5      1      3
  NFE2L2 WILD-TYPE     36     59     48     38
D11V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               36
  CLUS_2              5               59
  CLUS_3              1               48
  CLUS_4              3               38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0     11      1
  NFE2L2 WILD-TYPE     49    109     23
D11V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               49
  CLUS_2             11              109
  CLUS_3              1               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0      5      7
  NFE2L2 WILD-TYPE     61     50     71
D11V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               61
  CLUS_2              5               50
  CLUS_3              7               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED        0      1      6      3      2
  NFE2L2 WILD-TYPE     41     49     52     12     28
D11V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              1               49
  CLUS_3              6               52
  CLUS_4              3               12
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0      4      7
  NFE2L2 WILD-TYPE     56     56     61
D11V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               56
  CLUS_2              4               56
  CLUS_3              7               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED        0      5      4      2      0
  NFE2L2 WILD-TYPE     19     57     55     20     22
D11V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              5               57
  CLUS_3              4               55
  CLUS_4              2               20
  CLUS_5              0               22
[1] 5 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 = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        1     12     10     17     13
  PIK3CA WILD-TYPE      5     60     21     27     25
D12V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                5
  CLUS_2             12               60
  CLUS_3             10               21
  CLUS_4             17               27
  CLUS_5             13               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
  PIK3CA MUTATED       17     19     17
  PIK3CA WILD-TYPE     33     54     54
D12V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             17               33
  CLUS_2             19               54
  CLUS_3             17               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
  PIK3CA MUTATED       12      6     11
  PIK3CA WILD-TYPE     33     27     44
D12V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             12               33
  CLUS_2              6               27
  CLUS_3             11               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        9      8      4      3      5
  PIK3CA WILD-TYPE     18     32     28     15     11
D12V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               18
  CLUS_2              8               32
  CLUS_3              4               28
  CLUS_4              3               15
  CLUS_5              5               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11     19     16      6
  PIK3CA WILD-TYPE     28     45     33     35
D12V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               28
  CLUS_2             19               45
  CLUS_3             16               33
  CLUS_4              6               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       19     32      1
  PIK3CA WILD-TYPE     30     88     23
D12V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             19               30
  CLUS_2             32               88
  CLUS_3              1               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       21     12     20
  PIK3CA WILD-TYPE     40     43     58
D12V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             21               40
  CLUS_2             12               43
  CLUS_3             20               58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       14     17     13      4      5
  PIK3CA WILD-TYPE     27     33     45     11     25
D12V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             14               27
  CLUS_2             17               33
  CLUS_3             13               45
  CLUS_4              4               11
  CLUS_5              5               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
  PIK3CA MUTATED       20     14     15
  PIK3CA WILD-TYPE     36     46     53
D12V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             20               36
  CLUS_2             14               46
  CLUS_3             15               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 CLUS_5
  PIK3CA MUTATED        8     17     16      1      7
  PIK3CA WILD-TYPE     11     45     43     21     15
D12V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               11
  CLUS_2             17               45
  CLUS_3             16               43
  CLUS_4              1               21
  CLUS_5              7               15
[1] 5 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 = CASP8 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CASP8 MUTATED        0      4      3      2      0
  CASP8 WILD-TYPE      6     68     28     42     38
D13V1, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             4              68
  CLUS_3             3              28
  CLUS_4             2              42
  CLUS_5             0              38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        1      5      3
  CASP8 WILD-TYPE     49     68     68
D13V2, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              49
  CLUS_2             5              68
  CLUS_3             3              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        2      2      1
  CASP8 WILD-TYPE     43     31     54
D13V3, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             2              43
  CLUS_2             2              31
  CLUS_3             1              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 CLUS_5
  CASP8 MUTATED        1      0      2      2      0
  CASP8 WILD-TYPE     26     40     30     16     16
D13V4, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             0              40
  CLUS_3             2              30
  CLUS_4             2              16
  CLUS_5             0              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CASP8 MUTATED        0      5      1      3
  CASP8 WILD-TYPE     39     59     48     38
D13V5, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             5              59
  CLUS_3             1              48
  CLUS_4             3              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        1      6      2
  CASP8 WILD-TYPE     48    114     22
D13V6, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              48
  CLUS_2             6             114
  CLUS_3             2              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        3      2      4
  CASP8 WILD-TYPE     58     53     74
D13V7, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              58
  CLUS_2             2              53
  CLUS_3             4              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CASP8 MUTATED        0      3      3      1      2
  CASP8 WILD-TYPE     41     47     55     14     28
D13V8, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             3              47
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             2              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        2      1      5
  CASP8 WILD-TYPE     54     59     63
D13V9, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             2              54
  CLUS_2             1              59
  CLUS_3             5              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CASP8 MUTATED        1      2      4      1      0
  CASP8 WILD-TYPE     18     60     55     21     22
D13V10, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             2              60
  CLUS_3             4              55
  CLUS_4             1              21
  CLUS_5             0              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = FAT2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAT2 MUTATED        0      4      1      4      2
  FAT2 WILD-TYPE      6     68     30     40     36
D14V1, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            4             68
  CLUS_3            1             30
  CLUS_4            4             40
  CLUS_5            2             36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        1      7      3
  FAT2 WILD-TYPE     49     66     68
D14V2, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             49
  CLUS_2            7             66
  CLUS_3            3             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        3      2      3
  FAT2 WILD-TYPE     42     31     52
D14V3, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            3             42
  CLUS_2            2             31
  CLUS_3            3             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 CLUS_5
  FAT2 MUTATED        1      2      3      2      0
  FAT2 WILD-TYPE     26     38     29     16     16
D14V4, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             26
  CLUS_2            2             38
  CLUS_3            3             29
  CLUS_4            2             16
  CLUS_5            0             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAT2 MUTATED        1      5      1      4
  FAT2 WILD-TYPE     38     59     48     37
D14V5, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             38
  CLUS_2            5             59
  CLUS_3            1             48
  CLUS_4            4             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        1      9      1
  FAT2 WILD-TYPE     48    111     23
D14V6, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             48
  CLUS_2            9            111
  CLUS_3            1             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        2      3      6
  FAT2 WILD-TYPE     59     52     72
D14V7, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            2             59
  CLUS_2            3             52
  CLUS_3            6             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAT2 MUTATED        1      4      4      0      2
  FAT2 WILD-TYPE     40     46     54     15     28
D14V8, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            4             46
  CLUS_3            4             54
  CLUS_4            0             15
  CLUS_5            2             28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        3      2      6
  FAT2 WILD-TYPE     53     58     62
D14V9, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            3             53
  CLUS_2            2             58
  CLUS_3            6             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAT2 MUTATED        1      2      6      2      0
  FAT2 WILD-TYPE     18     60     53     20     22
D14V10, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             60
  CLUS_3            6             53
  CLUS_4            2             20
  CLUS_5            0             22
[1] 5 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 = ZNF750 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF750 MUTATED        0      2      0      5      2
  ZNF750 WILD-TYPE      6     70     31     39     36
D15V1, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2               70
  CLUS_3              0               31
  CLUS_4              5               39
  CLUS_5              2               36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        2      4      3
  ZNF750 WILD-TYPE     48     69     68
D15V2, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               48
  CLUS_2              4               69
  CLUS_3              3               68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        2      2      3
  ZNF750 WILD-TYPE     43     31     52
D15V3, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               43
  CLUS_2              2               31
  CLUS_3              3               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 CLUS_5
  ZNF750 MUTATED        3      1      3      0      0
  ZNF750 WILD-TYPE     24     39     29     18     16
D15V4, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              3               24
  CLUS_2              1               39
  CLUS_3              3               29
  CLUS_4              0               18
  CLUS_5              0               16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF750 MUTATED        1      4      1      3
  ZNF750 WILD-TYPE     38     60     48     38
D15V5, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              1               38
  CLUS_2              4               60
  CLUS_3              1               48
  CLUS_4              3               38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        1      8      0
  ZNF750 WILD-TYPE     48    112     24
D15V6, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              1               48
  CLUS_2              8              112
  CLUS_3              0               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
  ZNF750 MUTATED        2      1      6
  ZNF750 WILD-TYPE     59     54     72
D15V7, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               59
  CLUS_2              1               54
  CLUS_3              6               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF750 MUTATED        0      5      1      1      2
  ZNF750 WILD-TYPE     41     45     57     14     28
D15V8, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              5               45
  CLUS_3              1               57
  CLUS_4              1               14
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        2      1      5
  ZNF750 WILD-TYPE     54     59     63
D15V9, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              1               59
  CLUS_3              5               63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF750 MUTATED        0      1      5      1      1
  ZNF750 WILD-TYPE     19     61     54     21     21
D15V10, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              1               61
  CLUS_3              5               54
  CLUS_4              1               21
  CLUS_5              1               21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = C12ORF43 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C12ORF43 MUTATED        0      2      1      1      0
  C12ORF43 WILD-TYPE      6     70     30     43     38
D16V1, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                2                 70
  CLUS_3                1                 30
  CLUS_4                1                 43
  CLUS_5                0                 38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        0      2      2
  C12ORF43 WILD-TYPE     50     71     69
D16V2, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 50
  CLUS_2                2                 71
  CLUS_3                2                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        0      1      1
  C12ORF43 WILD-TYPE     45     32     54
D16V3, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                131 
        TCGA-C5-A0TN         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MN         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LT         TCGA-C5-A2LV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HE         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DG-A2KH         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KL         TCGA-DG-A2KM         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A1QS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3HU         TCGA-EA-A3QD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A439         TCGA-EA-A43B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5FO         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZD         TCGA-EA-A5ZE         TCGA-EA-A5ZF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EA-A78R         TCGA-EK-A2H1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2IP         TCGA-EK-A2PK         TCGA-EK-A2PL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2PM         TCGA-EK-A2R7         TCGA-EK-A2R8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2R9         TCGA-EK-A2RA         TCGA-EK-A2RC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RD         TCGA-EK-A2RE         TCGA-EK-A2RJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RK         TCGA-EK-A2RL         TCGA-EK-A2RM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EK-A3GK         TCGA-EK-A3GM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A3GN         TCGA-EX-A1H5         TCGA-EX-A449 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-EX-A69M         TCGA-FU-A23K 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A40J         TCGA-FU-A57G 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JJ         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LA         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JX-A3PZ         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AV         TCGA-LP-A4AW         TCGA-LP-A4AX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-LP-A5U3         TCGA-LP-A7HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A5YI         TCGA-MY-A5BF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-Q1-A6DW         TCGA-Q1-A73O 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73P         TCGA-Q1-A73Q         TCGA-Q1-A73R 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-R2-A69V         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PF         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C12ORF43 MUTATED        0      0      2      0      0
  C12ORF43 WILD-TYPE     27     40     30     18     16
D16V4, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                131 
        TCGA-C5-A0TN         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MN         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LT         TCGA-C5-A2LV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HE         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DG-A2KH         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KL         TCGA-DG-A2KM         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A1QS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3HU         TCGA-EA-A3QD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A439         TCGA-EA-A43B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5FO         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZD         TCGA-EA-A5ZE         TCGA-EA-A5ZF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EA-A78R         TCGA-EK-A2H1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2IP         TCGA-EK-A2PK         TCGA-EK-A2PL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2PM         TCGA-EK-A2R7         TCGA-EK-A2R8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2R9         TCGA-EK-A2RA         TCGA-EK-A2RC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RD         TCGA-EK-A2RE         TCGA-EK-A2RJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RK         TCGA-EK-A2RL         TCGA-EK-A2RM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EK-A3GK         TCGA-EK-A3GM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A3GN         TCGA-EX-A1H5         TCGA-EX-A449 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-EX-A69M         TCGA-FU-A23K 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A40J         TCGA-FU-A57G 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JJ         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LA         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JX-A3PZ         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AV         TCGA-LP-A4AW         TCGA-LP-A4AX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-LP-A5U3         TCGA-LP-A7HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A5YI         TCGA-MY-A5BF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-Q1-A6DW         TCGA-Q1-A73O 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73P         TCGA-Q1-A73Q         TCGA-Q1-A73R 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-R2-A69V         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PF         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C12ORF43 MUTATED        0      2      1      1
  C12ORF43 WILD-TYPE     39     62     48     40
D16V5, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                2                 62
  CLUS_3                1                 48
  CLUS_4                1                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        0      4      0
  C12ORF43 WILD-TYPE     49    116     24
D16V6, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                4                116
  CLUS_3                0                 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
  C12ORF43 MUTATED        0      2      2
  C12ORF43 WILD-TYPE     61     53     76
D16V7, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 61
  CLUS_2                2                 53
  CLUS_3                2                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C12ORF43 MUTATED        0      0      2      1      1
  C12ORF43 WILD-TYPE     41     50     56     14     29
D16V8, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 41
  CLUS_2                0                 50
  CLUS_3                2                 56
  CLUS_4                1                 14
  CLUS_5                1                 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
  C12ORF43 MUTATED        0      2      1
  C12ORF43 WILD-TYPE     56     58     67
D16V9, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                2                 58
  CLUS_3                1                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C12ORF43 MUTATED        0      2      0      1      0
  C12ORF43 WILD-TYPE     19     60     59     21     22
D16V10, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                2                 60
  CLUS_3                0                 59
  CLUS_4                1                 21
  CLUS_5                0                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = C3ORF70 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C3ORF70 MUTATED        0      1      1      1      1
  C3ORF70 WILD-TYPE      6     71     30     43     37
D17V1, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                71
  CLUS_3               1                30
  CLUS_4               1                43
  CLUS_5               1                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C3ORF70 MUTATED        3      1      0
  C3ORF70 WILD-TYPE     47     72     71
D17V2, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               3                47
  CLUS_2               1                72
  CLUS_3               0                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C3ORF70 MUTATED        0      1      2
  C3ORF70 WILD-TYPE     45     32     53
D17V3, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               0                45
  CLUS_2               1                32
  CLUS_3               2                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 CLUS_5
  C3ORF70 MUTATED        0      0      2      0      1
  C3ORF70 WILD-TYPE     27     40     30     18     15
D17V4, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               0                27
  CLUS_2               0                40
  CLUS_3               2                30
  CLUS_4               0                18
  CLUS_5               1                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C3ORF70 MUTATED        1      1      2      0
  C3ORF70 WILD-TYPE     38     63     47     41
D17V5, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               1                38
  CLUS_2               1                63
  CLUS_3               2                47
  CLUS_4               0                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C3ORF70 MUTATED        3      1      0
  C3ORF70 WILD-TYPE     46    119     24
D17V6, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               3                46
  CLUS_2               1               119
  CLUS_3               0                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
  C3ORF70 MUTATED        4      0      0
  C3ORF70 WILD-TYPE     57     55     78
D17V7, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               4                57
  CLUS_2               0                55
  CLUS_3               0                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C3ORF70 MUTATED        2      2      0      0      0
  C3ORF70 WILD-TYPE     39     48     58     15     30
D17V8, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               2                39
  CLUS_2               2                48
  CLUS_3               0                58
  CLUS_4               0                15
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  C3ORF70 MUTATED        4      0      0
  C3ORF70 WILD-TYPE     52     60     68
D17V9, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               4                52
  CLUS_2               0                60
  CLUS_3               0                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C3ORF70 MUTATED        3      0      1      0      0
  C3ORF70 WILD-TYPE     16     62     58     22     22
D17V10, multiclass
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  CLUS_1               3                16
  CLUS_2               0                62
  CLUS_3               1                58
  CLUS_4               0                22
  CLUS_5               0                22
[1] 5 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 = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BAP1 MUTATED        0      1      0      0      3
  BAP1 WILD-TYPE      6     71     31     44     35
D18V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1             71
  CLUS_3            0             31
  CLUS_4            0             44
  CLUS_5            3             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        0      3      1
  BAP1 WILD-TYPE     50     70     70
D18V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             50
  CLUS_2            3             70
  CLUS_3            1             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        0      1      1
  BAP1 WILD-TYPE     45     32     54
D18V3, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            131 
    TCGA-C5-A0TN     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1M5 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CK     TCGA-C5-A7X3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A439     TCGA-EA-A43B     TCGA-EA-A4BA     TCGA-EA-A50E 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2IP     TCGA-EK-A2PK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2PL     TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2R9     TCGA-EK-A2RA     TCGA-EK-A2RD     TCGA-EK-A2RE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-EK-A3GK     TCGA-EK-A3GM     TCGA-EK-A3GN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A40J     TCGA-FU-A57G     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A4S6     TCGA-IR-A3L7     TCGA-IR-A3LA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A5QV     TCGA-LP-A4AV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73P 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S     TCGA-R2-A69V 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BAP1 MUTATED        0      1      1      0      0
  BAP1 WILD-TYPE     27     39     31     18     16
D18V4, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            131 
    TCGA-C5-A0TN     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1M5 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CK     TCGA-C5-A7X3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A439     TCGA-EA-A43B     TCGA-EA-A4BA     TCGA-EA-A50E 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2IP     TCGA-EK-A2PK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2PL     TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2R9     TCGA-EK-A2RA     TCGA-EK-A2RD     TCGA-EK-A2RE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-EK-A3GK     TCGA-EK-A3GM     TCGA-EK-A3GN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A40J     TCGA-FU-A57G     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A4S6     TCGA-IR-A3L7     TCGA-IR-A3LA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A5QV     TCGA-LP-A4AV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73P 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S     TCGA-R2-A69V 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED        0      3      1      0
  BAP1 WILD-TYPE     39     61     48     41
D18V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             39
  CLUS_2            3             61
  CLUS_3            1             48
  CLUS_4            0             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        0      4      0
  BAP1 WILD-TYPE     49    116     24
D18V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             49
  CLUS_2            4            116
  CLUS_3            0             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
  BAP1 MUTATED        1      2      1
  BAP1 WILD-TYPE     60     53     77
D18V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             60
  CLUS_2            2             53
  CLUS_3            1             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BAP1 MUTATED        0      2      1      1      0
  BAP1 WILD-TYPE     41     48     57     14     30
D18V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            2             48
  CLUS_3            1             57
  CLUS_4            1             14
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        0      2      2
  BAP1 WILD-TYPE     56     58     66
D18V9, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             56
  CLUS_2            2             58
  CLUS_3            2             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BAP1 MUTATED        0      1      3      0      0
  BAP1 WILD-TYPE     19     61     56     22     22
D18V10, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            1             61
  CLUS_3            3             56
  CLUS_4            0             22
  CLUS_5            0             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = USP28 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  USP28 MUTATED        0      2      0      2      0
  USP28 WILD-TYPE      6     70     31     42     38
D19V1, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2              70
  CLUS_3             0              31
  CLUS_4             2              42
  CLUS_5             0              38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        1      3      0
  USP28 WILD-TYPE     49     70     71
D19V2, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              49
  CLUS_2             3              70
  CLUS_3             0              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        0      0      3
  USP28 WILD-TYPE     45     33     52
D19V3, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             0              45
  CLUS_2             0              33
  CLUS_3             3              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 CLUS_5
  USP28 MUTATED        0      2      1      0      0
  USP28 WILD-TYPE     27     38     31     18     16
D19V4, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             0              27
  CLUS_2             2              38
  CLUS_3             1              31
  CLUS_4             0              18
  CLUS_5             0              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  USP28 MUTATED        0      1      1      2
  USP28 WILD-TYPE     39     63     48     39
D19V5, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             1              63
  CLUS_3             1              48
  CLUS_4             2              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        1      3      0
  USP28 WILD-TYPE     48    117     24
D19V6, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              48
  CLUS_2             3             117
  CLUS_3             0              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
  USP28 MUTATED        1      0      3
  USP28 WILD-TYPE     60     55     75
D19V7, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              60
  CLUS_2             0              55
  CLUS_3             3              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  USP28 MUTATED        1      1      2      0      0
  USP28 WILD-TYPE     40     49     56     15     30
D19V8, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             1              49
  CLUS_3             2              56
  CLUS_4             0              15
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        1      0      3
  USP28 WILD-TYPE     55     60     65
D19V9, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              55
  CLUS_2             0              60
  CLUS_3             3              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  USP28 MUTATED        1      0      2      1      0
  USP28 WILD-TYPE     18     62     57     21     22
D19V10, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             0              62
  CLUS_3             2              57
  CLUS_4             1              21
  CLUS_5             0              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = IFNGR1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IFNGR1 MUTATED        0      0      1      3      2
  IFNGR1 WILD-TYPE      6     72     30     41     36
D20V1, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0               72
  CLUS_3              1               30
  CLUS_4              3               41
  CLUS_5              2               36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        2      2      2
  IFNGR1 WILD-TYPE     48     71     69
D20V2, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               48
  CLUS_2              2               71
  CLUS_3              2               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        0      1      2
  IFNGR1 WILD-TYPE     45     32     53
D20V3, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              0               45
  CLUS_2              1               32
  CLUS_3              2               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 CLUS_5
  IFNGR1 MUTATED        0      2      1      0      0
  IFNGR1 WILD-TYPE     27     38     31     18     16
D20V4, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              0               27
  CLUS_2              2               38
  CLUS_3              1               31
  CLUS_4              0               18
  CLUS_5              0               16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFNGR1 MUTATED        2      2      1      1
  IFNGR1 WILD-TYPE     37     62     48     40
D20V5, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               37
  CLUS_2              2               62
  CLUS_3              1               48
  CLUS_4              1               40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        2      4      0
  IFNGR1 WILD-TYPE     47    116     24
D20V6, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               47
  CLUS_2              4              116
  CLUS_3              0               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
  IFNGR1 MUTATED        3      0      3
  IFNGR1 WILD-TYPE     58     55     75
D20V7, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              3               58
  CLUS_2              0               55
  CLUS_3              3               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IFNGR1 MUTATED        1      3      0      2      0
  IFNGR1 WILD-TYPE     40     47     58     13     30
D20V8, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              1               40
  CLUS_2              3               47
  CLUS_3              0               58
  CLUS_4              2               13
  CLUS_5              0               30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        3      0      3
  IFNGR1 WILD-TYPE     53     60     65
D20V9, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              3               53
  CLUS_2              0               60
  CLUS_3              3               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IFNGR1 MUTATED        1      0      4      0      1
  IFNGR1 WILD-TYPE     18     62     55     22     21
D20V10, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              1               18
  CLUS_2              0               62
  CLUS_3              4               55
  CLUS_4              0               22
  CLUS_5              1               21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
