[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTPRAD-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/PRAD-TP/10667979/PRAD-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/10695255/transformed.cor.cli.txt"

nPatients in clinical file=425, in cluster file=261, common to both=261
[1] "Reduce the number of clustering variables from 41 to 38."
[1]  38 261
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            26            235 
  SPOP MUTATED SPOP WILD-TYPE 
            26            235 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            23            238 
  TP53 MUTATED TP53 WILD-TYPE 
            23            238 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            248 
  PTEN MUTATED PTEN WILD-TYPE 
            13            248 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              252 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              252 
[1] "TCEB3 MUTATION ANALYSIS"
[1] 3
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             257 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             257 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             249 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             249 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             6            255 
  BRAF MUTATED BRAF WILD-TYPE 
             6            255 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9              252 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9              252 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            257 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            257 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               8              253 
  FAM47C MUTATED FAM47C WILD-TYPE 
               8              253 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                5               256 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                5               256 
[1] "CNTNAP1 MUTATION ANALYSIS"
[1] 3
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                5               256 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                5               256 
[1] "MLLT10 MUTATION ANALYSIS"
[1] 3
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              257 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              257 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             255 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             255 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
             4            257 
  SMG7 MUTATED SMG7 WILD-TYPE 
             4            257 
[1] "EDC4 MUTATION ANALYSIS"
[1] 3
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            258 
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            258 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              257 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              257 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              7             254 
  CDK12 MUTATED CDK12 WILD-TYPE 
              7             254 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             6            255 
  RPTN MUTATED RPTN WILD-TYPE 
             6            255 
[1] "TNRC18 MUTATION ANALYSIS"
[1] 3
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              257 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              257 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
              5             256 
  MED15 MUTATED MED15 WILD-TYPE 
              5             256 
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              256 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              256 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             255 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             255 
[1] "RNF31 MUTATION ANALYSIS"
[1] 3
  RNF31 MUTATED RNF31 WILD-TYPE 
              4             257 
  RNF31 MUTATED RNF31 WILD-TYPE 
              4             257 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             257 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             257 
[1] "LMOD2 MUTATION ANALYSIS"
[1] 3
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             258 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             258 
[1] "FAM120B MUTATION ANALYSIS"
[1] 3
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               258 
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               258 
[1] "CLEC1A MUTATION ANALYSIS"
[1] 3
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               4              257 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               4              257 
[1] "ITGA2B MUTATION ANALYSIS"
[1] 3
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               3              258 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               3              258 
[1] "RNF17 MUTATION ANALYSIS"
[1] 3
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             258 
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             258 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              7             254 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              7             254 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              4             257 
  EOMES MUTATED EOMES WILD-TYPE 
              4             257 
[1] "MTF1 MUTATION ANALYSIS"
[1] 3
  MTF1 MUTATED MTF1 WILD-TYPE 
             3            258 
  MTF1 MUTATED MTF1 WILD-TYPE 
             3            258 
[1] "NTM MUTATION ANALYSIS"
[1] 3
  NTM MUTATED NTM WILD-TYPE 
            5           256 
  NTM MUTATED NTM WILD-TYPE 
            5           256 
[1] "FNBP4 MUTATION ANALYSIS"
[1] 3
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              3             258 
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              3             258 
[1] "CDKN1B MUTATION ANALYSIS"
[1] 3
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              257 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              257 
[1] "EIF2AK3 MUTATION ANALYSIS"
[1] 3
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4               257 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4               257 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              3             258 
  LARP1 MUTATED LARP1 WILD-TYPE 
              3             258 
[1] "terrence_modification_tag"
[1] TRUE
[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 261 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	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] "rownames(nsurv.mat)"
 [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"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 261 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, 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 = SPOP MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        5      9     11
  SPOP WILD-TYPE    152     50     31
D1V1, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            5            152
  CLUS_2            9             50
  CLUS_3           11             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       21      4      1
  SPOP WILD-TYPE     54     85     96
D1V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           21             54
  CLUS_2            4             85
  CLUS_3            1             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        4      3      8
  SPOP WILD-TYPE     38     56     55
D1V3, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             38
  CLUS_2            3             56
  CLUS_3            8             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        5      8      2
  SPOP WILD-TYPE     43     58     48
D1V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            5             43
  CLUS_2            8             58
  CLUS_3            2             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       19      6      0
  SPOP WILD-TYPE     62     78     93
D1V5, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           19             62
  CLUS_2            6             78
  CLUS_3            0             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       22      3      0
  SPOP WILD-TYPE     68     80     85
D1V6, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           22             68
  CLUS_2            3             80
  CLUS_3            0             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPOP MUTATED        4      0      8      3     11
  SPOP WILD-TYPE     44     18     51     52     68
D1V7, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             44
  CLUS_2            0             18
  CLUS_3            8             51
  CLUS_4            3             52
  CLUS_5           11             68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       11      2     13
  SPOP WILD-TYPE     81     44    108
D1V8, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           11             81
  CLUS_2            2             44
  CLUS_3           13            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        9     10      7
  SPOP WILD-TYPE     61     81     91
D1V9, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            9             61
  CLUS_2           10             81
  CLUS_3            7             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPOP MUTATED        6      1      7      3      9
  SPOP WILD-TYPE     36     20     44     59     74
D1V10, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            6             36
  CLUS_2            1             20
  CLUS_3            7             44
  CLUS_4            3             59
  CLUS_5            9             74
[1] 5 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 = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        4     19      0
  TP53 WILD-TYPE    153     40     42
D2V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4            153
  CLUS_2           19             40
  CLUS_3            0             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        6      5     12
  TP53 WILD-TYPE     69     84     85
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             69
  CLUS_2            5             84
  CLUS_3           12             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        0      3     10
  TP53 WILD-TYPE     42     56     53
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            3             56
  CLUS_3           10             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
  TP53 MUTATED        0     10      3
  TP53 WILD-TYPE     48     56     47
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             48
  CLUS_2           10             56
  CLUS_3            3             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
  TP53 MUTATED        5      3     15
  TP53 WILD-TYPE     76     81     78
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             76
  CLUS_2            3             81
  CLUS_3           15             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
  TP53 MUTATED        5      2     16
  TP53 WILD-TYPE     85     81     69
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             85
  CLUS_2            2             81
  CLUS_3           16             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
  TP53 MUTATED        2      1      6      5      9
  TP53 WILD-TYPE     46     17     53     50     70
D2V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             46
  CLUS_2            1             17
  CLUS_3            6             53
  CLUS_4            5             50
  CLUS_5            9             70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        5      1     17
  TP53 WILD-TYPE     87     45    104
D2V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             87
  CLUS_2            1             45
  CLUS_3           17            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8     10      5
  TP53 WILD-TYPE     62     81     93
D2V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             62
  CLUS_2           10             81
  CLUS_3            5             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        3      2      7      2      9
  TP53 WILD-TYPE     39     19     44     60     74
D2V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             39
  CLUS_2            2             19
  CLUS_3            7             44
  CLUS_4            2             60
  CLUS_5            9             74
[1] 5 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 = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        6      4      3
  PTEN WILD-TYPE    151     55     39
D3V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6            151
  CLUS_2            4             55
  CLUS_3            3             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      2      7
  PTEN WILD-TYPE     71     87     90
D3V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             71
  CLUS_2            2             87
  CLUS_3            7             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      1      3
  PTEN WILD-TYPE     38     58     60
D3V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             38
  CLUS_2            1             58
  CLUS_3            3             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
  PTEN MUTATED        4      3      1
  PTEN WILD-TYPE     44     63     49
D3V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             44
  CLUS_2            3             63
  CLUS_3            1             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
  PTEN MUTATED        5      1      7
  PTEN WILD-TYPE     76     83     86
D3V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             76
  CLUS_2            1             83
  CLUS_3            7             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      1      8
  PTEN WILD-TYPE     86     82     77
D3V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             86
  CLUS_2            1             82
  CLUS_3            8             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
  PTEN MUTATED        0      1      6      3      3
  PTEN WILD-TYPE     48     17     53     52     76
D3V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             48
  CLUS_2            1             17
  CLUS_3            6             53
  CLUS_4            3             52
  CLUS_5            3             76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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      1      9
  PTEN WILD-TYPE     89     45    112
D3V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             89
  CLUS_2            1             45
  CLUS_3            9            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      4      1
  PTEN WILD-TYPE     62     87     97
D3V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             62
  CLUS_2            4             87
  CLUS_3            1             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      0      6      3      4
  PTEN WILD-TYPE     42     21     45     59     79
D3V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             21
  CLUS_3            6             45
  CLUS_4            3             59
  CLUS_5            4             79
[1] 5 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 = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        4      2      3
  CTNNB1 WILD-TYPE    153     57     39
D4V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4              153
  CLUS_2              2               57
  CLUS_3              3               39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      0      6
  CTNNB1 WILD-TYPE     72     89     91
D4V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               72
  CLUS_2              0               89
  CLUS_3              6               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0      0      4
  CTNNB1 WILD-TYPE     42     59     59
D4V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               59
  CLUS_3              4               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0      4      0
  CTNNB1 WILD-TYPE     48     62     50
D4V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              4               62
  CLUS_3              0               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
  CTNNB1 MUTATED        3      0      6
  CTNNB1 WILD-TYPE     78     84     87
D4V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               78
  CLUS_2              0               84
  CLUS_3              6               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      1      5
  CTNNB1 WILD-TYPE     87     82     80
D4V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               87
  CLUS_2              1               82
  CLUS_3              5               80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        0      0      4      2      3
  CTNNB1 WILD-TYPE     48     18     55     53     76
D4V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              0               18
  CLUS_3              4               55
  CLUS_4              2               53
  CLUS_5              3               76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        2      0      7
  CTNNB1 WILD-TYPE     90     46    114
D4V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               90
  CLUS_2              0               46
  CLUS_3              7              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        5      3      1
  CTNNB1 WILD-TYPE     65     88     97
D4V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              5               65
  CLUS_2              3               88
  CLUS_3              1               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        2      0      4      0      3
  CTNNB1 WILD-TYPE     40     21     47     62     80
D4V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               40
  CLUS_2              0               21
  CLUS_3              4               47
  CLUS_4              0               62
  CLUS_5              3               80
[1] 5 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 = TCEB3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        2      2      0
  TCEB3 WILD-TYPE    155     57     42
D5V1, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             2             155
  CLUS_2             2              57
  CLUS_3             0              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        0      1      3
  TCEB3 WILD-TYPE     75     88     94
D5V2, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             1              88
  CLUS_3             3              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        0      0      3
  TCEB3 WILD-TYPE     42     59     60
D5V3, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              59
  CLUS_3             3              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
  TCEB3 MUTATED        1      2      0
  TCEB3 WILD-TYPE     47     64     50
D5V4, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             2              64
  CLUS_3             0              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
  TCEB3 MUTATED        0      1      3
  TCEB3 WILD-TYPE     81     83     90
D5V5, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             0              81
  CLUS_2             1              83
  CLUS_3             3              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        1      1      2
  TCEB3 WILD-TYPE     89     82     83
D5V6, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             1              82
  CLUS_3             2              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCEB3 MUTATED        0      0      2      2      0
  TCEB3 WILD-TYPE     48     18     57     53     79
D5V7, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             0              18
  CLUS_3             2              57
  CLUS_4             2              53
  CLUS_5             0              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        2      1      1
  TCEB3 WILD-TYPE     90     45    120
D5V8, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             2              90
  CLUS_2             1              45
  CLUS_3             1             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCEB3 MUTATED        1      0      3
  TCEB3 WILD-TYPE     69     91     95
D5V9, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             0              91
  CLUS_3             3              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCEB3 MUTATED        1      1      1      1      0
  TCEB3 WILD-TYPE     41     20     50     61     83
D5V10, multiclass
        clus
vv       TCEB3 MUTATED TCEB3 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             1              20
  CLUS_3             1              50
  CLUS_4             1              61
  CLUS_5             0              83
[1] 5 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 = FOXA1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        3      3      6
  FOXA1 WILD-TYPE    154     56     36
D6V1, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             3             154
  CLUS_2             3              56
  CLUS_3             6              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED       10      1      1
  FOXA1 WILD-TYPE     65     88     96
D6V2, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1            10              65
  CLUS_2             1              88
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      2      3
  FOXA1 WILD-TYPE     40     57     60
D6V3, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              57
  CLUS_3             3              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
  FOXA1 MUTATED        3      3      1
  FOXA1 WILD-TYPE     45     63     49
D6V4, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             3              63
  CLUS_3             1              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
  FOXA1 MUTATED        9      3      0
  FOXA1 WILD-TYPE     72     81     93
D6V5, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             9              72
  CLUS_2             3              81
  CLUS_3             0              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        9      2      1
  FOXA1 WILD-TYPE     81     81     84
D6V6, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             9              81
  CLUS_2             2              81
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXA1 MUTATED        2      0      4      1      5
  FOXA1 WILD-TYPE     46     18     55     54     74
D6V7, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             0              18
  CLUS_3             4              55
  CLUS_4             1              54
  CLUS_5             5              74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        1      1     10
  FOXA1 WILD-TYPE     91     45    111
D6V8, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             1              45
  CLUS_3            10             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        4      7      1
  FOXA1 WILD-TYPE     66     84     97
D6V9, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             7              84
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXA1 MUTATED        2      0      4      1      5
  FOXA1 WILD-TYPE     40     21     47     61     78
D6V10, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              21
  CLUS_3             4              47
  CLUS_4             1              61
  CLUS_5             5              78
[1] 5 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 = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      1      2
  BRAF WILD-TYPE    154     58     40
D7V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3            154
  CLUS_2            1             58
  CLUS_3            2             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      3      0
  BRAF WILD-TYPE     72     86     97
D7V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             72
  CLUS_2            3             86
  CLUS_3            0             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      2      1
  BRAF WILD-TYPE     41     57     62
D7V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             41
  CLUS_2            2             57
  CLUS_3            1             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
  BRAF MUTATED        1      2      1
  BRAF WILD-TYPE     47     64     49
D7V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             47
  CLUS_2            2             64
  CLUS_3            1             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
  BRAF MUTATED        5      1      0
  BRAF WILD-TYPE     76     83     93
D7V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            5             76
  CLUS_2            1             83
  CLUS_3            0             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      1      2
  BRAF WILD-TYPE     87     82     83
D7V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             87
  CLUS_2            1             82
  CLUS_3            2             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        0      0      4      1      1
  BRAF WILD-TYPE     48     18     55     54     78
D7V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             48
  CLUS_2            0             18
  CLUS_3            4             55
  CLUS_4            1             54
  CLUS_5            1             78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      1      2
  BRAF WILD-TYPE     89     45    119
D7V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             89
  CLUS_2            1             45
  CLUS_3            2            119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      1      2
  BRAF WILD-TYPE     67     90     96
D7V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             67
  CLUS_2            1             90
  CLUS_3            2             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        2      0      2      1      1
  BRAF WILD-TYPE     40     21     49     61     82
D7V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             21
  CLUS_3            2             49
  CLUS_4            1             61
  CLUS_5            1             82
[1] 5 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 = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        6      3      0
  PIK3CA WILD-TYPE    151     56     42
D8V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6              151
  CLUS_2              3               56
  CLUS_3              0               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        1      0      8
  PIK3CA WILD-TYPE     74     89     89
D8V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               74
  CLUS_2              0               89
  CLUS_3              8               89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        0      0      4
  PIK3CA WILD-TYPE     42     59     59
D8V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               59
  CLUS_3              4               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        0      4      0
  PIK3CA WILD-TYPE     48     62     50
D8V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               48
  CLUS_2              4               62
  CLUS_3              0               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
  PIK3CA MUTATED        2      0      7
  PIK3CA WILD-TYPE     79     84     86
D8V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               79
  CLUS_2              0               84
  CLUS_3              7               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        1      1      7
  PIK3CA WILD-TYPE     89     82     78
D8V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               89
  CLUS_2              1               82
  CLUS_3              7               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
  PIK3CA MUTATED        0      0      3      2      4
  PIK3CA WILD-TYPE     48     18     56     53     75
D8V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               48
  CLUS_2              0               18
  CLUS_3              3               56
  CLUS_4              2               53
  CLUS_5              4               75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        1      1      7
  PIK3CA WILD-TYPE     91     45    114
D8V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               91
  CLUS_2              1               45
  CLUS_3              7              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      4      1
  PIK3CA WILD-TYPE     66     87     97
D8V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               66
  CLUS_2              4               87
  CLUS_3              1               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      0      4      1      4
  PIK3CA WILD-TYPE     42     21     47     61     79
D8V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               21
  CLUS_3              4               47
  CLUS_4              1               61
  CLUS_5              4               79
[1] 5 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 = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        1      1      2
  IDH1 WILD-TYPE    156     58     40
D9V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1            156
  CLUS_2            1             58
  CLUS_3            2             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     71     89     97
D9V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             71
  CLUS_2            0             89
  CLUS_3            0             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      3      0
  IDH1 WILD-TYPE     42     56     63
D9V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            3             56
  CLUS_3            0             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
  IDH1 MUTATED        0      0      3
  IDH1 WILD-TYPE     48     66     47
D9V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            0             66
  CLUS_3            3             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
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     77     84     93
D9V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             77
  CLUS_2            0             84
  CLUS_3            0             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     86     83     85
D9V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             86
  CLUS_2            0             83
  CLUS_3            0             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH1 MUTATED        0      2      1      0      1
  IDH1 WILD-TYPE     48     16     58     55     78
D9V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            2             16
  CLUS_3            1             58
  CLUS_4            0             55
  CLUS_5            1             78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      3      1
  IDH1 WILD-TYPE     92     43    120
D9V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             92
  CLUS_2            3             43
  CLUS_3            1            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        1      2      1
  IDH1 WILD-TYPE     69     89     97
D9V9, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             69
  CLUS_2            2             89
  CLUS_3            1             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH1 MUTATED        0      2      1      0      1
  IDH1 WILD-TYPE     42     19     50     62     82
D9V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            2             19
  CLUS_3            1             50
  CLUS_4            0             62
  CLUS_5            1             82
[1] 5 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 = FAM47C MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        6      2      0
  FAM47C WILD-TYPE    151     57     42
D10V1, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              6              151
  CLUS_2              2               57
  CLUS_3              0               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        0      4      4
  FAM47C WILD-TYPE     75     85     93
D10V2, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0               75
  CLUS_2              4               85
  CLUS_3              4               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        1      1      1
  FAM47C WILD-TYPE     41     58     62
D10V3, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               41
  CLUS_2              1               58
  CLUS_3              1               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
  FAM47C MUTATED        1      1      1
  FAM47C WILD-TYPE     47     65     49
D10V4, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               47
  CLUS_2              1               65
  CLUS_3              1               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
  FAM47C MUTATED        2      2      4
  FAM47C WILD-TYPE     79     82     89
D10V5, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              2               79
  CLUS_2              2               82
  CLUS_3              4               89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        4      1      3
  FAM47C WILD-TYPE     86     82     82
D10V6, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              4               86
  CLUS_2              1               82
  CLUS_3              3               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM47C MUTATED        3      2      0      0      3
  FAM47C WILD-TYPE     45     16     59     55     76
D10V7, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              3               45
  CLUS_2              2               16
  CLUS_3              0               59
  CLUS_4              0               55
  CLUS_5              3               76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        3      2      3
  FAM47C WILD-TYPE     89     44    118
D10V8, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              3               89
  CLUS_2              2               44
  CLUS_3              3              118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        0      5      3
  FAM47C WILD-TYPE     70     86     95
D10V9, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0               70
  CLUS_2              5               86
  CLUS_3              3               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM47C MUTATED        2      1      0      1      4
  FAM47C WILD-TYPE     40     20     51     61     79
D10V10, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              2               40
  CLUS_2              1               20
  CLUS_3              0               51
  CLUS_4              1               61
  CLUS_5              4               79
[1] 5 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 = TP53BP1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        2      2      1
  TP53BP1 WILD-TYPE    155     57     41
D11V1, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               2               155
  CLUS_2               2                57
  CLUS_3               1                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        4      1      0
  TP53BP1 WILD-TYPE     71     88     97
D11V2, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               4                71
  CLUS_2               1                88
  CLUS_3               0                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        1      0      4
  TP53BP1 WILD-TYPE     41     59     59
D11V3, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               0                59
  CLUS_3               4                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        1      4      0
  TP53BP1 WILD-TYPE     47     62     50
D11V4, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               1                47
  CLUS_2               4                62
  CLUS_3               0                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
  TP53BP1 MUTATED        4      1      0
  TP53BP1 WILD-TYPE     77     83     93
D11V5, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               4                77
  CLUS_2               1                83
  CLUS_3               0                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        4      0      1
  TP53BP1 WILD-TYPE     86     83     84
D11V6, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               4                86
  CLUS_2               0                83
  CLUS_3               1                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53BP1 MUTATED        0      0      2      1      2
  TP53BP1 WILD-TYPE     48     18     57     54     77
D11V7, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               0                48
  CLUS_2               0                18
  CLUS_3               2                57
  CLUS_4               1                54
  CLUS_5               2                77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        1      2      2
  TP53BP1 WILD-TYPE     91     44    119
D11V8, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               1                91
  CLUS_2               2                44
  CLUS_3               2               119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TP53BP1 MUTATED        2      2      1
  TP53BP1 WILD-TYPE     68     89     97
D11V9, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               2                68
  CLUS_2               2                89
  CLUS_3               1                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53BP1 MUTATED        1      1      2      0      1
  TP53BP1 WILD-TYPE     41     20     49     62     82
D11V10, multiclass
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               1                20
  CLUS_3               2                49
  CLUS_4               0                62
  CLUS_5               1                82
[1] 5 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 = CNTNAP1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        1      1      2
  CNTNAP1 WILD-TYPE    156     58     40
D12V1, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               1               156
  CLUS_2               1                58
  CLUS_3               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        4      1      0
  CNTNAP1 WILD-TYPE     71     88     97
D12V2, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               4                71
  CLUS_2               1                88
  CLUS_3               0                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        0      1      0
  CNTNAP1 WILD-TYPE     42     58     63
D12V3, multiclass
[1] "Remove cluster labels:" "CNTNAP1 MUTATED"       
clus
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                1               163 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8474        TCGA-EJ-A46B 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-A65E        TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-7525        TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-8264        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-KK-A59Y        TCGA-KK-A59Z        TCGA-KK-A5A1 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        0      0      1
  CNTNAP1 WILD-TYPE     48     66     49
D12V4, multiclass
[1] "Remove cluster labels:" "CNTNAP1 MUTATED"       
clus
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                1               163 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8474        TCGA-EJ-A46B 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-EJ-A65E        TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-G9-7525        TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HC-8264        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
       TCGA-KK-A59Y        TCGA-KK-A59Z        TCGA-KK-A5A1 
"CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" "CNTNAP1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        3      1      0
  CNTNAP1 WILD-TYPE     78     83     93
D12V5, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               3                78
  CLUS_2               1                83
  CLUS_3               0                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        3      1      0
  CNTNAP1 WILD-TYPE     87     82     85
D12V6, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               3                87
  CLUS_2               1                82
  CLUS_3               0                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CNTNAP1 MUTATED        2      0      2      0      1
  CNTNAP1 WILD-TYPE     46     18     57     55     78
D12V7, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               2                46
  CLUS_2               0                18
  CLUS_3               2                57
  CLUS_4               0                55
  CLUS_5               1                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        2      0      3
  CNTNAP1 WILD-TYPE     90     46    118
D12V8, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               2                90
  CLUS_2               0                46
  CLUS_3               3               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CNTNAP1 MUTATED        2      2      1
  CNTNAP1 WILD-TYPE     68     89     97
D12V9, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               2                68
  CLUS_2               2                89
  CLUS_3               1                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CNTNAP1 MUTATED        1      0      1      0      3
  CNTNAP1 WILD-TYPE     41     21     50     62     80
D12V10, multiclass
        clus
vv       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               0                21
  CLUS_3               1                50
  CLUS_4               0                62
  CLUS_5               3                80
[1] 5 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 = MLLT10 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        1      2      1
  MLLT10 WILD-TYPE    156     57     41
D13V1, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              1              156
  CLUS_2              2               57
  CLUS_3              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        1      3      0
  MLLT10 WILD-TYPE     74     86     97
D13V2, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              3               86
  CLUS_3              0               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        2      1      1
  MLLT10 WILD-TYPE     40     58     62
D13V3, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              2               40
  CLUS_2              1               58
  CLUS_3              1               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
  MLLT10 MUTATED        2      1      1
  MLLT10 WILD-TYPE     46     65     49
D13V4, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              2               46
  CLUS_2              1               65
  CLUS_3              1               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
  MLLT10 MUTATED        1      1      2
  MLLT10 WILD-TYPE     80     83     91
D13V5, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              1               80
  CLUS_2              1               83
  CLUS_3              2               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        1      2      1
  MLLT10 WILD-TYPE     89     81     84
D13V6, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              1               89
  CLUS_2              2               81
  CLUS_3              1               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLLT10 MUTATED        2      0      0      2      0
  MLLT10 WILD-TYPE     46     18     59     53     79
D13V7, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              2               46
  CLUS_2              0               18
  CLUS_3              0               59
  CLUS_4              2               53
  CLUS_5              0               79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        3      0      1
  MLLT10 WILD-TYPE     89     46    120
D13V8, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              3               89
  CLUS_2              0               46
  CLUS_3              1              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MLLT10 MUTATED        1      0      3
  MLLT10 WILD-TYPE     69     91     95
D13V9, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              0               91
  CLUS_3              3               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLLT10 MUTATED        0      0      1      3      0
  MLLT10 WILD-TYPE     42     21     50     59     83
D13V10, multiclass
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               21
  CLUS_3              1               50
  CLUS_4              3               59
  CLUS_5              0               83
[1] 5 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 = ZMYM3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        5      0      1
  ZMYM3 WILD-TYPE    152     59     41
D14V1, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             5             152
  CLUS_2             0              59
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        2      0      4
  ZMYM3 WILD-TYPE     73     89     93
D14V2, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             0              89
  CLUS_3             4              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        0      2      3
  ZMYM3 WILD-TYPE     42     57     60
D14V3, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             2              57
  CLUS_3             3              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
  ZMYM3 MUTATED        0      3      2
  ZMYM3 WILD-TYPE     48     63     48
D14V4, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             3              63
  CLUS_3             2              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        2      0      4
  ZMYM3 WILD-TYPE     79     84     89
D14V5, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             2              79
  CLUS_2             0              84
  CLUS_3             4              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        1      0      5
  ZMYM3 WILD-TYPE     89     83     80
D14V6, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             0              83
  CLUS_3             5              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZMYM3 MUTATED        0      1      3      2      0
  ZMYM3 WILD-TYPE     48     17     56     53     79
D14V7, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             1              17
  CLUS_3             3              56
  CLUS_4             2              53
  CLUS_5             0              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        0      1      5
  ZMYM3 WILD-TYPE     92     45    116
D14V8, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             0              92
  CLUS_2             1              45
  CLUS_3             5             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ZMYM3 MUTATED        5      0      1
  ZMYM3 WILD-TYPE     65     91     97
D14V9, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             5              65
  CLUS_2             0              91
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZMYM3 MUTATED        0      1      3      2      0
  ZMYM3 WILD-TYPE     42     20     48     60     83
D14V10, multiclass
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              20
  CLUS_3             3              48
  CLUS_4             2              60
  CLUS_5             0              83
[1] 5 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 = SMG7 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        2      1      1
  SMG7 WILD-TYPE    155     58     41
D15V1, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            2            155
  CLUS_2            1             58
  CLUS_3            1             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        2      1      1
  SMG7 WILD-TYPE     73     88     96
D15V2, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            2             73
  CLUS_2            1             88
  CLUS_3            1             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        1      1      1
  SMG7 WILD-TYPE     41     58     62
D15V3, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            1             58
  CLUS_3            1             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
  SMG7 MUTATED        1      1      1
  SMG7 WILD-TYPE     47     65     49
D15V4, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            1             65
  CLUS_3            1             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
  SMG7 MUTATED        4      0      0
  SMG7 WILD-TYPE     77     84     93
D15V5, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            4             77
  CLUS_2            0             84
  CLUS_3            0             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        2      0      2
  SMG7 WILD-TYPE     88     83     83
D15V6, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            2             88
  CLUS_2            0             83
  CLUS_3            2             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMG7 MUTATED        0      1      1      1      1
  SMG7 WILD-TYPE     48     17     58     54     78
D15V7, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            1             17
  CLUS_3            1             58
  CLUS_4            1             54
  CLUS_5            1             78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        0      1      3
  SMG7 WILD-TYPE     92     45    118
D15V8, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            0             92
  CLUS_2            1             45
  CLUS_3            3            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMG7 MUTATED        2      2      0
  SMG7 WILD-TYPE     68     89     98
D15V9, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            2             89
  CLUS_3            0             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMG7 MUTATED        0      0      1      1      2
  SMG7 WILD-TYPE     42     21     50     61     81
D15V10, multiclass
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             21
  CLUS_3            1             50
  CLUS_4            1             61
  CLUS_5            2             81
[1] 5 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 = EDC4 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        0      2      1
  EDC4 WILD-TYPE    157     57     41
D16V1, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            0            157
  CLUS_2            2             57
  CLUS_3            1             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        3      0      0
  EDC4 WILD-TYPE     72     89     97
D16V2, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            3             72
  CLUS_2            0             89
  CLUS_3            0             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        0      1      0
  EDC4 WILD-TYPE     42     58     63
D16V3, multiclass
[1] "Remove cluster labels:" "EDC4 MUTATED"          
clus
  EDC4 MUTATED EDC4 WILD-TYPE 
             1            163 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7125     TCGA-EJ-7314 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7328     TCGA-EJ-7330 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468     TCGA-EJ-8469 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-8470     TCGA-EJ-8474     TCGA-EJ-A46B     TCGA-EJ-A46D 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-A46E     TCGA-EJ-A46F     TCGA-EJ-A46G     TCGA-EJ-A65E 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-A65M     TCGA-FC-7708     TCGA-FC-7961     TCGA-FC-A4JI 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-FC-A5OB     TCGA-G9-6329     TCGA-G9-6338     TCGA-G9-6342 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377     TCGA-G9-6378 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6384     TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-7510     TCGA-G9-7521     TCGA-G9-7522     TCGA-G9-7523 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-7525     TCGA-H9-7775     TCGA-HC-7077     TCGA-HC-7079 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7744     TCGA-HC-7748     TCGA-HC-7817 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-8264     TCGA-HI-7168     TCGA-HI-7169     TCGA-HI-7170 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HI-7171     TCGA-J4-8198     TCGA-J4-8200     TCGA-J9-A52C 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-J9-A52E     TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BO 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-KC-A4BR     TCGA-KC-A4BV     TCGA-KK-A59V     TCGA-KK-A59X 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-KK-A59Y     TCGA-KK-A59Z     TCGA-KK-A5A1 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        0      0      1
  EDC4 WILD-TYPE     48     66     49
D16V4, multiclass
[1] "Remove cluster labels:" "EDC4 MUTATED"          
clus
  EDC4 MUTATED EDC4 WILD-TYPE 
             1            163 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7125     TCGA-EJ-7314 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7328     TCGA-EJ-7330 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468     TCGA-EJ-8469 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-8470     TCGA-EJ-8474     TCGA-EJ-A46B     TCGA-EJ-A46D 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-A46E     TCGA-EJ-A46F     TCGA-EJ-A46G     TCGA-EJ-A65E 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-EJ-A65M     TCGA-FC-7708     TCGA-FC-7961     TCGA-FC-A4JI 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-FC-A5OB     TCGA-G9-6329     TCGA-G9-6338     TCGA-G9-6342 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377     TCGA-G9-6378 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-6384     TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-7510     TCGA-G9-7521     TCGA-G9-7522     TCGA-G9-7523 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-G9-7525     TCGA-H9-7775     TCGA-HC-7077     TCGA-HC-7079 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7744     TCGA-HC-7748     TCGA-HC-7817 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HC-8264     TCGA-HI-7168     TCGA-HI-7169     TCGA-HI-7170 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-HI-7171     TCGA-J4-8198     TCGA-J4-8200     TCGA-J9-A52C 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-J9-A52E     TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BO 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-KC-A4BR     TCGA-KC-A4BV     TCGA-KK-A59V     TCGA-KK-A59X 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
    TCGA-KK-A59Y     TCGA-KK-A59Z     TCGA-KK-A5A1 
"EDC4 WILD-TYPE" "EDC4 WILD-TYPE" "EDC4 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        1      1      1
  EDC4 WILD-TYPE     80     83     92
D16V5, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            1             80
  CLUS_2            1             83
  CLUS_3            1             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        2      0      1
  EDC4 WILD-TYPE     88     83     84
D16V6, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            2             88
  CLUS_2            0             83
  CLUS_3            1             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EDC4 MUTATED        0      0      0      0      3
  EDC4 WILD-TYPE     48     18     59     55     76
D16V7, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            0             18
  CLUS_3            0             59
  CLUS_4            0             55
  CLUS_5            3             76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        0      0      3
  EDC4 WILD-TYPE     92     46    118
D16V8, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            0             92
  CLUS_2            0             46
  CLUS_3            3            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EDC4 MUTATED        0      3      0
  EDC4 WILD-TYPE     70     88     98
D16V9, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            0             70
  CLUS_2            3             88
  CLUS_3            0             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EDC4 MUTATED        0      0      0      0      3
  EDC4 WILD-TYPE     42     21     51     62     80
D16V10, multiclass
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             21
  CLUS_3            0             51
  CLUS_4            0             62
  CLUS_5            3             80
[1] 5 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 = ZNF709 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        3      0      1
  ZNF709 WILD-TYPE    154     59     41
D17V1, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              3              154
  CLUS_2              0               59
  CLUS_3              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        1      1      2
  ZNF709 WILD-TYPE     74     88     95
D17V2, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               88
  CLUS_3              2               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        0      1      3
  ZNF709 WILD-TYPE     42     58     60
D17V3, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              1               58
  CLUS_3              3               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
  ZNF709 MUTATED        0      3      1
  ZNF709 WILD-TYPE     48     63     49
D17V4, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              3               63
  CLUS_3              1               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
  ZNF709 MUTATED        1      1      2
  ZNF709 WILD-TYPE     80     83     91
D17V5, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               80
  CLUS_2              1               83
  CLUS_3              2               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        0      1      3
  ZNF709 WILD-TYPE     90     82     82
D17V6, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               90
  CLUS_2              1               82
  CLUS_3              3               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF709 MUTATED        0      0      1      0      3
  ZNF709 WILD-TYPE     48     18     58     55     76
D17V7, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              0               18
  CLUS_3              1               58
  CLUS_4              0               55
  CLUS_5              3               76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        1      0      3
  ZNF709 WILD-TYPE     91     46    118
D17V8, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               91
  CLUS_2              0               46
  CLUS_3              3              118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        1      3      0
  ZNF709 WILD-TYPE     69     88     98
D17V9, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              3               88
  CLUS_3              0               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF709 MUTATED        0      0      1      0      3
  ZNF709 WILD-TYPE     42     21     50     62     80
D17V10, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               21
  CLUS_3              1               50
  CLUS_4              0               62
  CLUS_5              3               80
[1] 5 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 = CDK12 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        1      4      1
  CDK12 WILD-TYPE    156     55     41
D18V1, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1             156
  CLUS_2             4              55
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        4      1      2
  CDK12 WILD-TYPE     71     88     95
D18V2, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             4              71
  CLUS_2             1              88
  CLUS_3             2              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        0      0      4
  CDK12 WILD-TYPE     42     59     59
D18V3, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              59
  CLUS_3             4              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        0      4      0
  CDK12 WILD-TYPE     48     62     50
D18V4, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4              62
  CLUS_3             0              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
  CDK12 MUTATED        4      1      1
  CDK12 WILD-TYPE     77     83     92
D18V5, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             4              77
  CLUS_2             1              83
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        4      0      2
  CDK12 WILD-TYPE     86     83     83
D18V6, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             4              86
  CLUS_2             0              83
  CLUS_3             2              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDK12 MUTATED        2      0      3      0      2
  CDK12 WILD-TYPE     46     18     56     55     77
D18V7, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             0              18
  CLUS_3             3              56
  CLUS_4             0              55
  CLUS_5             2              77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        1      0      6
  CDK12 WILD-TYPE     91     46    115
D18V8, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             0              46
  CLUS_3             6             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        3      3      1
  CDK12 WILD-TYPE     67     88     97
D18V9, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             3              88
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDK12 MUTATED        1      0      3      0      3
  CDK12 WILD-TYPE     41     21     48     62     80
D18V10, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              21
  CLUS_3             3              48
  CLUS_4             0              62
  CLUS_5             3              80
[1] 5 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 = RPTN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        4      0      2
  RPTN WILD-TYPE    153     59     40
D19V1, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            4            153
  CLUS_2            0             59
  CLUS_3            2             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        3      2      1
  RPTN WILD-TYPE     72     87     96
D19V2, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            3             72
  CLUS_2            2             87
  CLUS_3            1             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        0      0      3
  RPTN WILD-TYPE     42     59     60
D19V3, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             59
  CLUS_3            3             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
  RPTN MUTATED        0      3      0
  RPTN WILD-TYPE     48     63     50
D19V4, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            0             48
  CLUS_2            3             63
  CLUS_3            0             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
  RPTN MUTATED        3      2      1
  RPTN WILD-TYPE     78     82     92
D19V5, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            3             78
  CLUS_2            2             82
  CLUS_3            1             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        3      1      2
  RPTN WILD-TYPE     87     82     83
D19V6, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            3             87
  CLUS_2            1             82
  CLUS_3            2             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPTN MUTATED        2      0      1      0      3
  RPTN WILD-TYPE     46     18     58     55     76
D19V7, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             46
  CLUS_2            0             18
  CLUS_3            1             58
  CLUS_4            0             55
  CLUS_5            3             76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        2      0      4
  RPTN WILD-TYPE     90     46    117
D19V8, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             90
  CLUS_2            0             46
  CLUS_3            4            117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPTN MUTATED        1      4      1
  RPTN WILD-TYPE     69     87     97
D19V9, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             69
  CLUS_2            4             87
  CLUS_3            1             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPTN MUTATED        2      0      1      0      3
  RPTN WILD-TYPE     40     21     50     62     80
D19V10, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             21
  CLUS_3            1             50
  CLUS_4            0             62
  CLUS_5            3             80
[1] 5 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 = TNRC18 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        1      3      0
  TNRC18 WILD-TYPE    156     56     42
D20V1, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              1              156
  CLUS_2              3               56
  CLUS_3              0               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        1      1      2
  TNRC18 WILD-TYPE     74     88     95
D20V2, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               88
  CLUS_3              2               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        1      0      0
  TNRC18 WILD-TYPE     41     59     63
D20V3, multiclass
[1] "Remove cluster labels:" "TNRC18 MUTATED"        
clus
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               1              163 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5502       TCGA-EJ-5503 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7125       TCGA-EJ-7314 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7328 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7331       TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7784       TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7789       TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7794       TCGA-EJ-7797       TCGA-EJ-8468       TCGA-EJ-8469 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-8470       TCGA-EJ-8474       TCGA-EJ-A46B       TCGA-EJ-A46D 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-A46E       TCGA-EJ-A46F       TCGA-EJ-A46G       TCGA-EJ-A65E 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-A65M       TCGA-FC-7708       TCGA-FC-7961       TCGA-FC-A4JI 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-FC-A5OB       TCGA-G9-6329       TCGA-G9-6338       TCGA-G9-6342 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6370 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-7510       TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-7525       TCGA-H9-7775       TCGA-HC-7077       TCGA-HC-7079 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7213       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7744       TCGA-HC-7748       TCGA-HC-7817 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-8264       TCGA-HI-7168       TCGA-HI-7169       TCGA-HI-7170 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HI-7171       TCGA-J4-8198       TCGA-J4-8200       TCGA-J9-A52C 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-J9-A52E       TCGA-KC-A4BL       TCGA-KC-A4BN       TCGA-KC-A4BO 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-KC-A4BR       TCGA-KC-A4BV       TCGA-KK-A59V       TCGA-KK-A59X 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-KK-A59Y       TCGA-KK-A59Z       TCGA-KK-A5A1 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        1      0      0
  TNRC18 WILD-TYPE     47     66     50
D20V4, multiclass
[1] "Remove cluster labels:" "TNRC18 MUTATED"        
clus
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               1              163 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5502       TCGA-EJ-5503 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7125       TCGA-EJ-7314 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7328 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7331       TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7784       TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7789       TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7794       TCGA-EJ-7797       TCGA-EJ-8468       TCGA-EJ-8469 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-8470       TCGA-EJ-8474       TCGA-EJ-A46B       TCGA-EJ-A46D 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-A46E       TCGA-EJ-A46F       TCGA-EJ-A46G       TCGA-EJ-A65E 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-A65M       TCGA-FC-7708       TCGA-FC-7961       TCGA-FC-A4JI 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-FC-A5OB       TCGA-G9-6329       TCGA-G9-6338       TCGA-G9-6342 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6370 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-7510       TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-7525       TCGA-H9-7775       TCGA-HC-7077       TCGA-HC-7079 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7213       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7744       TCGA-HC-7748       TCGA-HC-7817 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-8264       TCGA-HI-7168       TCGA-HI-7169       TCGA-HI-7170 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HI-7171       TCGA-J4-8198       TCGA-J4-8200       TCGA-J9-A52C 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-J9-A52E       TCGA-KC-A4BL       TCGA-KC-A4BN       TCGA-KC-A4BO 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-KC-A4BR       TCGA-KC-A4BV       TCGA-KK-A59V       TCGA-KK-A59X 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-KK-A59Y       TCGA-KK-A59Z       TCGA-KK-A5A1 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        2      1      1
  TNRC18 WILD-TYPE     79     83     92
D20V5, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              2               79
  CLUS_2              1               83
  CLUS_3              1               92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        0      1      3
  TNRC18 WILD-TYPE     90     82     82
D20V6, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              0               90
  CLUS_2              1               82
  CLUS_3              3               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TNRC18 MUTATED        0      0      2      0      2
  TNRC18 WILD-TYPE     48     18     57     55     77
D20V7, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              0               18
  CLUS_3              2               57
  CLUS_4              0               55
  CLUS_5              2               77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        1      1      2
  TNRC18 WILD-TYPE     91     45    119
D20V8, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              1               91
  CLUS_2              1               45
  CLUS_3              2              119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TNRC18 MUTATED        2      2      0
  TNRC18 WILD-TYPE     68     89     98
D20V9, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              2               89
  CLUS_3              0               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TNRC18 MUTATED        0      0      2      0      2
  TNRC18 WILD-TYPE     42     21     49     62     81
D20V10, multiclass
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               21
  CLUS_3              2               49
  CLUS_4              0               62
  CLUS_5              2               81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = MED15 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        4      0      1
  MED15 WILD-TYPE    153     59     41
D21V1, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             4             153
  CLUS_2             0              59
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        4      0      1
  MED15 WILD-TYPE     71     89     96
D21V2, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             4              71
  CLUS_2             0              89
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        0      2      3
  MED15 WILD-TYPE     42     57     60
D21V3, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             2              57
  CLUS_3             3              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
  MED15 MUTATED        1      3      1
  MED15 WILD-TYPE     47     63     49
D21V4, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             3              63
  CLUS_3             1              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
  MED15 MUTATED        3      1      1
  MED15 WILD-TYPE     78     83     92
D21V5, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             3              78
  CLUS_2             1              83
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        2      2      1
  MED15 WILD-TYPE     88     81     84
D21V6, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             2              88
  CLUS_2             2              81
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MED15 MUTATED        1      1      1      0      2
  MED15 WILD-TYPE     47     17     58     55     77
D21V7, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             1              17
  CLUS_3             1              58
  CLUS_4             0              55
  CLUS_5             2              77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        1      1      3
  MED15 WILD-TYPE     91     45    118
D21V8, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             1              45
  CLUS_3             3             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MED15 MUTATED        1      3      1
  MED15 WILD-TYPE     69     88     97
D21V9, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             3              88
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MED15 MUTATED        0      1      1      1      2
  MED15 WILD-TYPE     42     20     50     61     81
D21V10, multiclass
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              20
  CLUS_3             1              50
  CLUS_4             1              61
  CLUS_5             2              81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = NKX3-1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        3      0      1
  NKX3-1 WILD-TYPE    154     59     41
D22V1, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              3              154
  CLUS_2              0               59
  CLUS_3              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        1      1      3
  NKX3-1 WILD-TYPE     74     88     94
D22V2, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               88
  CLUS_3              3               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        4      0      1
  NKX3-1 WILD-TYPE     38     59     62
D22V3, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              4               38
  CLUS_2              0               59
  CLUS_3              1               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
  NKX3-1 MUTATED        4      1      0
  NKX3-1 WILD-TYPE     44     65     50
D22V4, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              4               44
  CLUS_2              1               65
  CLUS_3              0               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
  NKX3-1 MUTATED        2      1      2
  NKX3-1 WILD-TYPE     79     83     91
D22V5, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               79
  CLUS_2              1               83
  CLUS_3              2               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        2      1      2
  NKX3-1 WILD-TYPE     88     82     83
D22V6, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               88
  CLUS_2              1               82
  CLUS_3              2               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NKX3-1 MUTATED        0      1      0      4      0
  NKX3-1 WILD-TYPE     48     17     59     51     79
D22V7, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              1               17
  CLUS_3              0               59
  CLUS_4              4               51
  CLUS_5              0               79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        2      2      1
  NKX3-1 WILD-TYPE     90     44    120
D22V8, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               90
  CLUS_2              2               44
  CLUS_3              1              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        0      0      5
  NKX3-1 WILD-TYPE     70     91     93
D22V9, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              0               70
  CLUS_2              0               91
  CLUS_3              5               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NKX3-1 MUTATED        0      2      0      3      0
  NKX3-1 WILD-TYPE     42     19     51     59     83
D22V10, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              2               19
  CLUS_3              0               51
  CLUS_4              3               59
  CLUS_5              0               83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = KDM6A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        2      1      3
  KDM6A WILD-TYPE    155     58     39
D23V1, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             2             155
  CLUS_2             1              58
  CLUS_3             3              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        4      1      1
  KDM6A WILD-TYPE     71     88     96
D23V2, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              71
  CLUS_2             1              88
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        1      2      1
  KDM6A WILD-TYPE     41     57     62
D23V3, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              41
  CLUS_2             2              57
  CLUS_3             1              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
  KDM6A MUTATED        2      1      1
  KDM6A WILD-TYPE     46     65     49
D23V4, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             2              46
  CLUS_2             1              65
  CLUS_3             1              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
  KDM6A MUTATED        4      1      1
  KDM6A WILD-TYPE     77     83     92
D23V5, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              77
  CLUS_2             1              83
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        4      1      1
  KDM6A WILD-TYPE     86     82     84
D23V6, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              86
  CLUS_2             1              82
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KDM6A MUTATED        0      0      2      1      3
  KDM6A WILD-TYPE     48     18     57     54     76
D23V7, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             0              48
  CLUS_2             0              18
  CLUS_3             2              57
  CLUS_4             1              54
  CLUS_5             3              76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        1      4      1
  KDM6A WILD-TYPE     91     42    120
D23V8, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              91
  CLUS_2             4              42
  CLUS_3             1             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        2      3      1
  KDM6A WILD-TYPE     68     88     97
D23V9, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             2              68
  CLUS_2             3              88
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KDM6A MUTATED        0      1      1      1      3
  KDM6A WILD-TYPE     42     20     50     61     80
D23V10, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              20
  CLUS_3             1              50
  CLUS_4             1              61
  CLUS_5             3              80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = RNF31 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        3      0      0
  RNF31 WILD-TYPE    154     59     42
D24V1, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             3             154
  CLUS_2             0              59
  CLUS_3             0              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        2      2      0
  RNF31 WILD-TYPE     73     87     97
D24V2, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             2              87
  CLUS_3             0              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        0      2      2
  RNF31 WILD-TYPE     42     57     61
D24V3, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             2              57
  CLUS_3             2              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
  RNF31 MUTATED        0      2      2
  RNF31 WILD-TYPE     48     64     48
D24V4, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             2              64
  CLUS_3             2              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        1      2      0
  RNF31 WILD-TYPE     80     82     93
D24V5, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             1              80
  CLUS_2             2              82
  CLUS_3             0              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        0      2      1
  RNF31 WILD-TYPE     90     81     84
D24V6, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             2              81
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF31 MUTATED        0      0      2      0      2
  RNF31 WILD-TYPE     48     18     57     55     77
D24V7, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             0              18
  CLUS_3             2              57
  CLUS_4             0              55
  CLUS_5             2              77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        0      0      4
  RNF31 WILD-TYPE     92     46    117
D24V8, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              92
  CLUS_2             0              46
  CLUS_3             4             117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF31 MUTATED        2      2      0
  RNF31 WILD-TYPE     68     89     98
D24V9, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             2              68
  CLUS_2             2              89
  CLUS_3             0              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF31 MUTATED        0      0      2      0      2
  RNF31 WILD-TYPE     42     21     49     62     81
D24V10, multiclass
        clus
vv       RNF31 MUTATED RNF31 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              21
  CLUS_3             2              49
  CLUS_4             0              62
  CLUS_5             2              81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = ESCO1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        3      0      1
  ESCO1 WILD-TYPE    154     59     41
D25V1, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             3             154
  CLUS_2             0              59
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        1      2      1
  ESCO1 WILD-TYPE     74     87     96
D25V2, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             1              74
  CLUS_2             2              87
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        1      0      2
  ESCO1 WILD-TYPE     41     59     61
D25V3, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              59
  CLUS_3             2              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
  ESCO1 MUTATED        2      1      0
  ESCO1 WILD-TYPE     46     65     50
D25V4, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             1              65
  CLUS_3             0              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
  ESCO1 MUTATED        0      3      1
  ESCO1 WILD-TYPE     81     81     92
D25V5, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             0              81
  CLUS_2             3              81
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        0      3      1
  ESCO1 WILD-TYPE     90     80     84
D25V6, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             3              80
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ESCO1 MUTATED        2      0      0      2      0
  ESCO1 WILD-TYPE     46     18     59     53     79
D25V7, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             0              18
  CLUS_3             0              59
  CLUS_4             2              53
  CLUS_5             0              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        3      0      1
  ESCO1 WILD-TYPE     89     46    120
D25V8, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             3              89
  CLUS_2             0              46
  CLUS_3             1             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ESCO1 MUTATED        1      1      2
  ESCO1 WILD-TYPE     69     90     96
D25V9, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             1              90
  CLUS_3             2              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ESCO1 MUTATED        1      0      0      3      0
  ESCO1 WILD-TYPE     41     21     51     59     83
D25V10, multiclass
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              21
  CLUS_3             0              51
  CLUS_4             3              59
  CLUS_5             0              83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = LMOD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        3      0      0
  LMOD2 WILD-TYPE    154     59     42
D26V1, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             3             154
  CLUS_2             0              59
  CLUS_3             0              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      2      1
  LMOD2 WILD-TYPE     75     87     96
D26V2, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             2              87
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      1      1
  LMOD2 WILD-TYPE     42     58     62
D26V3, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46D 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      1      1
  LMOD2 WILD-TYPE     48     65     49
D26V4, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46D 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        1      1      1
  LMOD2 WILD-TYPE     80     83     92
D26V5, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              80
  CLUS_2             1              83
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        1      1      1
  LMOD2 WILD-TYPE     89     82     84
D26V6, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             1              82
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LMOD2 MUTATED        1      1      0      0      1
  LMOD2 WILD-TYPE     47     17     59     55     78
D26V7, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             1              17
  CLUS_3             0              59
  CLUS_4             0              55
  CLUS_5             1              78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        1      1      1
  LMOD2 WILD-TYPE     91     45    120
D26V8, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             1              45
  CLUS_3             1             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      1      2
  LMOD2 WILD-TYPE     70     90     96
D26V9, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             0              70
  CLUS_2             1              90
  CLUS_3             2              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LMOD2 MUTATED        1      1      0      0      1
  LMOD2 WILD-TYPE     41     20     51     62     82
D26V10, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             1              20
  CLUS_3             0              51
  CLUS_4             0              62
  CLUS_5             1              82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = FAM120B MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        1      1      1
  FAM120B WILD-TYPE    156     58     41
D27V1, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               1               156
  CLUS_2               1                58
  CLUS_3               1                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        1      1      1
  FAM120B WILD-TYPE     74     88     96
D27V2, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               1                74
  CLUS_2               1                88
  CLUS_3               1                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        0      1      1
  FAM120B WILD-TYPE     42     58     62
D27V3, multiclass
[1] "Remove cluster labels:" "FAM120B MUTATED"       
clus
  FAM120B MUTATED FAM120B WILD-TYPE 
                2               162 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7315 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8469 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-8470        TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-EJ-A65E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A65M        TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817        TCGA-HC-8264 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C        TCGA-J9-A52E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO        TCGA-KC-A4BR 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        1      1      0
  FAM120B WILD-TYPE     47     65     50
D27V4, multiclass
[1] "Remove cluster labels:" "FAM120B MUTATED"       
clus
  FAM120B MUTATED FAM120B WILD-TYPE 
                2               162 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7315 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8469 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-8470        TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-EJ-A65E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A65M        TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817        TCGA-HC-8264 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C        TCGA-J9-A52E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO        TCGA-KC-A4BR 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        2      0      1
  FAM120B WILD-TYPE     79     84     92
D27V5, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               2                79
  CLUS_2               0                84
  CLUS_3               1                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        1      0      2
  FAM120B WILD-TYPE     89     83     83
D27V6, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               1                89
  CLUS_2               0                83
  CLUS_3               2                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM120B MUTATED        0      0      0      0      3
  FAM120B WILD-TYPE     48     18     59     55     76
D27V7, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                48
  CLUS_2               0                18
  CLUS_3               0                59
  CLUS_4               0                55
  CLUS_5               3                76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        0      0      3
  FAM120B WILD-TYPE     92     46    118
D27V8, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                92
  CLUS_2               0                46
  CLUS_3               3               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM120B MUTATED        0      3      0
  FAM120B WILD-TYPE     70     88     98
D27V9, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                70
  CLUS_2               3                88
  CLUS_3               0                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM120B MUTATED        0      0      0      0      3
  FAM120B WILD-TYPE     42     21     51     62     80
D27V10, multiclass
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  CLUS_1               0                42
  CLUS_2               0                21
  CLUS_3               0                51
  CLUS_4               0                62
  CLUS_5               3                80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = CLEC1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        3      0      1
  CLEC1A WILD-TYPE    154     59     41
D28V1, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              3              154
  CLUS_2              0               59
  CLUS_3              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        0      1      3
  CLEC1A WILD-TYPE     75     88     94
D28V2, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              0               75
  CLUS_2              1               88
  CLUS_3              3               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        0      1      1
  CLEC1A WILD-TYPE     42     58     62
D28V3, multiclass
[1] "Remove cluster labels:" "CLEC1A MUTATED"        
clus
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               2              162 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5501       TCGA-EJ-5502       TCGA-EJ-5503       TCGA-EJ-5504 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7115       TCGA-EJ-7125       TCGA-EJ-7314       TCGA-EJ-7315 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7328       TCGA-EJ-7330 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7331       TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7784       TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7789       TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7794       TCGA-EJ-7797       TCGA-EJ-8468       TCGA-EJ-8469 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-8470       TCGA-EJ-8474       TCGA-EJ-A46B       TCGA-EJ-A46D 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-A46E       TCGA-EJ-A46F       TCGA-EJ-A46G       TCGA-EJ-A65E 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-A65M       TCGA-FC-7708       TCGA-FC-7961       TCGA-FC-A4JI 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-FC-A5OB       TCGA-G9-6329       TCGA-G9-6338       TCGA-G9-6342 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6370       TCGA-G9-6371 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-G9-7510 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523       TCGA-G9-7525 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-H9-7775       TCGA-HC-7077       TCGA-HC-7079       TCGA-HC-7081 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736       TCGA-HC-7740 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7748       TCGA-HC-7817       TCGA-HC-8264 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HI-7168       TCGA-HI-7169       TCGA-HI-7170       TCGA-HI-7171 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-J4-8198       TCGA-J4-8200       TCGA-J9-A52C       TCGA-J9-A52E 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KC-A4BL       TCGA-KC-A4BN       TCGA-KC-A4BO       TCGA-KC-A4BR 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KC-A4BV       TCGA-KK-A59V       TCGA-KK-A59X       TCGA-KK-A59Y 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KK-A59Z       TCGA-KK-A5A1 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        0      1      1
  CLEC1A WILD-TYPE     48     65     49
D28V4, multiclass
[1] "Remove cluster labels:" "CLEC1A MUTATED"        
clus
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               2              162 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5501       TCGA-EJ-5502       TCGA-EJ-5503       TCGA-EJ-5504 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7115       TCGA-EJ-7125       TCGA-EJ-7314       TCGA-EJ-7315 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7328       TCGA-EJ-7330 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7331       TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7784       TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7789       TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7794       TCGA-EJ-7797       TCGA-EJ-8468       TCGA-EJ-8469 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-8470       TCGA-EJ-8474       TCGA-EJ-A46B       TCGA-EJ-A46D 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-A46E       TCGA-EJ-A46F       TCGA-EJ-A46G       TCGA-EJ-A65E 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-A65M       TCGA-FC-7708       TCGA-FC-7961       TCGA-FC-A4JI 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-FC-A5OB       TCGA-G9-6329       TCGA-G9-6338       TCGA-G9-6342 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6370       TCGA-G9-6371 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-G9-7510 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523       TCGA-G9-7525 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-H9-7775       TCGA-HC-7077       TCGA-HC-7079       TCGA-HC-7081 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736       TCGA-HC-7740 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7748       TCGA-HC-7817       TCGA-HC-8264 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HI-7168       TCGA-HI-7169       TCGA-HI-7170       TCGA-HI-7171 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-J4-8198       TCGA-J4-8200       TCGA-J9-A52C       TCGA-J9-A52E 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KC-A4BL       TCGA-KC-A4BN       TCGA-KC-A4BO       TCGA-KC-A4BR 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KC-A4BV       TCGA-KK-A59V       TCGA-KK-A59X       TCGA-KK-A59Y 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-KK-A59Z       TCGA-KK-A5A1 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        0      3      1
  CLEC1A WILD-TYPE     81     81     92
D28V5, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              0               81
  CLUS_2              3               81
  CLUS_3              1               92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        1      1      2
  CLEC1A WILD-TYPE     89     82     83
D28V6, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              1               89
  CLUS_2              1               82
  CLUS_3              2               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLEC1A MUTATED        0      1      1      1      1
  CLEC1A WILD-TYPE     48     17     58     54     78
D28V7, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              0               48
  CLUS_2              1               17
  CLUS_3              1               58
  CLUS_4              1               54
  CLUS_5              1               78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        2      1      1
  CLEC1A WILD-TYPE     90     45    120
D28V8, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              2               90
  CLUS_2              1               45
  CLUS_3              1              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CLEC1A MUTATED        0      1      3
  CLEC1A WILD-TYPE     70     90     95
D28V9, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              0               70
  CLUS_2              1               90
  CLUS_3              3               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CLEC1A MUTATED        1      1      0      1      1
  CLEC1A WILD-TYPE     41     20     51     61     82
D28V10, multiclass
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  CLUS_1              1               41
  CLUS_2              1               20
  CLUS_3              0               51
  CLUS_4              1               61
  CLUS_5              1               82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = ITGA2B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        3      0      0
  ITGA2B WILD-TYPE    154     59     42
D29V1, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              3              154
  CLUS_2              0               59
  CLUS_3              0               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        1      1      1
  ITGA2B WILD-TYPE     74     88     96
D29V2, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               88
  CLUS_3              1               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        0      1      2
  ITGA2B WILD-TYPE     42     58     61
D29V3, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              0               42
  CLUS_2              1               58
  CLUS_3              2               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
  ITGA2B MUTATED        0      2      1
  ITGA2B WILD-TYPE     48     64     49
D29V4, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              0               48
  CLUS_2              2               64
  CLUS_3              1               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
  ITGA2B MUTATED        2      0      1
  ITGA2B WILD-TYPE     79     84     92
D29V5, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              2               79
  CLUS_2              0               84
  CLUS_3              1               92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        1      0      2
  ITGA2B WILD-TYPE     89     83     83
D29V6, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              1               89
  CLUS_2              0               83
  CLUS_3              2               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ITGA2B MUTATED        0      1      1      0      1
  ITGA2B WILD-TYPE     48     17     58     55     78
D29V7, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              0               48
  CLUS_2              1               17
  CLUS_3              1               58
  CLUS_4              0               55
  CLUS_5              1               78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        0      1      2
  ITGA2B WILD-TYPE     92     45    119
D29V8, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              0               92
  CLUS_2              1               45
  CLUS_3              2              119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ITGA2B MUTATED        1      1      1
  ITGA2B WILD-TYPE     69     90     97
D29V9, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              1               69
  CLUS_2              1               90
  CLUS_3              1               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ITGA2B MUTATED        0      0      2      0      1
  ITGA2B WILD-TYPE     42     21     49     62     82
D29V10, multiclass
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               21
  CLUS_3              2               49
  CLUS_4              0               62
  CLUS_5              1               82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = RNF17 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        1      1      1
  RNF17 WILD-TYPE    156     58     41
D30V1, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             1             156
  CLUS_2             1              58
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        0      1      2
  RNF17 WILD-TYPE     75     88     95
D30V2, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             1              88
  CLUS_3             2              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        3      0      0
  RNF17 WILD-TYPE     39     59     63
D30V3, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             0              59
  CLUS_3             0              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
  RNF17 MUTATED        3      0      0
  RNF17 WILD-TYPE     45     66     50
D30V4, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             0              66
  CLUS_3             0              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
  RNF17 MUTATED        0      0      3
  RNF17 WILD-TYPE     81     84     90
D30V5, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             0              81
  CLUS_2             0              84
  CLUS_3             3              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        0      1      2
  RNF17 WILD-TYPE     90     82     83
D30V6, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             1              82
  CLUS_3             2              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF17 MUTATED        1      0      0      1      1
  RNF17 WILD-TYPE     47     18     59     54     78
D30V7, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             0              18
  CLUS_3             0              59
  CLUS_4             1              54
  CLUS_5             1              78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        2      0      1
  RNF17 WILD-TYPE     90     46    120
D30V8, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             2              90
  CLUS_2             0              46
  CLUS_3             1             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RNF17 MUTATED        1      1      1
  RNF17 WILD-TYPE     69     90     97
D30V9, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             1              90
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RNF17 MUTATED        0      0      0      3      0
  RNF17 WILD-TYPE     42     21     51     59     83
D30V10, multiclass
        clus
vv       RNF17 MUTATED RNF17 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              21
  CLUS_3             0              51
  CLUS_4             3              59
  CLUS_5             0              83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = RP1L1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        5      1      1
  RP1L1 WILD-TYPE    152     58     41
D31V1, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             5             152
  CLUS_2             1              58
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        2      3      2
  RP1L1 WILD-TYPE     73     86     95
D31V2, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             3              86
  CLUS_3             2              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        0      2      3
  RP1L1 WILD-TYPE     42     57     60
D31V3, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             2              57
  CLUS_3             3              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
  RP1L1 MUTATED        0      3      2
  RP1L1 WILD-TYPE     48     63     48
D31V4, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             3              63
  CLUS_3             2              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        2      3      2
  RP1L1 WILD-TYPE     79     81     91
D31V5, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             2              79
  CLUS_2             3              81
  CLUS_3             2              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        3      1      3
  RP1L1 WILD-TYPE     87     82     82
D31V6, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             1              82
  CLUS_3             3              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RP1L1 MUTATED        0      0      5      1      1
  RP1L1 WILD-TYPE     48     18     54     54     78
D31V7, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             0              18
  CLUS_3             5              54
  CLUS_4             1              54
  CLUS_5             1              78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        2      1      4
  RP1L1 WILD-TYPE     90     45    117
D31V8, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             2              90
  CLUS_2             1              45
  CLUS_3             4             117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RP1L1 MUTATED        5      1      1
  RP1L1 WILD-TYPE     65     90     97
D31V9, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             5              65
  CLUS_2             1              90
  CLUS_3             1              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RP1L1 MUTATED        3      0      3      0      1
  RP1L1 WILD-TYPE     39     21     48     62     82
D31V10, multiclass
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             0              21
  CLUS_3             3              48
  CLUS_4             0              62
  CLUS_5             1              82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = EOMES MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        3      0      1
  EOMES WILD-TYPE    154     59     41
D32V1, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3             154
  CLUS_2             0              59
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        2      1      1
  EOMES WILD-TYPE     73     88     96
D32V2, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              73
  CLUS_2             1              88
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        0      1      2
  EOMES WILD-TYPE     42     58     61
D32V3, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              58
  CLUS_3             2              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
  EOMES MUTATED        0      2      1
  EOMES WILD-TYPE     48     64     49
D32V4, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             0              48
  CLUS_2             2              64
  CLUS_3             1              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
  EOMES MUTATED        2      2      0
  EOMES WILD-TYPE     79     82     93
D32V5, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              79
  CLUS_2             2              82
  CLUS_3             0              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        3      0      1
  EOMES WILD-TYPE     87     83     84
D32V6, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3              87
  CLUS_2             0              83
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EOMES MUTATED        0      2      2      0      0
  EOMES WILD-TYPE     48     16     57     55     79
D32V7, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             0              48
  CLUS_2             2              16
  CLUS_3             2              57
  CLUS_4             0              55
  CLUS_5             0              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        2      2      0
  EOMES WILD-TYPE     90     44    121
D32V8, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              90
  CLUS_2             2              44
  CLUS_3             0             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        1      1      2
  EOMES WILD-TYPE     69     90     96
D32V9, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              69
  CLUS_2             1              90
  CLUS_3             2              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EOMES MUTATED        2      2      0      0      0
  EOMES WILD-TYPE     40     19     51     62     83
D32V10, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              19
  CLUS_3             0              51
  CLUS_4             0              62
  CLUS_5             0              83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = MTF1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        3      0      0
  MTF1 WILD-TYPE    154     59     42
D33V1, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            3            154
  CLUS_2            0             59
  CLUS_3            0             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        1      2      0
  MTF1 WILD-TYPE     74     87     97
D33V2, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            1             74
  CLUS_2            2             87
  CLUS_3            0             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        0      1      1
  MTF1 WILD-TYPE     42     58     62
D33V3, multiclass
[1] "Remove cluster labels:" "MTF1 MUTATED"          
clus
  MTF1 MUTATED MTF1 WILD-TYPE 
             2            162 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7125     TCGA-EJ-7314 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7328 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8474     TCGA-EJ-A46B 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A46D     TCGA-EJ-A46E     TCGA-EJ-A46F     TCGA-EJ-A46G 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A65E     TCGA-EJ-A65M     TCGA-FC-7708     TCGA-FC-7961 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-FC-A4JI     TCGA-FC-A5OB     TCGA-G9-6329     TCGA-G9-6338 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6351     TCGA-G9-6353 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6494     TCGA-G9-6496 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521     TCGA-G9-7522 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-7525     TCGA-H9-7775     TCGA-HC-7077     TCGA-HC-7079 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7744     TCGA-HC-7748     TCGA-HC-7817 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-8264     TCGA-HI-7168     TCGA-HI-7169     TCGA-HI-7170 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HI-7171     TCGA-J4-8198     TCGA-J4-8200     TCGA-J9-A52E 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BO     TCGA-KC-A4BR 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KC-A4BV     TCGA-KK-A59V     TCGA-KK-A59X     TCGA-KK-A59Y 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KK-A59Z     TCGA-KK-A5A1 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        0      1      1
  MTF1 WILD-TYPE     48     65     49
D33V4, multiclass
[1] "Remove cluster labels:" "MTF1 MUTATED"          
clus
  MTF1 MUTATED MTF1 WILD-TYPE 
             2            162 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7125     TCGA-EJ-7314 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7328 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8474     TCGA-EJ-A46B 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A46D     TCGA-EJ-A46E     TCGA-EJ-A46F     TCGA-EJ-A46G 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A65E     TCGA-EJ-A65M     TCGA-FC-7708     TCGA-FC-7961 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-FC-A4JI     TCGA-FC-A5OB     TCGA-G9-6329     TCGA-G9-6338 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6351     TCGA-G9-6353 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6494     TCGA-G9-6496 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521     TCGA-G9-7522 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-7525     TCGA-H9-7775     TCGA-HC-7077     TCGA-HC-7079 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7744     TCGA-HC-7748     TCGA-HC-7817 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-8264     TCGA-HI-7168     TCGA-HI-7169     TCGA-HI-7170 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HI-7171     TCGA-J4-8198     TCGA-J4-8200     TCGA-J9-A52E 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BO     TCGA-KC-A4BR 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KC-A4BV     TCGA-KK-A59V     TCGA-KK-A59X     TCGA-KK-A59Y 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KK-A59Z     TCGA-KK-A5A1 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        2      1      0
  MTF1 WILD-TYPE     79     83     93
D33V5, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            2             79
  CLUS_2            1             83
  CLUS_3            0             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        3      0      0
  MTF1 WILD-TYPE     87     83     85
D33V6, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            3             87
  CLUS_2            0             83
  CLUS_3            0             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MTF1 MUTATED        0      1      2      0      0
  MTF1 WILD-TYPE     48     17     57     55     79
D33V7, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            1             17
  CLUS_3            2             57
  CLUS_4            0             55
  CLUS_5            0             79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        1      2      0
  MTF1 WILD-TYPE     91     44    121
D33V8, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            1             91
  CLUS_2            2             44
  CLUS_3            0            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTF1 MUTATED        1      1      1
  MTF1 WILD-TYPE     69     90     97
D33V9, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            1             69
  CLUS_2            1             90
  CLUS_3            1             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MTF1 MUTATED        1      2      0      0      0
  MTF1 WILD-TYPE     41     19     51     62     83
D33V10, multiclass
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            2             19
  CLUS_3            0             51
  CLUS_4            0             62
  CLUS_5            0             83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = NTM MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        3      1      1
  NTM WILD-TYPE    154     58     41
D34V1, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           3           154
  CLUS_2           1            58
  CLUS_3           1            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        0      2      3
  NTM WILD-TYPE     75     87     94
D34V2, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           0            75
  CLUS_2           2            87
  CLUS_3           3            94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        1      0      4
  NTM WILD-TYPE     41     59     59
D34V3, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           1            41
  CLUS_2           0            59
  CLUS_3           4            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        2      3      0
  NTM WILD-TYPE     46     63     50
D34V4, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           2            46
  CLUS_2           3            63
  CLUS_3           0            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
  NTM MUTATED        0      2      3
  NTM WILD-TYPE     81     82     90
D34V5, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           0            81
  CLUS_2           2            82
  CLUS_3           3            90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        0      3      2
  NTM WILD-TYPE     90     80     83
D34V6, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           0            90
  CLUS_2           3            80
  CLUS_3           2            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NTM MUTATED        1      0      0      2      2
  NTM WILD-TYPE     47     18     59     53     77
D34V7, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           1            47
  CLUS_2           0            18
  CLUS_3           0            59
  CLUS_4           2            53
  CLUS_5           2            77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        2      0      3
  NTM WILD-TYPE     90     46    118
D34V8, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           2            90
  CLUS_2           0            46
  CLUS_3           3           118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NTM MUTATED        1      2      2
  NTM WILD-TYPE     69     89     96
D34V9, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           1            69
  CLUS_2           2            89
  CLUS_3           2            96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NTM MUTATED        0      0      0      3      2
  NTM WILD-TYPE     42     21     51     59     81
D34V10, multiclass
        clus
vv       NTM MUTATED NTM WILD-TYPE
  CLUS_1           0            42
  CLUS_2           0            21
  CLUS_3           0            51
  CLUS_4           3            59
  CLUS_5           2            81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = FNBP4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        1      1      1
  FNBP4 WILD-TYPE    156     58     41
D35V1, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             1             156
  CLUS_2             1              58
  CLUS_3             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        2      0      1
  FNBP4 WILD-TYPE     73     89     96
D35V2, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             0              89
  CLUS_3             1              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        0      1      1
  FNBP4 WILD-TYPE     42     58     62
D35V3, multiclass
[1] "Remove cluster labels:" "FNBP4 MUTATED"         
clus
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7525 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079      TCGA-HC-7081 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        0      1      1
  FNBP4 WILD-TYPE     48     65     49
D35V4, multiclass
[1] "Remove cluster labels:" "FNBP4 MUTATED"         
clus
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7525 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079      TCGA-HC-7081 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        2      0      1
  FNBP4 WILD-TYPE     79     84     92
D35V5, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             2              79
  CLUS_2             0              84
  CLUS_3             1              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        2      0      1
  FNBP4 WILD-TYPE     88     83     84
D35V6, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             2              88
  CLUS_2             0              83
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FNBP4 MUTATED        0      1      1      0      1
  FNBP4 WILD-TYPE     48     17     58     55     78
D35V7, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             1              17
  CLUS_3             1              58
  CLUS_4             0              55
  CLUS_5             1              78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        0      1      2
  FNBP4 WILD-TYPE     92     45    119
D35V8, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             0              92
  CLUS_2             1              45
  CLUS_3             2             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FNBP4 MUTATED        1      2      0
  FNBP4 WILD-TYPE     69     89     98
D35V9, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             2              89
  CLUS_3             0              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FNBP4 MUTATED        0      1      2      0      0
  FNBP4 WILD-TYPE     42     20     49     62     83
D35V10, multiclass
        clus
vv       FNBP4 MUTATED FNBP4 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              20
  CLUS_3             2              49
  CLUS_4             0              62
  CLUS_5             0              83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = CDKN1B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        2      1      1
  CDKN1B WILD-TYPE    155     58     41
D36V1, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              2              155
  CLUS_2              1               58
  CLUS_3              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        3      0      1
  CDKN1B WILD-TYPE     72     89     96
D36V2, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              3               72
  CLUS_2              0               89
  CLUS_3              1               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        1      0      3
  CDKN1B WILD-TYPE     41     59     60
D36V3, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               41
  CLUS_2              0               59
  CLUS_3              3               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
  CDKN1B MUTATED        1      3      0
  CDKN1B WILD-TYPE     47     63     50
D36V4, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               47
  CLUS_2              3               63
  CLUS_3              0               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
  CDKN1B MUTATED        3      0      1
  CDKN1B WILD-TYPE     78     84     92
D36V5, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              3               78
  CLUS_2              0               84
  CLUS_3              1               92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        2      0      2
  CDKN1B WILD-TYPE     88     83     83
D36V6, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              2               88
  CLUS_2              0               83
  CLUS_3              2               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN1B MUTATED        0      0      1      2      1
  CDKN1B WILD-TYPE     48     18     58     53     78
D36V7, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              0               48
  CLUS_2              0               18
  CLUS_3              1               58
  CLUS_4              2               53
  CLUS_5              1               78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        0      2      2
  CDKN1B WILD-TYPE     92     44    119
D36V8, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              0               92
  CLUS_2              2               44
  CLUS_3              2              119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        2      1      1
  CDKN1B WILD-TYPE     68     90     97
D36V9, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              2               68
  CLUS_2              1               90
  CLUS_3              1               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN1B MUTATED        0      1      2      0      1
  CDKN1B WILD-TYPE     42     20     49     62     82
D36V10, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              0               42
  CLUS_2              1               20
  CLUS_3              2               49
  CLUS_4              0               62
  CLUS_5              1               82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = EIF2AK3 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        3      1      0
  EIF2AK3 WILD-TYPE    154     58     42
D37V1, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               3               154
  CLUS_2               1                58
  CLUS_3               0                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        0      3      1
  EIF2AK3 WILD-TYPE     75     86     96
D37V2, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               0                75
  CLUS_2               3                86
  CLUS_3               1                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        1      0      1
  EIF2AK3 WILD-TYPE     41     59     62
D37V3, multiclass
[1] "Remove cluster labels:" "EIF2AK3 MUTATED"       
clus
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                2               162 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5763 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8470 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-EJ-A65E        TCGA-EJ-A65M 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI        TCGA-FC-A5OB 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817        TCGA-HC-8264 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C        TCGA-J9-A52E 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO        TCGA-KC-A4BR 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        1      1      0
  EIF2AK3 WILD-TYPE     47     65     50
D37V4, multiclass
[1] "Remove cluster labels:" "EIF2AK3 MUTATED"       
clus
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                2               162 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5763 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8470 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-EJ-A65E        TCGA-EJ-A65M 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A4JI        TCGA-FC-A5OB 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-7817        TCGA-HC-8264 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-J4-8198        TCGA-J4-8200        TCGA-J9-A52C        TCGA-J9-A52E 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO        TCGA-KC-A4BR 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KC-A4BV        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        0      2      2
  EIF2AK3 WILD-TYPE     81     82     91
D37V5, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               0                81
  CLUS_2               2                82
  CLUS_3               2                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        1      2      1
  EIF2AK3 WILD-TYPE     89     81     84
D37V6, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               1                89
  CLUS_2               2                81
  CLUS_3               1                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EIF2AK3 MUTATED        1      0      0      0      3
  EIF2AK3 WILD-TYPE     47     18     59     55     76
D37V7, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               1                47
  CLUS_2               0                18
  CLUS_3               0                59
  CLUS_4               0                55
  CLUS_5               3                76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        1      1      2
  EIF2AK3 WILD-TYPE     91     45    119
D37V8, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               1                91
  CLUS_2               1                45
  CLUS_3               2               119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  EIF2AK3 MUTATED        0      3      1
  EIF2AK3 WILD-TYPE     70     88     97
D37V9, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               0                70
  CLUS_2               3                88
  CLUS_3               1                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EIF2AK3 MUTATED        0      0      0      1      3
  EIF2AK3 WILD-TYPE     42     21     51     61     80
D37V10, multiclass
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  CLUS_1               0                42
  CLUS_2               0                21
  CLUS_3               0                51
  CLUS_4               1                61
  CLUS_5               3                80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = LARP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        3      0      0
  LARP1 WILD-TYPE    154     59     42
D38V1, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             3             154
  CLUS_2             0              59
  CLUS_3             0              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        1      2      0
  LARP1 WILD-TYPE     74     87     97
D38V2, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             1              74
  CLUS_2             2              87
  CLUS_3             0              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        1      0      1
  LARP1 WILD-TYPE     41     59     62
D38V3, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5521      TCGA-EJ-5522 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5530 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8470 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D      TCGA-EJ-A46E 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E      TCGA-EJ-A65M 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI      TCGA-FC-A5OB 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370      TCGA-G9-6371 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-G9-7510 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523      TCGA-G9-7525 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079      TCGA-HC-7081 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      1      1
  LARP1 WILD-TYPE     48     65     49
D38V4, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5521      TCGA-EJ-5522 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5530 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8470 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D      TCGA-EJ-A46E 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E      TCGA-EJ-A65M 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI      TCGA-FC-A5OB 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370      TCGA-G9-6371 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-G9-7510 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523      TCGA-G9-7525 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079      TCGA-HC-7081 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      1      2
  LARP1 WILD-TYPE     81     83     91
D38V5, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0              81
  CLUS_2             1              83
  CLUS_3             2              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      2      1
  LARP1 WILD-TYPE     90     81     84
D38V6, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             2              81
  CLUS_3             1              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LARP1 MUTATED        2      0      0      1      0
  LARP1 WILD-TYPE     46     18     59     54     79
D38V7, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             0              18
  CLUS_3             0              59
  CLUS_4             1              54
  CLUS_5             0              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        3      0      0
  LARP1 WILD-TYPE     89     46    121
D38V8, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             3              89
  CLUS_2             0              46
  CLUS_3             0             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        1      0      2
  LARP1 WILD-TYPE     69     91     96
D38V9, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             1              69
  CLUS_2             0              91
  CLUS_3             2              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LARP1 MUTATED        0      0      0      2      1
  LARP1 WILD-TYPE     42     21     51     60     82
D38V10, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              21
  CLUS_3             0              51
  CLUS_4             2              60
  CLUS_5             1              82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
