[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"      "-oTOV-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/OV-TP/10671262/OV-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/10686039/transformed.cor.cli.txt"

nPatients in clinical file=586, in cluster file=316, common to both=316
[1]  19 316
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           273             43 
  TP53 MUTATED TP53 WILD-TYPE 
           273             43 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
[1] "FAM86B2 MUTATION ANALYSIS"
[1] 3
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                6               310 
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                6               310 
[1] "TBP MUTATION ANALYSIS"
[1] 3
  TBP MUTATED TBP WILD-TYPE 
            4           312 
  TBP MUTATED TBP WILD-TYPE 
            4           312 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4              312 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4              312 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
[1] "C10ORF140 MUTATION ANALYSIS"
[1] 3
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  5                 311 
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  5                 311 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             11             305 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             11             305 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             308 
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             308 
[1] "OR4F21 MUTATION ANALYSIS"
[1] 3
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               3              313 
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               3              313 
[1] "C9ORF171 MUTATION ANALYSIS"
[1] 3
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                311 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                311 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             11             305 
  HYDIN MUTATED HYDIN WILD-TYPE 
             11             305 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            8           308 
  RB1 MUTATED RB1 WILD-TYPE 
            8           308 
[1] "GART MUTATION ANALYSIS"
[1] 3
  GART MUTATED GART WILD-TYPE 
             3            313 
  GART MUTATED GART WILD-TYPE 
             3            313 
[1] "SRC MUTATION ANALYSIS"
[1] 3
  SRC MUTATED SRC WILD-TYPE 
            4           312 
  SRC MUTATED SRC WILD-TYPE 
            4           312 
[1] "ZNF236 MUTATION ANALYSIS"
[1] 3
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               7              309 
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               7              309 
[1] "NBPF16 MUTATION ANALYSIS"
[1] 3
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               4              312 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               4              312 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                7               309 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                7               309 
[1] "SON MUTATION ANALYSIS"
[1] 3
  SON MUTATED SON WILD-TYPE 
            8           308 
  SON MUTATED SON WILD-TYPE 
            8           308 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "RPPA_CNMF"                  
 [7] "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF"               
 [9] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[11] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[13] "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 13 rows and 316 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIR_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "RPPA_CNMF"                  
 [7] "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF"               
 [9] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[11] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[13] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 316 columns, 0 survival variables, and 13 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=10, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED      103    100     70
  TP53 WILD-TYPE     16     15     12
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          103             16
  CLUS_2          100             15
  CLUS_3           70             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED      156     77     40
  TP53 WILD-TYPE     17     17      9
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          156             17
  CLUS_2           77             17
  CLUS_3           40              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       82     80    111
  TP53 WILD-TYPE     10     16     17
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           82             10
  CLUS_2           80             16
  CLUS_3          111             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED       43      25     28     47     19     37     18     14
  TP53 WILD-TYPE      8       3      5      6      1      7      2      2
                vv
clus             CLUS_8 CLUS_9
  TP53 MUTATED       16     26
  TP53 WILD-TYPE      5      4
D1V4, multiclass
         clus
vv        TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            43              8
  CLUS_10           25              3
  CLUS_2            28              5
  CLUS_3            47              6
  CLUS_4            19              1
  CLUS_5            37              7
  CLUS_6            18              2
  CLUS_7            14              2
  CLUS_8            16              5
  CLUS_9            26              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       96     93     80
  TP53 WILD-TYPE     16     10     16
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           96             16
  CLUS_2           93             10
  CLUS_3           80             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       63     88     33
  TP53 WILD-TYPE     13      8      5
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           63             13
  CLUS_2           88              8
  CLUS_3           33              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       54     44     57     29
  TP53 WILD-TYPE     13      4      7      2
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           54             13
  CLUS_2           44              4
  CLUS_3           57              7
  CLUS_4           29              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       60     36     45
  TP53 WILD-TYPE     10      4      6
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           60             10
  CLUS_2           36              4
  CLUS_3           45              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       58     68     15
  TP53 WILD-TYPE      8      8      4
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           58              8
  CLUS_2           68              8
  CLUS_3           15              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       65    106     78
  TP53 WILD-TYPE     14     13     11
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           65             14
  CLUS_2          106             13
  CLUS_3           78             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       64     38     85     62
  TP53 WILD-TYPE     10      8     14      6
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           64             10
  CLUS_2           38              8
  CLUS_3           85             14
  CLUS_4           62              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       51    111     87
  TP53 WILD-TYPE     13     13     12
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           51             13
  CLUS_2          111             13
  CLUS_3           87             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       94     99     56
  TP53 WILD-TYPE     17     14      7
D1V13, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           94             17
  CLUS_2           99             14
  CLUS_3           56              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = BRCA1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        4      7      1
  BRCA1 WILD-TYPE    115    108     81
D2V1, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4             115
  CLUS_2             7             108
  CLUS_3             1              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        7      2      3
  BRCA1 WILD-TYPE    166     92     46
D2V2, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             7             166
  CLUS_2             2              92
  CLUS_3             3              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        1      4      7
  BRCA1 WILD-TYPE     91     92    121
D2V3, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             4              92
  CLUS_3             7             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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BRCA1 MUTATED        0       2      1      4      1      3      0      0
  BRCA1 WILD-TYPE     51      26     32     49     19     41     20     16
                 vv
clus              CLUS_8 CLUS_9
  BRCA1 MUTATED        1      0
  BRCA1 WILD-TYPE     20     30
D2V4, multiclass
         clus
vv        BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1              0              51
  CLUS_10             2              26
  CLUS_2              1              32
  CLUS_3              4              49
  CLUS_4              1              19
  CLUS_5              3              41
  CLUS_6              0              20
  CLUS_7              0              16
  CLUS_8              1              20
  CLUS_9              0              30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        6      4      2
  BRCA1 WILD-TYPE    106     99     94
D2V5, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             6             106
  CLUS_2             4              99
  CLUS_3             2              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
  BRCA1 MUTATED        3      3      3
  BRCA1 WILD-TYPE     73     93     35
D2V6, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              73
  CLUS_2             3              93
  CLUS_3             3              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRCA1 MUTATED        1      1      4      3
  BRCA1 WILD-TYPE     66     47     60     28
D2V7, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             1              66
  CLUS_2             1              47
  CLUS_3             4              60
  CLUS_4             3              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        4      2      2
  BRCA1 WILD-TYPE     66     38     49
D2V8, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             2              38
  CLUS_3             2              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
  BRCA1 MUTATED        4      3      1
  BRCA1 WILD-TYPE     62     73     18
D2V9, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4              62
  CLUS_2             3              73
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        3      3      4
  BRCA1 WILD-TYPE     76    116     85
D2V10, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             3             116
  CLUS_3             4              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
  BRCA1 MUTATED        4      0      2      4
  BRCA1 WILD-TYPE     70     46     97     64
D2V11, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4              70
  CLUS_2             0              46
  CLUS_3             2              97
  CLUS_4             4              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA1 MUTATED        3      2      5
  BRCA1 WILD-TYPE     61    122     94
D2V12, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              61
  CLUS_2             2             122
  CLUS_3             5              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
  BRCA1 MUTATED        4      5      1
  BRCA1 WILD-TYPE    107    108     62
D2V13, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4             107
  CLUS_2             5             108
  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"

Clustering(3) Variable = FAM86B2 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        2      1      3
  FAM86B2 WILD-TYPE    117    114     79
D3V1, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               2               117
  CLUS_2               1               114
  CLUS_3               3                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        2      3      1
  FAM86B2 WILD-TYPE    171     91     48
D3V2, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               2               171
  CLUS_2               3                91
  CLUS_3               1                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
  FAM86B2 MUTATED        3      0      3
  FAM86B2 WILD-TYPE     89     96    125
D3V3, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               3                89
  CLUS_2               0                96
  CLUS_3               3               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FAM86B2 MUTATED        2       0      0      2      1      0      1      0
  FAM86B2 WILD-TYPE     49      28     33     51     19     44     19     16
                   vv
clus                CLUS_8 CLUS_9
  FAM86B2 MUTATED        0      0
  FAM86B2 WILD-TYPE     21     30
D3V4, multiclass
         clus
vv        FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1                2                49
  CLUS_10               0                28
  CLUS_2                0                33
  CLUS_3                2                51
  CLUS_4                1                19
  CLUS_5                0                44
  CLUS_6                1                19
  CLUS_7                0                16
  CLUS_8                0                21
  CLUS_9                0                30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        3      2      1
  FAM86B2 WILD-TYPE    109    101     95
D3V5, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               3               109
  CLUS_2               2               101
  CLUS_3               1                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
  FAM86B2 MUTATED        2      2      1
  FAM86B2 WILD-TYPE     74     94     37
D3V6, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               2                74
  CLUS_2               2                94
  CLUS_3               1                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM86B2 MUTATED        4      0      0      1
  FAM86B2 WILD-TYPE     63     48     64     30
D3V7, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               4                63
  CLUS_2               0                48
  CLUS_3               0                64
  CLUS_4               1                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        0      0      0
  FAM86B2 WILD-TYPE     70     40     51
D3V8, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        0      0      0
  FAM86B2 WILD-TYPE     66     76     19
D3V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        1      3      0
  FAM86B2 WILD-TYPE     78    116     89
D3V10, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               1                78
  CLUS_2               3               116
  CLUS_3               0                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 CLUS_4
  FAM86B2 MUTATED        1      1      2      0
  FAM86B2 WILD-TYPE     73     45     97     68
D3V11, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               1                73
  CLUS_2               1                45
  CLUS_3               2                97
  CLUS_4               0                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        1      3      0
  FAM86B2 WILD-TYPE     63    121     99
D3V12, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               1                63
  CLUS_2               3               121
  CLUS_3               0                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM86B2 MUTATED        3      0      1
  FAM86B2 WILD-TYPE    108    113     62
D3V13, multiclass
        clus
vv       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  CLUS_1               3               108
  CLUS_2               0               113
  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"

Clustering(4) Variable = TBP MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      1
  TBP WILD-TYPE    117    114     81
D4V1, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2           117
  CLUS_2           1           114
  CLUS_3           1            81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        3      1      0
  TBP WILD-TYPE    170     93     49
D4V2, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           3           170
  CLUS_2           1            93
  CLUS_3           0            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
  TBP MUTATED        2      1      1
  TBP WILD-TYPE     90     95    127
D4V3, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            90
  CLUS_2           1            95
  CLUS_3           1           127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TBP MUTATED        1       0      0      0      0      1      0      2      0
  TBP WILD-TYPE     50      28     33     53     20     43     20     14     21
               vv
clus            CLUS_9
  TBP MUTATED        0
  TBP WILD-TYPE     30
D4V4, multiclass
         clus
vv        TBP MUTATED TBP WILD-TYPE
  CLUS_1            1            50
  CLUS_10           0            28
  CLUS_2            0            33
  CLUS_3            0            53
  CLUS_4            0            20
  CLUS_5            1            43
  CLUS_6            0            20
  CLUS_7            2            14
  CLUS_8            0            21
  CLUS_9            0            30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        4      0      0
  TBP WILD-TYPE    108    103     96
D4V5, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           4           108
  CLUS_2           0           103
  CLUS_3           0            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
  TBP MUTATED        3      0      0
  TBP WILD-TYPE     73     96     38
D4V6, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           3            73
  CLUS_2           0            96
  CLUS_3           0            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TBP MUTATED        2      0      1      0
  TBP WILD-TYPE     65     48     63     31
D4V7, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            65
  CLUS_2           0            48
  CLUS_3           1            63
  CLUS_4           0            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      1      1
  TBP WILD-TYPE     69     39     50
D4V8, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            69
  CLUS_2           1            39
  CLUS_3           1            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
  TBP MUTATED        1      2      0
  TBP WILD-TYPE     65     74     19
D4V9, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            65
  CLUS_2           2            74
  CLUS_3           0            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      1
  TBP WILD-TYPE     77    118     88
D4V10, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            77
  CLUS_2           1           118
  CLUS_3           1            88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TBP MUTATED        1      0      2      1
  TBP WILD-TYPE     73     46     97     67
D4V11, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            73
  CLUS_2           0            46
  CLUS_3           2            97
  CLUS_4           1            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      2      1
  TBP WILD-TYPE     63    122     98
D4V12, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            63
  CLUS_2           2           122
  CLUS_3           1            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
  TBP MUTATED        2      1      1
  TBP WILD-TYPE    109    112     62
D4V13, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2           109
  CLUS_2           1           112
  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"

Clustering(5) Variable = NBPF10 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        1      2      1
  NBPF10 WILD-TYPE    118    113     81
D5V1, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1              118
  CLUS_2              2              113
  CLUS_3              1               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        2      1      1
  NBPF10 WILD-TYPE    171     93     48
D5V2, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2              171
  CLUS_2              1               93
  CLUS_3              1               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
  NBPF10 MUTATED        2      2      0
  NBPF10 WILD-TYPE     90     94    128
D5V3, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2               90
  CLUS_2              2               94
  CLUS_3              0              128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NBPF10 MUTATED        2       1      0      0      0      1      0      0
  NBPF10 WILD-TYPE     49      27     33     53     20     43     20     16
                  vv
clus               CLUS_8 CLUS_9
  NBPF10 MUTATED        0      0
  NBPF10 WILD-TYPE     21     30
D5V4, multiclass
         clus
vv        NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1               2               49
  CLUS_10              1               27
  CLUS_2               0               33
  CLUS_3               0               53
  CLUS_4               0               20
  CLUS_5               1               43
  CLUS_6               0               20
  CLUS_7               0               16
  CLUS_8               0               21
  CLUS_9               0               30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        1      2      1
  NBPF10 WILD-TYPE    111    101     95
D5V5, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1              111
  CLUS_2              2              101
  CLUS_3              1               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
  NBPF10 MUTATED        2      1      1
  NBPF10 WILD-TYPE     74     95     37
D5V6, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2               74
  CLUS_2              1               95
  CLUS_3              1               37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NBPF10 MUTATED        1      2      0      1
  NBPF10 WILD-TYPE     66     46     64     30
D5V7, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1               66
  CLUS_2              2               46
  CLUS_3              0               64
  CLUS_4              1               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        0      2      1
  NBPF10 WILD-TYPE     70     38     50
D5V8, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              0               70
  CLUS_2              2               38
  CLUS_3              1               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
  NBPF10 MUTATED        1      2      0
  NBPF10 WILD-TYPE     65     74     19
D5V9, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              2               74
  CLUS_3              0               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        1      1      2
  NBPF10 WILD-TYPE     78    118     87
D5V10, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1               78
  CLUS_2              1              118
  CLUS_3              2               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 CLUS_4
  NBPF10 MUTATED        0      0      2      2
  NBPF10 WILD-TYPE     74     46     97     66
D5V11, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              0               74
  CLUS_2              0               46
  CLUS_3              2               97
  CLUS_4              2               66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF10 MUTATED        1      1      2
  NBPF10 WILD-TYPE     63    123     97
D5V12, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              1               63
  CLUS_2              1              123
  CLUS_3              2               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
  NBPF10 MUTATED        2      2      0
  NBPF10 WILD-TYPE    109    111     63
D5V13, multiclass
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  CLUS_1              2              109
  CLUS_2              2              111
  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"

Clustering(6) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4      4      6
  NF1 WILD-TYPE    115    111     76
D6V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4           115
  CLUS_2           4           111
  CLUS_3           6            76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        6      7      1
  NF1 WILD-TYPE    167     87     48
D6V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           6           167
  CLUS_2           7            87
  CLUS_3           1            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
  NF1 MUTATED        3      5      6
  NF1 WILD-TYPE     89     91    122
D6V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            89
  CLUS_2           5            91
  CLUS_3           6           122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NF1 MUTATED        3       0      0      1      0      4      0      2      1
  NF1 WILD-TYPE     48      28     33     52     20     40     20     14     20
               vv
clus            CLUS_9
  NF1 MUTATED        3
  NF1 WILD-TYPE     27
D6V4, multiclass
         clus
vv        NF1 MUTATED NF1 WILD-TYPE
  CLUS_1            3            48
  CLUS_10           0            28
  CLUS_2            0            33
  CLUS_3            1            52
  CLUS_4            0            20
  CLUS_5            4            40
  CLUS_6            0            20
  CLUS_7            2            14
  CLUS_8            1            20
  CLUS_9            3            27
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        7      4      3
  NF1 WILD-TYPE    105     99     93
D6V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           7           105
  CLUS_2           4            99
  CLUS_3           3            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
  NF1 MUTATED        4      1      3
  NF1 WILD-TYPE     72     95     35
D6V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            72
  CLUS_2           1            95
  CLUS_3           3            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        5      0      2      1
  NF1 WILD-TYPE     62     48     62     30
D6V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            62
  CLUS_2           0            48
  CLUS_3           2            62
  CLUS_4           1            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4      0      2
  NF1 WILD-TYPE     66     40     49
D6V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            66
  CLUS_2           0            40
  CLUS_3           2            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
  NF1 MUTATED        5      0      1
  NF1 WILD-TYPE     61     76     18
D6V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            61
  CLUS_2           0            76
  CLUS_3           1            18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4      7      3
  NF1 WILD-TYPE     75    112     86
D6V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            75
  CLUS_2           7           112
  CLUS_3           3            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 CLUS_4
  NF1 MUTATED        6      1      4      3
  NF1 WILD-TYPE     68     45     95     65
D6V11, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           6            68
  CLUS_2           1            45
  CLUS_3           4            95
  CLUS_4           3            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        2      8      4
  NF1 WILD-TYPE     62    116     95
D6V12, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            62
  CLUS_2           8           116
  CLUS_3           4            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
  NF1 MUTATED        9      4      1
  NF1 WILD-TYPE    102    109     62
D6V13, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           9           102
  CLUS_2           4           109
  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"

Clustering(7) Variable = C10ORF140 MUTATION ANALYSIS
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        1      1      3
  C10ORF140 WILD-TYPE    118    114     79
D7V1, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 1                 118
  CLUS_2                 1                 114
  CLUS_3                 3                  79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        1      4      0
  C10ORF140 WILD-TYPE    172     90     49
D7V2, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 1                 172
  CLUS_2                 4                  90
  CLUS_3                 0                  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
  C10ORF140 MUTATED        2      1      2
  C10ORF140 WILD-TYPE     90     95    126
D7V3, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 2                  90
  CLUS_2                 1                  95
  CLUS_3                 2                 126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  C10ORF140 MUTATED        2       0      0      1      0      2      0      0
  C10ORF140 WILD-TYPE     49      28     33     52     20     42     20     16
                     vv
clus                  CLUS_8 CLUS_9
  C10ORF140 MUTATED        0      0
  C10ORF140 WILD-TYPE     21     30
D7V4, multiclass
         clus
vv        C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                  2                  49
  CLUS_10                 0                  28
  CLUS_2                  0                  33
  CLUS_3                  1                  52
  CLUS_4                  0                  20
  CLUS_5                  2                  42
  CLUS_6                  0                  20
  CLUS_7                  0                  16
  CLUS_8                  0                  21
  CLUS_9                  0                  30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        3      2      0
  C10ORF140 WILD-TYPE    109    101     96
D7V5, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 3                 109
  CLUS_2                 2                 101
  CLUS_3                 0                  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
  C10ORF140 MUTATED        2      1      0
  C10ORF140 WILD-TYPE     74     95     38
D7V6, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 2                  74
  CLUS_2                 1                  95
  CLUS_3                 0                  38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C10ORF140 MUTATED        2      1      0      0
  C10ORF140 WILD-TYPE     65     47     64     31
D7V7, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 2                  65
  CLUS_2                 1                  47
  CLUS_3                 0                  64
  CLUS_4                 0                  31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        1      0      1
  C10ORF140 WILD-TYPE     69     40     50
D7V8, multiclass
[1] "Remove cluster labels:" "C10ORF140 MUTATED"     
clus
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  2                 159 
         TCGA-04-1348          TCGA-04-1357          TCGA-04-1362 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-04-1364          TCGA-04-1365          TCGA-04-1514 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-0366          TCGA-09-0369          TCGA-09-1662 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-1666          TCGA-09-1669          TCGA-09-2044 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-2045          TCGA-09-2051          TCGA-09-2056 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-10-0928          TCGA-13-0730          TCGA-13-0800 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0890          TCGA-13-0893          TCGA-13-0897 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0899          TCGA-13-0913          TCGA-13-0920 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0924          TCGA-13-1403          TCGA-13-1405 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1410          TCGA-13-1481          TCGA-13-1497 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1498          TCGA-13-1505          TCGA-13-1506 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1507          TCGA-13-1512          TCGA-13-2060 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-1023          TCGA-23-1026          TCGA-23-1027 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-1120          TCGA-23-1122          TCGA-23-1123 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-2077          TCGA-23-2081          TCGA-24-0975 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1103          TCGA-24-1413          TCGA-24-1416 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1417          TCGA-24-1418          TCGA-24-1419 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1423          TCGA-24-1424          TCGA-24-1427 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1428          TCGA-24-1436          TCGA-24-1469 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1474          TCGA-24-1544          TCGA-24-1548 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1549          TCGA-24-1551          TCGA-24-1552 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1553          TCGA-24-1555          TCGA-24-1556 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1557          TCGA-24-1558          TCGA-24-1560 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1562          TCGA-24-1563          TCGA-24-1564 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1567          TCGA-24-1603          TCGA-24-1604 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1616          TCGA-24-2019          TCGA-24-2024 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2035          TCGA-24-2038          TCGA-24-2254 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2261          TCGA-24-2267          TCGA-24-2271 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2281          TCGA-24-2288          TCGA-24-2290 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2298          TCGA-25-1313          TCGA-25-1315 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1316          TCGA-25-1317          TCGA-25-1318 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1319          TCGA-25-1321          TCGA-25-1322 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1324          TCGA-25-1326          TCGA-25-1328 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1329          TCGA-25-1623          TCGA-25-1625 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1627          TCGA-25-1630          TCGA-25-1631 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1632          TCGA-25-1633          TCGA-25-1634 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1635          TCGA-25-2391          TCGA-25-2392 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-2393          TCGA-25-2396          TCGA-25-2399 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-2400          TCGA-25-2404          TCGA-25-2409 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-29-2427          TCGA-30-1862          TCGA-30-1891 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-31-1953          TCGA-36-1568          TCGA-36-1570 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-36-1571          TCGA-36-1574          TCGA-36-1575 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-36-1577          TCGA-36-1578          TCGA-36-1580 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-57-1582          TCGA-57-1583          TCGA-57-1584 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-57-1993          TCGA-59-2348          TCGA-59-2350 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-59-2351          TCGA-59-2352          TCGA-59-2355 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-59-2363          TCGA-61-1728          TCGA-61-1736 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-1919          TCGA-61-1995          TCGA-61-1998 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2000          TCGA-61-2008          TCGA-61-2009 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2012          TCGA-61-2016          TCGA-61-2088 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2092          TCGA-61-2094          TCGA-61-2097 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2102          TCGA-61-2104          TCGA-61-2109 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2110          TCGA-61-2111          TCGA-61-2113 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        1      1      0
  C10ORF140 WILD-TYPE     65     75     19
D7V9, multiclass
[1] "Remove cluster labels:" "C10ORF140 MUTATED"     
clus
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  2                 159 
         TCGA-04-1348          TCGA-04-1357          TCGA-04-1362 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-04-1364          TCGA-04-1365          TCGA-04-1514 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-0366          TCGA-09-0369          TCGA-09-1662 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-1666          TCGA-09-1669          TCGA-09-2044 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-09-2045          TCGA-09-2051          TCGA-09-2056 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-10-0928          TCGA-13-0730          TCGA-13-0800 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0890          TCGA-13-0893          TCGA-13-0897 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0899          TCGA-13-0913          TCGA-13-0920 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-0924          TCGA-13-1403          TCGA-13-1405 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1410          TCGA-13-1481          TCGA-13-1497 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1498          TCGA-13-1505          TCGA-13-1506 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-13-1507          TCGA-13-1512          TCGA-13-2060 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-1023          TCGA-23-1026          TCGA-23-1027 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-1120          TCGA-23-1122          TCGA-23-1123 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-23-2077          TCGA-23-2081          TCGA-24-0975 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1103          TCGA-24-1413          TCGA-24-1416 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1417          TCGA-24-1418          TCGA-24-1419 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1423          TCGA-24-1424          TCGA-24-1427 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1428          TCGA-24-1436          TCGA-24-1469 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1474          TCGA-24-1544          TCGA-24-1548 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1549          TCGA-24-1551          TCGA-24-1552 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1553          TCGA-24-1555          TCGA-24-1556 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1557          TCGA-24-1558          TCGA-24-1560 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1562          TCGA-24-1563          TCGA-24-1564 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1567          TCGA-24-1603          TCGA-24-1604 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-1616          TCGA-24-2019          TCGA-24-2024 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2035          TCGA-24-2038          TCGA-24-2254 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2261          TCGA-24-2267          TCGA-24-2271 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2281          TCGA-24-2288          TCGA-24-2290 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-24-2298          TCGA-25-1313          TCGA-25-1315 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1316          TCGA-25-1317          TCGA-25-1318 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1319          TCGA-25-1321          TCGA-25-1322 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1324          TCGA-25-1326          TCGA-25-1328 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1329          TCGA-25-1623          TCGA-25-1625 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1627          TCGA-25-1630          TCGA-25-1631 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1632          TCGA-25-1633          TCGA-25-1634 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-1635          TCGA-25-2391          TCGA-25-2392 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-2393          TCGA-25-2396          TCGA-25-2399 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-25-2400          TCGA-25-2404          TCGA-25-2409 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-29-2427          TCGA-30-1862          TCGA-30-1891 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-31-1953          TCGA-36-1568          TCGA-36-1570 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-36-1571          TCGA-36-1574          TCGA-36-1575 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-36-1577          TCGA-36-1578          TCGA-36-1580 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-57-1582          TCGA-57-1583          TCGA-57-1584 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-57-1993          TCGA-59-2348          TCGA-59-2350 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-59-2351          TCGA-59-2352          TCGA-59-2355 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-59-2363          TCGA-61-1728          TCGA-61-1736 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-1919          TCGA-61-1995          TCGA-61-1998 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2000          TCGA-61-2008          TCGA-61-2009 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2012          TCGA-61-2016          TCGA-61-2088 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2092          TCGA-61-2094          TCGA-61-2097 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2102          TCGA-61-2104          TCGA-61-2109 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
         TCGA-61-2110          TCGA-61-2111          TCGA-61-2113 
"C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" "C10ORF140 WILD-TYPE" 
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        3      1      0
  C10ORF140 WILD-TYPE     76    118     89
D7V10, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 3                  76
  CLUS_2                 1                 118
  CLUS_3                 0                  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 CLUS_4
  C10ORF140 MUTATED        1      0      3      0
  C10ORF140 WILD-TYPE     73     46     96     68
D7V11, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 1                  73
  CLUS_2                 0                  46
  CLUS_3                 3                  96
  CLUS_4                 0                  68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        3      1      0
  C10ORF140 WILD-TYPE     61    123     99
D7V12, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 3                  61
  CLUS_2                 1                 123
  CLUS_3                 0                  99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  C10ORF140 MUTATED        3      0      1
  C10ORF140 WILD-TYPE    108    113     62
D7V13, multiclass
        clus
vv       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  CLUS_1                 3                 108
  CLUS_2                 0                 113
  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"

Clustering(8) Variable = BRCA2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        5      2      4
  BRCA2 WILD-TYPE    114    113     78
D8V1, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             5             114
  CLUS_2             2             113
  CLUS_3             4              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
  BRCA2 MUTATED        7      3      1
  BRCA2 WILD-TYPE    166     91     48
D8V2, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             7             166
  CLUS_2             3              91
  CLUS_3             1              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
  BRCA2 MUTATED        3      4      4
  BRCA2 WILD-TYPE     89     92    124
D8V3, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             3              89
  CLUS_2             4              92
  CLUS_3             4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BRCA2 MUTATED        3       1      0      1      0      2      2      1
  BRCA2 WILD-TYPE     48      27     33     52     20     42     18     15
                 vv
clus              CLUS_8 CLUS_9
  BRCA2 MUTATED        0      1
  BRCA2 WILD-TYPE     21     29
D8V4, multiclass
         clus
vv        BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1              3              48
  CLUS_10             1              27
  CLUS_2              0              33
  CLUS_3              1              52
  CLUS_4              0              20
  CLUS_5              2              42
  CLUS_6              2              18
  CLUS_7              1              15
  CLUS_8              0              21
  CLUS_9              1              29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        5      4      2
  BRCA2 WILD-TYPE    107     99     94
D8V5, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             5             107
  CLUS_2             4              99
  CLUS_3             2              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
  BRCA2 MUTATED        1      3      0
  BRCA2 WILD-TYPE     75     93     38
D8V6, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             1              75
  CLUS_2             3              93
  CLUS_3             0              38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRCA2 MUTATED        2      1      0      1
  BRCA2 WILD-TYPE     65     47     64     30
D8V7, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             2              65
  CLUS_2             1              47
  CLUS_3             0              64
  CLUS_4             1              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        4      2      0
  BRCA2 WILD-TYPE     66     38     51
D8V8, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             2              38
  CLUS_3             0              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        4      2      0
  BRCA2 WILD-TYPE     62     74     19
D8V9, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             4              62
  CLUS_2             2              74
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        3      4      3
  BRCA2 WILD-TYPE     76    115     86
D8V10, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             4             115
  CLUS_3             3              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 CLUS_4
  BRCA2 MUTATED        4      2      3      1
  BRCA2 WILD-TYPE     70     44     96     67
D8V11, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             4              70
  CLUS_2             2              44
  CLUS_3             3              96
  CLUS_4             1              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  BRCA2 MUTATED        2      5      3
  BRCA2 WILD-TYPE     62    119     96
D8V12, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             2              62
  CLUS_2             5             119
  CLUS_3             3              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
  BRCA2 MUTATED        4      3      3
  BRCA2 WILD-TYPE    107    110     60
D8V13, multiclass
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  CLUS_1             4             107
  CLUS_2             3             110
  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"

Clustering(9) Variable = CDK12 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        2      6      0
  CDK12 WILD-TYPE    117    109     82
D9V1, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             2             117
  CLUS_2             6             109
  CLUS_3             0              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
  CDK12 MUTATED        7      1      0
  CDK12 WILD-TYPE    166     93     49
D9V2, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             7             166
  CLUS_2             1              93
  CLUS_3             0              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
  CDK12 MUTATED        4      1      3
  CDK12 WILD-TYPE     88     95    125
D9V3, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             4              88
  CLUS_2             1              95
  CLUS_3             3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CDK12 MUTATED        3       0      0      2      0      1      0      1
  CDK12 WILD-TYPE     48      28     33     51     20     43     20     15
                 vv
clus              CLUS_8 CLUS_9
  CDK12 MUTATED        0      1
  CDK12 WILD-TYPE     21     29
D9V4, multiclass
         clus
vv        CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1              3              48
  CLUS_10             0              28
  CLUS_2              0              33
  CLUS_3              2              51
  CLUS_4              0              20
  CLUS_5              1              43
  CLUS_6              0              20
  CLUS_7              1              15
  CLUS_8              0              21
  CLUS_9              1              29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      2
  CDK12 WILD-TYPE    109    100     94
D9V5, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             3             109
  CLUS_2             3             100
  CLUS_3             2              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
  CDK12 MUTATED        3      2      0
  CDK12 WILD-TYPE     73     94     38
D9V6, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             3              73
  CLUS_2             2              94
  CLUS_3             0              38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDK12 MUTATED        1      0      1      3
  CDK12 WILD-TYPE     66     48     63     28
D9V7, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1              66
  CLUS_2             0              48
  CLUS_3             1              63
  CLUS_4             3              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        3      1      0
  CDK12 WILD-TYPE     67     39     51
D9V8, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             1              39
  CLUS_3             0              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        2      2      0
  CDK12 WILD-TYPE     64     74     19
D9V9, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             2              74
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDK12 MUTATED        1      4      3
  CDK12 WILD-TYPE     78    115     86
D9V10, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1              78
  CLUS_2             4             115
  CLUS_3             3              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 CLUS_4
  CDK12 MUTATED        3      2      1      2
  CDK12 WILD-TYPE     71     44     98     66
D9V11, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             3              71
  CLUS_2             2              44
  CLUS_3             1              98
  CLUS_4             2              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      4      3
  CDK12 WILD-TYPE     63    120     96
D9V12, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             1              63
  CLUS_2             4             120
  CLUS_3             3              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
  CDK12 MUTATED        2      4      2
  CDK12 WILD-TYPE    109    109     61
D9V13, multiclass
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  CLUS_1             2             109
  CLUS_2             4             109
  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"

Clustering(10) Variable = OR4F21 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        1      2      0
  OR4F21 WILD-TYPE    118    113     82
D10V1, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              1              118
  CLUS_2              2              113
  CLUS_3              0               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
  OR4F21 MUTATED        2      1      0
  OR4F21 WILD-TYPE    171     93     49
D10V2, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              2              171
  CLUS_2              1               93
  CLUS_3              0               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
  OR4F21 MUTATED        1      0      2
  OR4F21 WILD-TYPE     91     96    126
D10V3, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              1               91
  CLUS_2              0               96
  CLUS_3              2              126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  OR4F21 MUTATED        1       0      0      2      0      0      0      0
  OR4F21 WILD-TYPE     50      28     33     51     20     44     20     16
                  vv
clus               CLUS_8 CLUS_9
  OR4F21 MUTATED        0      0
  OR4F21 WILD-TYPE     21     30
D10V4, multiclass
         clus
vv        OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1               1               50
  CLUS_10              0               28
  CLUS_2               0               33
  CLUS_3               2               51
  CLUS_4               0               20
  CLUS_5               0               44
  CLUS_6               0               20
  CLUS_7               0               16
  CLUS_8               0               21
  CLUS_9               0               30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        1      1      1
  OR4F21 WILD-TYPE    111    102     95
D10V5, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              1              111
  CLUS_2              1              102
  CLUS_3              1               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
  OR4F21 MUTATED        1      2      0
  OR4F21 WILD-TYPE     75     94     38
D10V6, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              1               75
  CLUS_2              2               94
  CLUS_3              0               38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR4F21 MUTATED        0      0      2      1
  OR4F21 WILD-TYPE     67     48     62     30
D10V7, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              0               67
  CLUS_2              0               48
  CLUS_3              2               62
  CLUS_4              1               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        2      0      0
  OR4F21 WILD-TYPE     68     40     51
D10V8, multiclass
[1] "Remove cluster labels:" "OR4F21 MUTATED"        
clus
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               2              159 
      TCGA-04-1348       TCGA-04-1357       TCGA-04-1362       TCGA-04-1364 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1365       TCGA-04-1514       TCGA-09-0366       TCGA-09-0369 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-1662       TCGA-09-1666       TCGA-09-1669       TCGA-09-2044 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-2045       TCGA-09-2051       TCGA-09-2056       TCGA-10-0928 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0730       TCGA-13-0800       TCGA-13-0890       TCGA-13-0893 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0897       TCGA-13-0899       TCGA-13-0913       TCGA-13-0916 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0920       TCGA-13-0924       TCGA-13-1403       TCGA-13-1405 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1410       TCGA-13-1481       TCGA-13-1497       TCGA-13-1498 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1505       TCGA-13-1506       TCGA-13-1507       TCGA-13-1512 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-2060       TCGA-23-1023       TCGA-23-1026       TCGA-23-1027 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1120       TCGA-23-1122       TCGA-23-1123       TCGA-23-2077 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-2081       TCGA-24-0975       TCGA-24-1103       TCGA-24-1413 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1416       TCGA-24-1417       TCGA-24-1418       TCGA-24-1419 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1423       TCGA-24-1424       TCGA-24-1427       TCGA-24-1428 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1436       TCGA-24-1469       TCGA-24-1474       TCGA-24-1544 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1548       TCGA-24-1549       TCGA-24-1551       TCGA-24-1552 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1553       TCGA-24-1555       TCGA-24-1556       TCGA-24-1557 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1558       TCGA-24-1560       TCGA-24-1562       TCGA-24-1563 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1564       TCGA-24-1567       TCGA-24-1603       TCGA-24-1604 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1616       TCGA-24-2019       TCGA-24-2024       TCGA-24-2035 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2038       TCGA-24-2254       TCGA-24-2261       TCGA-24-2262 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2267       TCGA-24-2271       TCGA-24-2281       TCGA-24-2288 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2290       TCGA-24-2298       TCGA-25-1313       TCGA-25-1315 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1316       TCGA-25-1317       TCGA-25-1318       TCGA-25-1319 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1321       TCGA-25-1322       TCGA-25-1324       TCGA-25-1326 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1328       TCGA-25-1329       TCGA-25-1623       TCGA-25-1625 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1627       TCGA-25-1630       TCGA-25-1631       TCGA-25-1632 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1633       TCGA-25-1634       TCGA-25-1635       TCGA-25-2391 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2392       TCGA-25-2393       TCGA-25-2396       TCGA-25-2399 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2400       TCGA-25-2404       TCGA-25-2409       TCGA-29-2427 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-30-1862       TCGA-30-1891       TCGA-31-1953       TCGA-36-1568 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1570       TCGA-36-1571       TCGA-36-1574       TCGA-36-1575 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1577       TCGA-36-1578       TCGA-36-1580       TCGA-57-1582 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-57-1583       TCGA-57-1584       TCGA-57-1993       TCGA-59-2348 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-59-2350       TCGA-59-2352       TCGA-59-2355       TCGA-59-2363 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-1728       TCGA-61-1736       TCGA-61-1919       TCGA-61-1995 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-1998       TCGA-61-2008       TCGA-61-2009       TCGA-61-2012 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2016       TCGA-61-2088       TCGA-61-2092       TCGA-61-2094 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2097       TCGA-61-2102       TCGA-61-2104       TCGA-61-2109 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2110       TCGA-61-2111       TCGA-61-2113 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        1      1      0
  OR4F21 WILD-TYPE     65     75     19
D10V9, multiclass
[1] "Remove cluster labels:" "OR4F21 MUTATED"        
clus
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               2              159 
      TCGA-04-1348       TCGA-04-1357       TCGA-04-1362       TCGA-04-1364 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1365       TCGA-04-1514       TCGA-09-0366       TCGA-09-0369 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-1662       TCGA-09-1666       TCGA-09-1669       TCGA-09-2044 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-2045       TCGA-09-2051       TCGA-09-2056       TCGA-10-0928 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0730       TCGA-13-0800       TCGA-13-0890       TCGA-13-0893 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0897       TCGA-13-0899       TCGA-13-0913       TCGA-13-0916 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0920       TCGA-13-0924       TCGA-13-1403       TCGA-13-1405 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1410       TCGA-13-1481       TCGA-13-1497       TCGA-13-1498 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1505       TCGA-13-1506       TCGA-13-1507       TCGA-13-1512 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-2060       TCGA-23-1023       TCGA-23-1026       TCGA-23-1027 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1120       TCGA-23-1122       TCGA-23-1123       TCGA-23-2077 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-2081       TCGA-24-0975       TCGA-24-1103       TCGA-24-1413 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1416       TCGA-24-1417       TCGA-24-1418       TCGA-24-1419 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1423       TCGA-24-1424       TCGA-24-1427       TCGA-24-1428 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1436       TCGA-24-1469       TCGA-24-1474       TCGA-24-1544 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1548       TCGA-24-1549       TCGA-24-1551       TCGA-24-1552 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1553       TCGA-24-1555       TCGA-24-1556       TCGA-24-1557 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1558       TCGA-24-1560       TCGA-24-1562       TCGA-24-1563 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1564       TCGA-24-1567       TCGA-24-1603       TCGA-24-1604 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1616       TCGA-24-2019       TCGA-24-2024       TCGA-24-2035 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2038       TCGA-24-2254       TCGA-24-2261       TCGA-24-2262 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2267       TCGA-24-2271       TCGA-24-2281       TCGA-24-2288 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2290       TCGA-24-2298       TCGA-25-1313       TCGA-25-1315 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1316       TCGA-25-1317       TCGA-25-1318       TCGA-25-1319 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1321       TCGA-25-1322       TCGA-25-1324       TCGA-25-1326 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1328       TCGA-25-1329       TCGA-25-1623       TCGA-25-1625 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1627       TCGA-25-1630       TCGA-25-1631       TCGA-25-1632 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1633       TCGA-25-1634       TCGA-25-1635       TCGA-25-2391 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2392       TCGA-25-2393       TCGA-25-2396       TCGA-25-2399 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2400       TCGA-25-2404       TCGA-25-2409       TCGA-29-2427 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-30-1862       TCGA-30-1891       TCGA-31-1953       TCGA-36-1568 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1570       TCGA-36-1571       TCGA-36-1574       TCGA-36-1575 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1577       TCGA-36-1578       TCGA-36-1580       TCGA-57-1582 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-57-1583       TCGA-57-1584       TCGA-57-1993       TCGA-59-2348 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-59-2350       TCGA-59-2352       TCGA-59-2355       TCGA-59-2363 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-1728       TCGA-61-1736       TCGA-61-1919       TCGA-61-1995 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-1998       TCGA-61-2008       TCGA-61-2009       TCGA-61-2012 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2016       TCGA-61-2088       TCGA-61-2092       TCGA-61-2094 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2097       TCGA-61-2102       TCGA-61-2104       TCGA-61-2109 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2110       TCGA-61-2111       TCGA-61-2113 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        0      2      1
  OR4F21 WILD-TYPE     79    117     88
D10V10, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              0               79
  CLUS_2              2              117
  CLUS_3              1               88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  OR4F21 MUTATED        0      0      2      1
  OR4F21 WILD-TYPE     74     46     97     67
D10V11, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              0               74
  CLUS_2              0               46
  CLUS_3              2               97
  CLUS_4              1               67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  OR4F21 MUTATED        0      2      1
  OR4F21 WILD-TYPE     64    122     98
D10V12, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              0               64
  CLUS_2              2              122
  CLUS_3              1               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
  OR4F21 MUTATED        1      1      1
  OR4F21 WILD-TYPE    110    112     62
D10V13, multiclass
        clus
vv       OR4F21 MUTATED OR4F21 WILD-TYPE
  CLUS_1              1              110
  CLUS_2              1              112
  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"

Clustering(11) Variable = C9ORF171 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        0      0      5
  C9ORF171 WILD-TYPE    119    115     77
D11V1, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                0                119
  CLUS_2                0                115
  CLUS_3                5                 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
  C9ORF171 MUTATED        0      5      0
  C9ORF171 WILD-TYPE    173     89     49
D11V2, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                0                173
  CLUS_2                5                 89
  CLUS_3                0                 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
  C9ORF171 MUTATED        3      1      1
  C9ORF171 WILD-TYPE     89     95    127
D11V3, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                3                 89
  CLUS_2                1                 95
  CLUS_3                1                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  C9ORF171 MUTATED        1       0      0      1      2      0      0      0
  C9ORF171 WILD-TYPE     50      28     33     52     18     44     20     16
                    vv
clus                 CLUS_8 CLUS_9
  C9ORF171 MUTATED        0      1
  C9ORF171 WILD-TYPE     21     29
D11V4, multiclass
         clus
vv        C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                 1                 50
  CLUS_10                0                 28
  CLUS_2                 0                 33
  CLUS_3                 1                 52
  CLUS_4                 2                 18
  CLUS_5                 0                 44
  CLUS_6                 0                 20
  CLUS_7                 0                 16
  CLUS_8                 0                 21
  CLUS_9                 1                 29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        2      2      1
  C9ORF171 WILD-TYPE    110    101     95
D11V5, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                2                110
  CLUS_2                2                101
  CLUS_3                1                 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
  C9ORF171 MUTATED        3      1      0
  C9ORF171 WILD-TYPE     73     95     38
D11V6, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                3                 73
  CLUS_2                1                 95
  CLUS_3                0                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C9ORF171 MUTATED        2      0      2      0
  C9ORF171 WILD-TYPE     65     48     62     31
D11V7, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                0                 48
  CLUS_3                2                 62
  CLUS_4                0                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        1      0      0
  C9ORF171 WILD-TYPE     69     40     51
D11V8, multiclass
[1] "Remove cluster labels:" "C9ORF171 MUTATED"      
clus
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 1                160 
        TCGA-04-1348         TCGA-04-1357         TCGA-04-1362 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-04-1364         TCGA-04-1365         TCGA-04-1514 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-0366         TCGA-09-0369         TCGA-09-1662 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-1666         TCGA-09-1669         TCGA-09-2044 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-2045         TCGA-09-2051         TCGA-09-2056 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-10-0928         TCGA-13-0730         TCGA-13-0800 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0890         TCGA-13-0893         TCGA-13-0897 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0899         TCGA-13-0913         TCGA-13-0916 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0920         TCGA-13-0924         TCGA-13-1403 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1405         TCGA-13-1410         TCGA-13-1481 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1497         TCGA-13-1498         TCGA-13-1505 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1506         TCGA-13-1507         TCGA-13-1512 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-2060         TCGA-23-1023         TCGA-23-1026 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-23-1027         TCGA-23-1120         TCGA-23-1122 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-23-1123         TCGA-23-2077         TCGA-23-2081 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-0975         TCGA-24-1103         TCGA-24-1413 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1416         TCGA-24-1417         TCGA-24-1418 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1419         TCGA-24-1423         TCGA-24-1424 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1427         TCGA-24-1428         TCGA-24-1436 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1469         TCGA-24-1474         TCGA-24-1544 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1548         TCGA-24-1549         TCGA-24-1551 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1552         TCGA-24-1553         TCGA-24-1555 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1556         TCGA-24-1557         TCGA-24-1558 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1560         TCGA-24-1562         TCGA-24-1563 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1564         TCGA-24-1567         TCGA-24-1603 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1604         TCGA-24-1616         TCGA-24-2019 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2024         TCGA-24-2038         TCGA-24-2254 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2261         TCGA-24-2262         TCGA-24-2267 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2271         TCGA-24-2281         TCGA-24-2288 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2298         TCGA-25-1313 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1315         TCGA-25-1316         TCGA-25-1317 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1318         TCGA-25-1319         TCGA-25-1321 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1322         TCGA-25-1324         TCGA-25-1326 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1328         TCGA-25-1329         TCGA-25-1623 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1625         TCGA-25-1627         TCGA-25-1630 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1631         TCGA-25-1632         TCGA-25-1633 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1634         TCGA-25-1635         TCGA-25-2391 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2392         TCGA-25-2393         TCGA-25-2396 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2409         TCGA-29-2427         TCGA-30-1862 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-30-1891         TCGA-31-1953         TCGA-36-1568 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1570         TCGA-36-1571         TCGA-36-1574 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1575         TCGA-36-1577         TCGA-36-1578 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1580         TCGA-57-1582         TCGA-57-1583 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-57-1584         TCGA-57-1993         TCGA-59-2348 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-59-2350         TCGA-59-2351         TCGA-59-2352 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-59-2355         TCGA-59-2363         TCGA-61-1728 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-1736         TCGA-61-1919         TCGA-61-1995 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-1998         TCGA-61-2000         TCGA-61-2008 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2009         TCGA-61-2012         TCGA-61-2016 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2088         TCGA-61-2092         TCGA-61-2094 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2097         TCGA-61-2102         TCGA-61-2104 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2110         TCGA-61-2111 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2113 
"C9ORF171 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        1      0      0
  C9ORF171 WILD-TYPE     65     76     19
D11V9, multiclass
[1] "Remove cluster labels:" "C9ORF171 MUTATED"      
clus
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 1                160 
        TCGA-04-1348         TCGA-04-1357         TCGA-04-1362 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-04-1364         TCGA-04-1365         TCGA-04-1514 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-0366         TCGA-09-0369         TCGA-09-1662 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-1666         TCGA-09-1669         TCGA-09-2044 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-09-2045         TCGA-09-2051         TCGA-09-2056 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-10-0928         TCGA-13-0730         TCGA-13-0800 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0890         TCGA-13-0893         TCGA-13-0897 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0899         TCGA-13-0913         TCGA-13-0916 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-0920         TCGA-13-0924         TCGA-13-1403 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1405         TCGA-13-1410         TCGA-13-1481 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1497         TCGA-13-1498         TCGA-13-1505 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-1506         TCGA-13-1507         TCGA-13-1512 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-13-2060         TCGA-23-1023         TCGA-23-1026 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-23-1027         TCGA-23-1120         TCGA-23-1122 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-23-1123         TCGA-23-2077         TCGA-23-2081 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-0975         TCGA-24-1103         TCGA-24-1413 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1416         TCGA-24-1417         TCGA-24-1418 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1419         TCGA-24-1423         TCGA-24-1424 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1427         TCGA-24-1428         TCGA-24-1436 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1469         TCGA-24-1474         TCGA-24-1544 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1548         TCGA-24-1549         TCGA-24-1551 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1552         TCGA-24-1553         TCGA-24-1555 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1556         TCGA-24-1557         TCGA-24-1558 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1560         TCGA-24-1562         TCGA-24-1563 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1564         TCGA-24-1567         TCGA-24-1603 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-1604         TCGA-24-1616         TCGA-24-2019 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2024         TCGA-24-2038         TCGA-24-2254 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2261         TCGA-24-2262         TCGA-24-2267 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2271         TCGA-24-2281         TCGA-24-2288 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2298         TCGA-25-1313 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1315         TCGA-25-1316         TCGA-25-1317 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1318         TCGA-25-1319         TCGA-25-1321 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1322         TCGA-25-1324         TCGA-25-1326 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1328         TCGA-25-1329         TCGA-25-1623 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1625         TCGA-25-1627         TCGA-25-1630 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1631         TCGA-25-1632         TCGA-25-1633 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-1634         TCGA-25-1635         TCGA-25-2391 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2392         TCGA-25-2393         TCGA-25-2396 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-25-2409         TCGA-29-2427         TCGA-30-1862 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-30-1891         TCGA-31-1953         TCGA-36-1568 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1570         TCGA-36-1571         TCGA-36-1574 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1575         TCGA-36-1577         TCGA-36-1578 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-36-1580         TCGA-57-1582         TCGA-57-1583 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-57-1584         TCGA-57-1993         TCGA-59-2348 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-59-2350         TCGA-59-2351         TCGA-59-2352 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-59-2355         TCGA-59-2363         TCGA-61-1728 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-1736         TCGA-61-1919         TCGA-61-1995 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-1998         TCGA-61-2000         TCGA-61-2008 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2009         TCGA-61-2012         TCGA-61-2016 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2088         TCGA-61-2092         TCGA-61-2094 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2097         TCGA-61-2102         TCGA-61-2104 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2110         TCGA-61-2111 
"C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" "C9ORF171 WILD-TYPE" 
        TCGA-61-2113 
"C9ORF171 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        2      2      0
  C9ORF171 WILD-TYPE     77    117     89
D11V10, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                2                117
  CLUS_3                0                 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 CLUS_4
  C9ORF171 MUTATED        1      0      3      0
  C9ORF171 WILD-TYPE     73     46     96     68
D11V11, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                1                 73
  CLUS_2                0                 46
  CLUS_3                3                 96
  CLUS_4                0                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        2      2      0
  C9ORF171 WILD-TYPE     62    122     99
D11V12, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                2                122
  CLUS_3                0                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C9ORF171 MUTATED        4      0      0
  C9ORF171 WILD-TYPE    107    113     63
D11V13, multiclass
        clus
vv       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  CLUS_1                4                107
  CLUS_2                0                113
  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"

Clustering(12) Variable = HYDIN MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        6      3      2
  HYDIN WILD-TYPE    113    112     80
D12V1, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             6             113
  CLUS_2             3             112
  CLUS_3             2              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
  HYDIN MUTATED        4      2      5
  HYDIN WILD-TYPE    169     92     44
D12V2, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             4             169
  CLUS_2             2              92
  CLUS_3             5              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        1      3      7
  HYDIN WILD-TYPE     91     93    121
D12V3, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             1              91
  CLUS_2             3              93
  CLUS_3             7             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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  HYDIN MUTATED        0       0      2      3      0      2      2      0
  HYDIN WILD-TYPE     51      28     31     50     20     42     18     16
                 vv
clus              CLUS_8 CLUS_9
  HYDIN MUTATED        1      1
  HYDIN WILD-TYPE     20     29
D12V4, multiclass
         clus
vv        HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1              0              51
  CLUS_10             0              28
  CLUS_2              2              31
  CLUS_3              3              50
  CLUS_4              0              20
  CLUS_5              2              42
  CLUS_6              2              18
  CLUS_7              0              16
  CLUS_8              1              20
  CLUS_9              1              29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        4      5      2
  HYDIN WILD-TYPE    108     98     94
D12V5, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             4             108
  CLUS_2             5              98
  CLUS_3             2              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
  HYDIN MUTATED        1      3      1
  HYDIN WILD-TYPE     75     93     37
D12V6, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             1              75
  CLUS_2             3              93
  CLUS_3             1              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HYDIN MUTATED        1      0      2      2
  HYDIN WILD-TYPE     66     48     62     29
D12V7, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             1              66
  CLUS_2             0              48
  CLUS_3             2              62
  CLUS_4             2              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        1      1      1
  HYDIN WILD-TYPE     69     39     50
D12V8, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             1              69
  CLUS_2             1              39
  CLUS_3             1              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
  HYDIN MUTATED        1      2      0
  HYDIN WILD-TYPE     65     74     19
D12V9, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             1              65
  CLUS_2             2              74
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        3      5      2
  HYDIN WILD-TYPE     76    114     87
D12V10, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             3              76
  CLUS_2             5             114
  CLUS_3             2              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 CLUS_4
  HYDIN MUTATED        2      2      5      1
  HYDIN WILD-TYPE     72     44     94     67
D12V11, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             2              72
  CLUS_2             2              44
  CLUS_3             5              94
  CLUS_4             1              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HYDIN MUTATED        2      6      2
  HYDIN WILD-TYPE     62    118     97
D12V12, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             2              62
  CLUS_2             6             118
  CLUS_3             2              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
  HYDIN MUTATED        4      3      3
  HYDIN WILD-TYPE    107    110     60
D12V13, multiclass
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  CLUS_1             4             107
  CLUS_2             3             110
  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"

Clustering(13) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        4      2      2
  RB1 WILD-TYPE    115    113     80
D13V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4           115
  CLUS_2           2           113
  CLUS_3           2            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
  RB1 MUTATED        3      2      3
  RB1 WILD-TYPE    170     92     46
D13V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3           170
  CLUS_2           2            92
  CLUS_3           3            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      1      5
  RB1 WILD-TYPE     90     95    123
D13V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            90
  CLUS_2           1            95
  CLUS_3           5           123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RB1 MUTATED        0       1      0      2      1      1      1      1      1
  RB1 WILD-TYPE     51      27     33     51     19     43     19     15     20
               vv
clus            CLUS_9
  RB1 MUTATED        0
  RB1 WILD-TYPE     30
D13V4, multiclass
         clus
vv        RB1 MUTATED RB1 WILD-TYPE
  CLUS_1            0            51
  CLUS_10           1            27
  CLUS_2            0            33
  CLUS_3            2            51
  CLUS_4            1            19
  CLUS_5            1            43
  CLUS_6            1            19
  CLUS_7            1            15
  CLUS_8            1            20
  CLUS_9            0            30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      2      4
  RB1 WILD-TYPE    110    101     92
D13V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2           110
  CLUS_2           2           101
  CLUS_3           4            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
  RB1 MUTATED        3      3      1
  RB1 WILD-TYPE     73     93     37
D13V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            73
  CLUS_2           3            93
  CLUS_3           1            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      1      3      1
  RB1 WILD-TYPE     65     47     61     30
D13V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            65
  CLUS_2           1            47
  CLUS_3           3            61
  CLUS_4           1            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      0      1
  RB1 WILD-TYPE     69     40     50
D13V8, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1474    TCGA-24-1544    TCGA-24-1548 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603    TCGA-24-1604 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035    TCGA-24-2038 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267    TCGA-24-2271 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298    TCGA-25-1313 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1318    TCGA-25-1319 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-2391 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2392    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      1      0
  RB1 WILD-TYPE     65     75     19
D13V9, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1474    TCGA-24-1544    TCGA-24-1548 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603    TCGA-24-1604 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035    TCGA-24-2038 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267    TCGA-24-2271 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298    TCGA-25-1313 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1318    TCGA-25-1319 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-2391 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2392    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      5      2
  RB1 WILD-TYPE     78    114     87
D13V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            78
  CLUS_2           5           114
  CLUS_3           2            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 CLUS_4
  RB1 MUTATED        3      0      3      2
  RB1 WILD-TYPE     71     46     96     66
D13V11, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            71
  CLUS_2           0            46
  CLUS_3           3            96
  CLUS_4           2            66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      5      2
  RB1 WILD-TYPE     63    119     97
D13V12, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            63
  CLUS_2           5           119
  CLUS_3           2            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
  RB1 MUTATED        3      2      3
  RB1 WILD-TYPE    108    111     60
D13V13, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3           108
  CLUS_2           2           111
  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"

Clustering(14) Variable = GART MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        1      1      1
  GART WILD-TYPE    118    114     81
D14V1, multiclass
        clus
vv       GART MUTATED GART WILD-TYPE
  CLUS_1            1            118
  CLUS_2            1            114
  CLUS_3            1             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        1      1      1
  GART WILD-TYPE    172     93     48
D14V2, multiclass
        clus
vv       GART MUTATED GART WILD-TYPE
  CLUS_1            1            172
  CLUS_2            1             93
  CLUS_3            1             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
  GART MUTATED        1      0      2
  GART WILD-TYPE     91     96    126
D14V3, multiclass
        clus
vv       GART MUTATED GART WILD-TYPE
  CLUS_1            1             91
  CLUS_2            0             96
  CLUS_3            2            126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GART MUTATED        0       0      0      2      1      0      0      0
  GART WILD-TYPE     51      28     33     51     19     44     20     16
                vv
clus             CLUS_8 CLUS_9
  GART MUTATED        0      0
  GART WILD-TYPE     21     30
D14V4, multiclass
         clus
vv        GART MUTATED GART WILD-TYPE
  CLUS_1             0             51
  CLUS_10            0             28
  CLUS_2             0             33
  CLUS_3             2             51
  CLUS_4             1             19
  CLUS_5             0             44
  CLUS_6             0             20
  CLUS_7             0             16
  CLUS_8             0             21
  CLUS_9             0             30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        0      3      0
  GART WILD-TYPE    112    100     96
D14V5, multiclass
        clus
vv       GART MUTATED GART WILD-TYPE
  CLUS_1            0            112
  CLUS_2            3            100
  CLUS_3            0             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
  GART MUTATED        1      0      1
  GART WILD-TYPE     75     96     37
D14V6, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            208 
    TCGA-04-1336     TCGA-04-1342     TCGA-04-1343     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1356     TCGA-04-1357     TCGA-04-1361 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1362     TCGA-04-1514     TCGA-04-1517     TCGA-04-1525 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-1662     TCGA-09-1665     TCGA-09-1666 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2044     TCGA-09-2045     TCGA-09-2049     TCGA-09-2051 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0931     TCGA-10-0933 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0720     TCGA-13-0793     TCGA-13-0800     TCGA-13-0804 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0884     TCGA-13-0886     TCGA-13-0887     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0894     TCGA-13-0897     TCGA-13-0899     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0906     TCGA-13-0910     TCGA-13-0911     TCGA-13-0913 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0916     TCGA-13-0920     TCGA-13-1404     TCGA-13-1405 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1498     TCGA-13-1499 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1501     TCGA-13-1504     TCGA-13-1505     TCGA-13-1506 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1507     TCGA-13-1509     TCGA-13-1512     TCGA-13-2060 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1110     TCGA-23-1122     TCGA-23-1123     TCGA-23-1124 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0970     TCGA-24-0979     TCGA-24-0980 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0982     TCGA-24-1103     TCGA-24-1104     TCGA-24-1105 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1416     TCGA-24-1417     TCGA-24-1419     TCGA-24-1422 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1423     TCGA-24-1424     TCGA-24-1427     TCGA-24-1428 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1431     TCGA-24-1434     TCGA-24-1435     TCGA-24-1436 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1463     TCGA-24-1464     TCGA-24-1466     TCGA-24-1469 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1470     TCGA-24-1471     TCGA-24-1474     TCGA-24-1544 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1545     TCGA-24-1548     TCGA-24-1549     TCGA-24-1551 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1552     TCGA-24-1553     TCGA-24-1555     TCGA-24-1556 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1557     TCGA-24-1558     TCGA-24-1560     TCGA-24-1562 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1563     TCGA-24-1564     TCGA-24-1565     TCGA-24-1567 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1603     TCGA-24-1604     TCGA-24-1614     TCGA-24-1616 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2024     TCGA-24-2030     TCGA-24-2038     TCGA-24-2254 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2260     TCGA-24-2261     TCGA-24-2262     TCGA-24-2267 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2271     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1318     TCGA-25-1319 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1320     TCGA-25-1321     TCGA-25-1322     TCGA-25-1326 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1328     TCGA-25-1329     TCGA-25-1623     TCGA-25-1625 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1626     TCGA-25-1627     TCGA-25-1628     TCGA-25-1630 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1631     TCGA-25-1633     TCGA-25-1635     TCGA-25-2042 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2391     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-31-1950     TCGA-36-1568     TCGA-36-1569     TCGA-36-1570 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1571     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-59-2348     TCGA-59-2351 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2352     TCGA-59-2354     TCGA-59-2363     TCGA-61-1736 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1919     TCGA-61-1995     TCGA-61-2000     TCGA-61-2003 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2009     TCGA-61-2012     TCGA-61-2088     TCGA-61-2092 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2094     TCGA-61-2095     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2111     TCGA-61-2113 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GART MUTATED        1      0      0      1
  GART WILD-TYPE     66     48     64     30
D14V7, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            208 
    TCGA-04-1336     TCGA-04-1342     TCGA-04-1343     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1356     TCGA-04-1357     TCGA-04-1361 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1362     TCGA-04-1514     TCGA-04-1517     TCGA-04-1525 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-1662     TCGA-09-1665     TCGA-09-1666 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2044     TCGA-09-2045     TCGA-09-2049     TCGA-09-2051 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0931     TCGA-10-0933 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0720     TCGA-13-0793     TCGA-13-0800     TCGA-13-0804 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0884     TCGA-13-0886     TCGA-13-0887     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0894     TCGA-13-0897     TCGA-13-0899     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0906     TCGA-13-0910     TCGA-13-0911     TCGA-13-0913 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0916     TCGA-13-0920     TCGA-13-1404     TCGA-13-1405 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1498     TCGA-13-1499 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1501     TCGA-13-1504     TCGA-13-1505     TCGA-13-1506 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1507     TCGA-13-1509     TCGA-13-1512     TCGA-13-2060 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1110     TCGA-23-1122     TCGA-23-1123     TCGA-23-1124 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0970     TCGA-24-0979     TCGA-24-0980 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0982     TCGA-24-1103     TCGA-24-1104     TCGA-24-1105 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1416     TCGA-24-1417     TCGA-24-1419     TCGA-24-1422 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1423     TCGA-24-1424     TCGA-24-1427     TCGA-24-1428 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1431     TCGA-24-1434     TCGA-24-1435     TCGA-24-1436 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1463     TCGA-24-1464     TCGA-24-1466     TCGA-24-1469 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1470     TCGA-24-1471     TCGA-24-1474     TCGA-24-1544 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1545     TCGA-24-1548     TCGA-24-1549     TCGA-24-1551 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1552     TCGA-24-1553     TCGA-24-1555     TCGA-24-1556 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1557     TCGA-24-1558     TCGA-24-1560     TCGA-24-1562 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1563     TCGA-24-1564     TCGA-24-1565     TCGA-24-1567 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1603     TCGA-24-1604     TCGA-24-1614     TCGA-24-1616 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2024     TCGA-24-2030     TCGA-24-2038     TCGA-24-2254 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2260     TCGA-24-2261     TCGA-24-2262     TCGA-24-2267 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2271     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1318     TCGA-25-1319 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1320     TCGA-25-1321     TCGA-25-1322     TCGA-25-1326 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1328     TCGA-25-1329     TCGA-25-1623     TCGA-25-1625 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1626     TCGA-25-1627     TCGA-25-1628     TCGA-25-1630 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1631     TCGA-25-1633     TCGA-25-1635     TCGA-25-2042 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2391     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-31-1950     TCGA-36-1568     TCGA-36-1569     TCGA-36-1570 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1571     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-59-2348     TCGA-59-2351 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2352     TCGA-59-2354     TCGA-59-2363     TCGA-61-1736 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1919     TCGA-61-1995     TCGA-61-2000     TCGA-61-2003 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2009     TCGA-61-2012     TCGA-61-2088     TCGA-61-2092 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2094     TCGA-61-2095     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2111     TCGA-61-2113 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        0      1      1
  GART WILD-TYPE     70     39     50
D14V8, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            159 
    TCGA-04-1348     TCGA-04-1357     TCGA-04-1362     TCGA-04-1364 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-09-0366     TCGA-09-0369     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1666     TCGA-09-1669     TCGA-09-2044     TCGA-09-2045 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2051     TCGA-09-2056     TCGA-10-0928     TCGA-13-0730 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0800     TCGA-13-0890     TCGA-13-0893     TCGA-13-0897 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0899     TCGA-13-0913     TCGA-13-0916     TCGA-13-0920 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0924     TCGA-13-1403     TCGA-13-1405     TCGA-13-1410 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1481     TCGA-13-1497     TCGA-13-1498     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1512     TCGA-13-2060 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1023     TCGA-23-1026     TCGA-23-1027     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-2077     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0975     TCGA-24-1103     TCGA-24-1413     TCGA-24-1416 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1417     TCGA-24-1418     TCGA-24-1419     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1427     TCGA-24-1428     TCGA-24-1436 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1474     TCGA-24-1544     TCGA-24-1548 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1549     TCGA-24-1551     TCGA-24-1552     TCGA-24-1553 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1555     TCGA-24-1556     TCGA-24-1557     TCGA-24-1558 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1560     TCGA-24-1562     TCGA-24-1563     TCGA-24-1564 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1616 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2019     TCGA-24-2024     TCGA-24-2035     TCGA-24-2038 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2254     TCGA-24-2261     TCGA-24-2262     TCGA-24-2267 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2271     TCGA-24-2281     TCGA-24-2288     TCGA-24-2290 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2298     TCGA-25-1313     TCGA-25-1315     TCGA-25-1316 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1317     TCGA-25-1318     TCGA-25-1319     TCGA-25-1321 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1322     TCGA-25-1324     TCGA-25-1326     TCGA-25-1328 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1329     TCGA-25-1623     TCGA-25-1625     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1630     TCGA-25-1631     TCGA-25-1633     TCGA-25-1634 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1635     TCGA-25-2391     TCGA-25-2392     TCGA-25-2393 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2396     TCGA-25-2399     TCGA-25-2400     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2409     TCGA-29-2427     TCGA-30-1862     TCGA-30-1891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-31-1953     TCGA-36-1568     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1577     TCGA-36-1578 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1580     TCGA-57-1582     TCGA-57-1583     TCGA-57-1584 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1993     TCGA-59-2348     TCGA-59-2350     TCGA-59-2351 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2352     TCGA-59-2355     TCGA-59-2363     TCGA-61-1728 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1736     TCGA-61-1919     TCGA-61-1995     TCGA-61-1998 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2000     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2097     TCGA-61-2102     TCGA-61-2104     TCGA-61-2109 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2110     TCGA-61-2111     TCGA-61-2113 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        1      1      0
  GART WILD-TYPE     65     75     19
D14V9, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            159 
    TCGA-04-1348     TCGA-04-1357     TCGA-04-1362     TCGA-04-1364 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-09-0366     TCGA-09-0369     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1666     TCGA-09-1669     TCGA-09-2044     TCGA-09-2045 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2051     TCGA-09-2056     TCGA-10-0928     TCGA-13-0730 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0800     TCGA-13-0890     TCGA-13-0893     TCGA-13-0897 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0899     TCGA-13-0913     TCGA-13-0916     TCGA-13-0920 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0924     TCGA-13-1403     TCGA-13-1405     TCGA-13-1410 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1481     TCGA-13-1497     TCGA-13-1498     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1512     TCGA-13-2060 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1023     TCGA-23-1026     TCGA-23-1027     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-2077     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0975     TCGA-24-1103     TCGA-24-1413     TCGA-24-1416 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1417     TCGA-24-1418     TCGA-24-1419     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1427     TCGA-24-1428     TCGA-24-1436 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1474     TCGA-24-1544     TCGA-24-1548 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1549     TCGA-24-1551     TCGA-24-1552     TCGA-24-1553 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1555     TCGA-24-1556     TCGA-24-1557     TCGA-24-1558 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1560     TCGA-24-1562     TCGA-24-1563     TCGA-24-1564 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1616 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2019     TCGA-24-2024     TCGA-24-2035     TCGA-24-2038 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2254     TCGA-24-2261     TCGA-24-2262     TCGA-24-2267 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2271     TCGA-24-2281     TCGA-24-2288     TCGA-24-2290 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2298     TCGA-25-1313     TCGA-25-1315     TCGA-25-1316 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1317     TCGA-25-1318     TCGA-25-1319     TCGA-25-1321 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1322     TCGA-25-1324     TCGA-25-1326     TCGA-25-1328 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1329     TCGA-25-1623     TCGA-25-1625     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1630     TCGA-25-1631     TCGA-25-1633     TCGA-25-1634 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1635     TCGA-25-2391     TCGA-25-2392     TCGA-25-2393 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2396     TCGA-25-2399     TCGA-25-2400     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2409     TCGA-29-2427     TCGA-30-1862     TCGA-30-1891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-31-1953     TCGA-36-1568     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1577     TCGA-36-1578 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1580     TCGA-57-1582     TCGA-57-1583     TCGA-57-1584 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1993     TCGA-59-2348     TCGA-59-2350     TCGA-59-2351 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2352     TCGA-59-2355     TCGA-59-2363     TCGA-61-1728 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1736     TCGA-61-1919     TCGA-61-1995     TCGA-61-1998 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2000     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2097     TCGA-61-2102     TCGA-61-2104     TCGA-61-2109 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2110     TCGA-61-2111     TCGA-61-2113 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        0      2      0
  GART WILD-TYPE     79    117     89
D14V10, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            285 
    TCGA-04-1331     TCGA-04-1332     TCGA-04-1336     TCGA-04-1337 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1342     TCGA-04-1346     TCGA-04-1347     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1350     TCGA-04-1356     TCGA-04-1357 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1361     TCGA-04-1362     TCGA-04-1364     TCGA-04-1367 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-04-1517     TCGA-04-1525     TCGA-04-1530 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-0366     TCGA-09-1661     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1665     TCGA-09-1666     TCGA-09-1669     TCGA-09-2044 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2045     TCGA-09-2050     TCGA-09-2051     TCGA-09-2053 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0927     TCGA-10-0928 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-10-0933     TCGA-10-0934     TCGA-13-0714     TCGA-13-0720 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0723     TCGA-13-0724     TCGA-13-0751     TCGA-13-0755 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0760     TCGA-13-0791     TCGA-13-0792     TCGA-13-0800 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0883     TCGA-13-0884     TCGA-13-0885     TCGA-13-0886 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0887     TCGA-13-0889     TCGA-13-0890     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0893     TCGA-13-0894     TCGA-13-0900     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0904     TCGA-13-0905     TCGA-13-0906     TCGA-13-0910 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0911     TCGA-13-0912     TCGA-13-0913     TCGA-13-0916 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0919     TCGA-13-0920     TCGA-13-0923     TCGA-13-0924 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1403     TCGA-13-1404     TCGA-13-1405     TCGA-13-1407 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1497     TCGA-13-1498 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1509     TCGA-13-1510 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1512     TCGA-13-2060     TCGA-20-0987     TCGA-20-0990 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-20-0991     TCGA-23-1021     TCGA-23-1022     TCGA-23-1023 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1026     TCGA-23-1027     TCGA-23-1028     TCGA-23-1030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1032     TCGA-23-1110     TCGA-23-1118     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-1124     TCGA-23-2072 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0968     TCGA-24-0970     TCGA-24-0975 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0979     TCGA-24-0982     TCGA-24-1103     TCGA-24-1104 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1105     TCGA-24-1413     TCGA-24-1416     TCGA-24-1417 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1418     TCGA-24-1419     TCGA-24-1422     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1425     TCGA-24-1426     TCGA-24-1427 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1428     TCGA-24-1431     TCGA-24-1434     TCGA-24-1435 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1436     TCGA-24-1463     TCGA-24-1464     TCGA-24-1466 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1470     TCGA-24-1471     TCGA-24-1474 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1544     TCGA-24-1545     TCGA-24-1548     TCGA-24-1549 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1551     TCGA-24-1552     TCGA-24-1553     TCGA-24-1555 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1556     TCGA-24-1557     TCGA-24-1558     TCGA-24-1560 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1562     TCGA-24-1563     TCGA-24-1564     TCGA-24-1565 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1614 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1616     TCGA-24-2019     TCGA-24-2024     TCGA-24-2030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2035     TCGA-24-2038     TCGA-24-2254     TCGA-24-2260 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2261     TCGA-24-2262     TCGA-24-2267     TCGA-24-2271 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2280     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1317     TCGA-25-1318 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1319     TCGA-25-1320     TCGA-25-1321     TCGA-25-1322 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1324     TCGA-25-1326     TCGA-25-1328     TCGA-25-1329 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1623     TCGA-25-1625     TCGA-25-1626     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1628     TCGA-25-1630     TCGA-25-1631     TCGA-25-1633 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1634     TCGA-25-1635     TCGA-25-2042     TCGA-25-2391 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2392     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1853 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-30-1862     TCGA-30-1891     TCGA-31-1953     TCGA-31-1959 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1568     TCGA-36-1569     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-57-1582     TCGA-57-1583 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1584     TCGA-57-1993     TCGA-59-2348     TCGA-59-2350 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2351     TCGA-59-2352     TCGA-59-2354     TCGA-59-2355 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2363     TCGA-61-1728     TCGA-61-1736     TCGA-61-1919 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1995     TCGA-61-1998     TCGA-61-2000     TCGA-61-2002 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2003     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2095     TCGA-61-2097     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2110     TCGA-61-2111 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2113 
"GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GART MUTATED        0      0      2      0
  GART WILD-TYPE     74     46     97     68
D14V11, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            285 
    TCGA-04-1331     TCGA-04-1332     TCGA-04-1336     TCGA-04-1337 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1342     TCGA-04-1346     TCGA-04-1347     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1350     TCGA-04-1356     TCGA-04-1357 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1361     TCGA-04-1362     TCGA-04-1364     TCGA-04-1367 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-04-1517     TCGA-04-1525     TCGA-04-1530 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-0366     TCGA-09-1661     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1665     TCGA-09-1666     TCGA-09-1669     TCGA-09-2044 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2045     TCGA-09-2050     TCGA-09-2051     TCGA-09-2053 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0927     TCGA-10-0928 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-10-0933     TCGA-10-0934     TCGA-13-0714     TCGA-13-0720 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0723     TCGA-13-0724     TCGA-13-0751     TCGA-13-0755 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0760     TCGA-13-0791     TCGA-13-0792     TCGA-13-0800 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0883     TCGA-13-0884     TCGA-13-0885     TCGA-13-0886 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0887     TCGA-13-0889     TCGA-13-0890     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0893     TCGA-13-0894     TCGA-13-0900     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0904     TCGA-13-0905     TCGA-13-0906     TCGA-13-0910 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0911     TCGA-13-0912     TCGA-13-0913     TCGA-13-0916 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0919     TCGA-13-0920     TCGA-13-0923     TCGA-13-0924 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1403     TCGA-13-1404     TCGA-13-1405     TCGA-13-1407 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1497     TCGA-13-1498 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1509     TCGA-13-1510 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1512     TCGA-13-2060     TCGA-20-0987     TCGA-20-0990 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-20-0991     TCGA-23-1021     TCGA-23-1022     TCGA-23-1023 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1026     TCGA-23-1027     TCGA-23-1028     TCGA-23-1030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1032     TCGA-23-1110     TCGA-23-1118     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-1124     TCGA-23-2072 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0968     TCGA-24-0970     TCGA-24-0975 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0979     TCGA-24-0982     TCGA-24-1103     TCGA-24-1104 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1105     TCGA-24-1413     TCGA-24-1416     TCGA-24-1417 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1418     TCGA-24-1419     TCGA-24-1422     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1425     TCGA-24-1426     TCGA-24-1427 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1428     TCGA-24-1431     TCGA-24-1434     TCGA-24-1435 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1436     TCGA-24-1463     TCGA-24-1464     TCGA-24-1466 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1470     TCGA-24-1471     TCGA-24-1474 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1544     TCGA-24-1545     TCGA-24-1548     TCGA-24-1549 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1551     TCGA-24-1552     TCGA-24-1553     TCGA-24-1555 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1556     TCGA-24-1557     TCGA-24-1558     TCGA-24-1560 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1562     TCGA-24-1563     TCGA-24-1564     TCGA-24-1565 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1614 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1616     TCGA-24-2019     TCGA-24-2024     TCGA-24-2030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2035     TCGA-24-2038     TCGA-24-2254     TCGA-24-2260 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2261     TCGA-24-2262     TCGA-24-2267     TCGA-24-2271 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2280     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1317     TCGA-25-1318 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1319     TCGA-25-1320     TCGA-25-1321     TCGA-25-1322 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1324     TCGA-25-1326     TCGA-25-1328     TCGA-25-1329 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1623     TCGA-25-1625     TCGA-25-1626     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1628     TCGA-25-1630     TCGA-25-1631     TCGA-25-1633 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1634     TCGA-25-1635     TCGA-25-2042     TCGA-25-2391 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2392     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1853 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-30-1862     TCGA-30-1891     TCGA-31-1953     TCGA-31-1959 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1568     TCGA-36-1569     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-57-1582     TCGA-57-1583 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1584     TCGA-57-1993     TCGA-59-2348     TCGA-59-2350 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2351     TCGA-59-2352     TCGA-59-2354     TCGA-59-2355 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2363     TCGA-61-1728     TCGA-61-1736     TCGA-61-1919 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1995     TCGA-61-1998     TCGA-61-2000     TCGA-61-2002 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2003     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2095     TCGA-61-2097     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2110     TCGA-61-2111 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2113 
"GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        0      1      1
  GART WILD-TYPE     64    123     98
D14V12, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            285 
    TCGA-04-1331     TCGA-04-1332     TCGA-04-1336     TCGA-04-1337 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1342     TCGA-04-1346     TCGA-04-1347     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1350     TCGA-04-1356     TCGA-04-1357 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1361     TCGA-04-1362     TCGA-04-1364     TCGA-04-1367 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-04-1517     TCGA-04-1525     TCGA-04-1530 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-0366     TCGA-09-1661     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1665     TCGA-09-1666     TCGA-09-1669     TCGA-09-2044 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2045     TCGA-09-2050     TCGA-09-2051     TCGA-09-2053 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0927     TCGA-10-0928 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-10-0933     TCGA-10-0934     TCGA-13-0714     TCGA-13-0720 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0723     TCGA-13-0724     TCGA-13-0751     TCGA-13-0755 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0760     TCGA-13-0791     TCGA-13-0792     TCGA-13-0800 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0883     TCGA-13-0884     TCGA-13-0885     TCGA-13-0886 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0887     TCGA-13-0889     TCGA-13-0890     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0893     TCGA-13-0894     TCGA-13-0900     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0904     TCGA-13-0905     TCGA-13-0906     TCGA-13-0910 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0911     TCGA-13-0912     TCGA-13-0913     TCGA-13-0916 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0919     TCGA-13-0920     TCGA-13-0923     TCGA-13-0924 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1403     TCGA-13-1404     TCGA-13-1405     TCGA-13-1407 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1497     TCGA-13-1498 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1509     TCGA-13-1510 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1512     TCGA-13-2060     TCGA-20-0987     TCGA-20-0990 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-20-0991     TCGA-23-1021     TCGA-23-1022     TCGA-23-1023 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1026     TCGA-23-1027     TCGA-23-1028     TCGA-23-1030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1032     TCGA-23-1110     TCGA-23-1118     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-1124     TCGA-23-2072 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0968     TCGA-24-0970     TCGA-24-0975 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0979     TCGA-24-0982     TCGA-24-1103     TCGA-24-1104 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1105     TCGA-24-1413     TCGA-24-1416     TCGA-24-1417 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1418     TCGA-24-1419     TCGA-24-1422     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1425     TCGA-24-1426     TCGA-24-1427 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1428     TCGA-24-1431     TCGA-24-1434     TCGA-24-1435 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1436     TCGA-24-1463     TCGA-24-1464     TCGA-24-1466 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1470     TCGA-24-1471     TCGA-24-1474 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1544     TCGA-24-1545     TCGA-24-1548     TCGA-24-1549 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1551     TCGA-24-1552     TCGA-24-1553     TCGA-24-1555 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1556     TCGA-24-1557     TCGA-24-1558     TCGA-24-1560 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1562     TCGA-24-1563     TCGA-24-1564     TCGA-24-1565 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1614 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1616     TCGA-24-2019     TCGA-24-2024     TCGA-24-2030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2035     TCGA-24-2038     TCGA-24-2254     TCGA-24-2260 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2261     TCGA-24-2262     TCGA-24-2267     TCGA-24-2271 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2280     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1317     TCGA-25-1318 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1319     TCGA-25-1320     TCGA-25-1321     TCGA-25-1322 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1324     TCGA-25-1326     TCGA-25-1328     TCGA-25-1329 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1623     TCGA-25-1625     TCGA-25-1626     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1628     TCGA-25-1630     TCGA-25-1631     TCGA-25-1633 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1634     TCGA-25-1635     TCGA-25-2042     TCGA-25-2391 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2392     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1853 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-30-1862     TCGA-30-1891     TCGA-31-1953     TCGA-31-1959 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1568     TCGA-36-1569     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-57-1582     TCGA-57-1583 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1584     TCGA-57-1993     TCGA-59-2348     TCGA-59-2350 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2351     TCGA-59-2352     TCGA-59-2354     TCGA-59-2355 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2363     TCGA-61-1728     TCGA-61-1736     TCGA-61-1919 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1995     TCGA-61-1998     TCGA-61-2000     TCGA-61-2002 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2003     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2095     TCGA-61-2097     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2110     TCGA-61-2111 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2113 
"GART WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GART MUTATED        0      1      1
  GART WILD-TYPE    111    112     62
D14V13, multiclass
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2            285 
    TCGA-04-1331     TCGA-04-1332     TCGA-04-1336     TCGA-04-1337 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1342     TCGA-04-1346     TCGA-04-1347     TCGA-04-1348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1349     TCGA-04-1350     TCGA-04-1356     TCGA-04-1357 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1361     TCGA-04-1362     TCGA-04-1364     TCGA-04-1367 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1514     TCGA-04-1517     TCGA-04-1525     TCGA-04-1530 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-04-1542     TCGA-09-0366     TCGA-09-1661     TCGA-09-1662 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-1665     TCGA-09-1666     TCGA-09-1669     TCGA-09-2044 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2045     TCGA-09-2050     TCGA-09-2051     TCGA-09-2053 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-09-2056     TCGA-10-0926     TCGA-10-0927     TCGA-10-0928 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-10-0933     TCGA-10-0934     TCGA-13-0714     TCGA-13-0720 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0723     TCGA-13-0724     TCGA-13-0751     TCGA-13-0755 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0760     TCGA-13-0791     TCGA-13-0792     TCGA-13-0800 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0883     TCGA-13-0884     TCGA-13-0885     TCGA-13-0886 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0887     TCGA-13-0889     TCGA-13-0890     TCGA-13-0891 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0893     TCGA-13-0894     TCGA-13-0900     TCGA-13-0903 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0904     TCGA-13-0905     TCGA-13-0906     TCGA-13-0910 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0911     TCGA-13-0912     TCGA-13-0913     TCGA-13-0916 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-0919     TCGA-13-0920     TCGA-13-0923     TCGA-13-0924 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1403     TCGA-13-1404     TCGA-13-1405     TCGA-13-1407 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1408     TCGA-13-1409     TCGA-13-1410     TCGA-13-1411 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1477     TCGA-13-1481     TCGA-13-1482 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1487     TCGA-13-1488 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1489     TCGA-13-1491     TCGA-13-1492     TCGA-13-1494 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1495     TCGA-13-1496     TCGA-13-1497     TCGA-13-1498 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1505 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1509     TCGA-13-1510 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-13-1512     TCGA-13-2060     TCGA-20-0987     TCGA-20-0990 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-20-0991     TCGA-23-1021     TCGA-23-1022     TCGA-23-1023 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1026     TCGA-23-1027     TCGA-23-1028     TCGA-23-1030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1032     TCGA-23-1110     TCGA-23-1118     TCGA-23-1120 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-1122     TCGA-23-1123     TCGA-23-1124     TCGA-23-2072 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-23-2077     TCGA-23-2078     TCGA-23-2079     TCGA-23-2081 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0966     TCGA-24-0968     TCGA-24-0970     TCGA-24-0975 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-0979     TCGA-24-0982     TCGA-24-1103     TCGA-24-1104 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1105     TCGA-24-1413     TCGA-24-1416     TCGA-24-1417 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1418     TCGA-24-1419     TCGA-24-1422     TCGA-24-1423 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1424     TCGA-24-1425     TCGA-24-1426     TCGA-24-1427 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1428     TCGA-24-1431     TCGA-24-1434     TCGA-24-1435 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1436     TCGA-24-1463     TCGA-24-1464     TCGA-24-1466 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1469     TCGA-24-1470     TCGA-24-1471     TCGA-24-1474 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1544     TCGA-24-1545     TCGA-24-1548     TCGA-24-1549 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1551     TCGA-24-1552     TCGA-24-1553     TCGA-24-1555 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1556     TCGA-24-1557     TCGA-24-1558     TCGA-24-1560 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1562     TCGA-24-1563     TCGA-24-1564     TCGA-24-1565 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1567     TCGA-24-1603     TCGA-24-1604     TCGA-24-1614 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-1616     TCGA-24-2019     TCGA-24-2024     TCGA-24-2030 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2035     TCGA-24-2038     TCGA-24-2254     TCGA-24-2260 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2261     TCGA-24-2262     TCGA-24-2267     TCGA-24-2271 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2280     TCGA-24-2281     TCGA-24-2288     TCGA-24-2289 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-24-2290     TCGA-24-2293     TCGA-24-2298     TCGA-25-1313 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1315     TCGA-25-1316     TCGA-25-1317     TCGA-25-1318 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1319     TCGA-25-1320     TCGA-25-1321     TCGA-25-1322 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1324     TCGA-25-1326     TCGA-25-1328     TCGA-25-1329 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1623     TCGA-25-1625     TCGA-25-1626     TCGA-25-1627 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1628     TCGA-25-1630     TCGA-25-1631     TCGA-25-1633 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-1634     TCGA-25-1635     TCGA-25-2042     TCGA-25-2391 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2392     TCGA-25-2393     TCGA-25-2396     TCGA-25-2398 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2399     TCGA-25-2400     TCGA-25-2401     TCGA-25-2404 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-25-2408     TCGA-25-2409     TCGA-29-2427     TCGA-30-1853 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-30-1862     TCGA-30-1891     TCGA-31-1953     TCGA-31-1959 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1568     TCGA-36-1569     TCGA-36-1570     TCGA-36-1571 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1574     TCGA-36-1575     TCGA-36-1576     TCGA-36-1577 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-36-1578     TCGA-36-1580     TCGA-57-1582     TCGA-57-1583 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-57-1584     TCGA-57-1993     TCGA-59-2348     TCGA-59-2350 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2351     TCGA-59-2352     TCGA-59-2354     TCGA-59-2355 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-59-2363     TCGA-61-1728     TCGA-61-1736     TCGA-61-1919 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-1995     TCGA-61-1998     TCGA-61-2000     TCGA-61-2002 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2003     TCGA-61-2008     TCGA-61-2009     TCGA-61-2012 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2016     TCGA-61-2088     TCGA-61-2092     TCGA-61-2094 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2095     TCGA-61-2097     TCGA-61-2101     TCGA-61-2102 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2104     TCGA-61-2109     TCGA-61-2110     TCGA-61-2111 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-61-2113 
"GART WILD-TYPE" 

Clustering(15) Variable = SRC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      2      1
  SRC WILD-TYPE    118    113     81
D15V1, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1           118
  CLUS_2           2           113
  CLUS_3           1            81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        3      1      0
  SRC WILD-TYPE    170     93     49
D15V2, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           3           170
  CLUS_2           1            93
  CLUS_3           0            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
  SRC MUTATED        0      2      2
  SRC WILD-TYPE     92     94    126
D15V3, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            92
  CLUS_2           2            94
  CLUS_3           2           126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SRC MUTATED        0       1      0      0      0      1      0      0      0
  SRC WILD-TYPE     51      27     33     53     20     43     20     16     21
               vv
clus            CLUS_9
  SRC MUTATED        2
  SRC WILD-TYPE     28
D15V4, multiclass
         clus
vv        SRC MUTATED SRC WILD-TYPE
  CLUS_1            0            51
  CLUS_10           1            27
  CLUS_2            0            33
  CLUS_3            0            53
  CLUS_4            0            20
  CLUS_5            1            43
  CLUS_6            0            20
  CLUS_7            0            16
  CLUS_8            0            21
  CLUS_9            2            28
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      3      1
  SRC WILD-TYPE    112    100     95
D15V5, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0           112
  CLUS_2           3           100
  CLUS_3           1            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
  SRC MUTATED        1      1      0
  SRC WILD-TYPE     75     95     38
D15V6, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           208 
   TCGA-04-1336    TCGA-04-1338    TCGA-04-1342    TCGA-04-1343    TCGA-04-1348 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1349    TCGA-04-1356    TCGA-04-1357    TCGA-04-1361    TCGA-04-1362 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-04-1517    TCGA-04-1542    TCGA-09-1662    TCGA-09-1665 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1666    TCGA-09-2044    TCGA-09-2045    TCGA-09-2049    TCGA-09-2051 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-2056    TCGA-10-0926    TCGA-10-0931    TCGA-10-0933    TCGA-13-0720 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0800    TCGA-13-0804    TCGA-13-0884    TCGA-13-0886 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897    TCGA-13-0899 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0903    TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0913 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0916    TCGA-13-0920    TCGA-13-1404    TCGA-13-1405    TCGA-13-1408 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1409    TCGA-13-1410    TCGA-13-1411    TCGA-13-1412    TCGA-13-1477 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1481    TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1487 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1488    TCGA-13-1489    TCGA-13-1491    TCGA-13-1492    TCGA-13-1494 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1495    TCGA-13-1496    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1504    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507    TCGA-13-1509 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1110    TCGA-23-1122    TCGA-23-1123 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1124    TCGA-23-2077    TCGA-23-2078    TCGA-23-2079    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0966    TCGA-24-0970    TCGA-24-0979    TCGA-24-0980    TCGA-24-0982 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1103    TCGA-24-1104    TCGA-24-1105    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1419    TCGA-24-1422    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1431    TCGA-24-1434    TCGA-24-1435    TCGA-24-1436 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1463    TCGA-24-1464    TCGA-24-1466    TCGA-24-1469    TCGA-24-1470 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1471    TCGA-24-1474    TCGA-24-1544    TCGA-24-1545    TCGA-24-1548 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1565    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1614    TCGA-24-1616    TCGA-24-2024    TCGA-24-2030 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2260    TCGA-24-2261    TCGA-24-2262 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2267    TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2289 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2290    TCGA-24-2293    TCGA-24-2298    TCGA-25-1313    TCGA-25-1315 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1316    TCGA-25-1319    TCGA-25-1320    TCGA-25-1321    TCGA-25-1322 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1326    TCGA-25-1328    TCGA-25-1329    TCGA-25-1623    TCGA-25-1625 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1626    TCGA-25-1627    TCGA-25-1628    TCGA-25-1630    TCGA-25-1631 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1632    TCGA-25-1633    TCGA-25-1635    TCGA-25-2042    TCGA-25-2391 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2393    TCGA-25-2396    TCGA-25-2398    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2401    TCGA-25-2404    TCGA-25-2408    TCGA-25-2409    TCGA-29-2427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-30-1891    TCGA-31-1950    TCGA-36-1568    TCGA-36-1569    TCGA-36-1570 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1571    TCGA-36-1575    TCGA-36-1576    TCGA-36-1577    TCGA-36-1578 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1580    TCGA-59-2348    TCGA-59-2351    TCGA-59-2352    TCGA-59-2354 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2363    TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2003    TCGA-61-2009    TCGA-61-2012    TCGA-61-2088    TCGA-61-2092 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2094    TCGA-61-2095    TCGA-61-2101    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRC MUTATED        0      0      2      0
  SRC WILD-TYPE     67     48     62     31
D15V7, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           208 
   TCGA-04-1336    TCGA-04-1338    TCGA-04-1342    TCGA-04-1343    TCGA-04-1348 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1349    TCGA-04-1356    TCGA-04-1357    TCGA-04-1361    TCGA-04-1362 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-04-1517    TCGA-04-1542    TCGA-09-1662    TCGA-09-1665 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1666    TCGA-09-2044    TCGA-09-2045    TCGA-09-2049    TCGA-09-2051 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-2056    TCGA-10-0926    TCGA-10-0931    TCGA-10-0933    TCGA-13-0720 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0800    TCGA-13-0804    TCGA-13-0884    TCGA-13-0886 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897    TCGA-13-0899 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0903    TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0913 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0916    TCGA-13-0920    TCGA-13-1404    TCGA-13-1405    TCGA-13-1408 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1409    TCGA-13-1410    TCGA-13-1411    TCGA-13-1412    TCGA-13-1477 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1481    TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1487 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1488    TCGA-13-1489    TCGA-13-1491    TCGA-13-1492    TCGA-13-1494 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1495    TCGA-13-1496    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1504    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507    TCGA-13-1509 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1110    TCGA-23-1122    TCGA-23-1123 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1124    TCGA-23-2077    TCGA-23-2078    TCGA-23-2079    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0966    TCGA-24-0970    TCGA-24-0979    TCGA-24-0980    TCGA-24-0982 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1103    TCGA-24-1104    TCGA-24-1105    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1419    TCGA-24-1422    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1431    TCGA-24-1434    TCGA-24-1435    TCGA-24-1436 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1463    TCGA-24-1464    TCGA-24-1466    TCGA-24-1469    TCGA-24-1470 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1471    TCGA-24-1474    TCGA-24-1544    TCGA-24-1545    TCGA-24-1548 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1565    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1614    TCGA-24-1616    TCGA-24-2024    TCGA-24-2030 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2260    TCGA-24-2261    TCGA-24-2262 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2267    TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2289 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2290    TCGA-24-2293    TCGA-24-2298    TCGA-25-1313    TCGA-25-1315 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1316    TCGA-25-1319    TCGA-25-1320    TCGA-25-1321    TCGA-25-1322 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1326    TCGA-25-1328    TCGA-25-1329    TCGA-25-1623    TCGA-25-1625 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1626    TCGA-25-1627    TCGA-25-1628    TCGA-25-1630    TCGA-25-1631 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1632    TCGA-25-1633    TCGA-25-1635    TCGA-25-2042    TCGA-25-2391 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2393    TCGA-25-2396    TCGA-25-2398    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2401    TCGA-25-2404    TCGA-25-2408    TCGA-25-2409    TCGA-29-2427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-30-1891    TCGA-31-1950    TCGA-36-1568    TCGA-36-1569    TCGA-36-1570 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1571    TCGA-36-1575    TCGA-36-1576    TCGA-36-1577    TCGA-36-1578 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1580    TCGA-59-2348    TCGA-59-2351    TCGA-59-2352    TCGA-59-2354 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2363    TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2003    TCGA-61-2009    TCGA-61-2012    TCGA-61-2088    TCGA-61-2092 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2094    TCGA-61-2095    TCGA-61-2101    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      1      0
  SRC WILD-TYPE     69     39     51
D15V8, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1469    TCGA-24-1474    TCGA-24-1544 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1548    TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1555    TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1562    TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1313    TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1319 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-1635 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2391    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      2      0
  SRC WILD-TYPE     66     74     19
D15V9, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1469    TCGA-24-1474    TCGA-24-1544 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1548    TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1555    TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1562    TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1313    TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1319 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-1635 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2391    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      2
  SRC WILD-TYPE     79    118     87
D15V10, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            79
  CLUS_2           1           118
  CLUS_3           2            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 CLUS_4
  SRC MUTATED        0      1      1      1
  SRC WILD-TYPE     74     45     98     67
D15V11, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            74
  CLUS_2           1            45
  CLUS_3           1            98
  CLUS_4           1            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      2
  SRC WILD-TYPE     64    123     97
D15V12, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            64
  CLUS_2           1           123
  CLUS_3           2            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
  SRC MUTATED        1      2      0
  SRC WILD-TYPE    110    111     63
D15V13, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1           110
  CLUS_2           2           111
  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"

Clustering(16) Variable = ZNF236 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        3      2      2
  ZNF236 WILD-TYPE    116    113     80
D16V1, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              3              116
  CLUS_2              2              113
  CLUS_3              2               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
  ZNF236 MUTATED        4      2      1
  ZNF236 WILD-TYPE    169     92     48
D16V2, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              4              169
  CLUS_2              2               92
  CLUS_3              1               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
  ZNF236 MUTATED        3      2      2
  ZNF236 WILD-TYPE     89     94    126
D16V3, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              3               89
  CLUS_2              2               94
  CLUS_3              2              126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZNF236 MUTATED        0       2      0      1      1      2      1      0
  ZNF236 WILD-TYPE     51      26     33     52     19     42     19     16
                  vv
clus               CLUS_8 CLUS_9
  ZNF236 MUTATED        0      0
  ZNF236 WILD-TYPE     21     30
D16V4, multiclass
         clus
vv        ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1               0               51
  CLUS_10              2               26
  CLUS_2               0               33
  CLUS_3               1               52
  CLUS_4               1               19
  CLUS_5               2               42
  CLUS_6               1               19
  CLUS_7               0               16
  CLUS_8               0               21
  CLUS_9               0               30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        4      1      2
  ZNF236 WILD-TYPE    108    102     94
D16V5, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              4              108
  CLUS_2              1              102
  CLUS_3              2               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
  ZNF236 MUTATED        0      3      1
  ZNF236 WILD-TYPE     76     93     37
D16V6, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              0               76
  CLUS_2              3               93
  CLUS_3              1               37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF236 MUTATED        1      2      1      0
  ZNF236 WILD-TYPE     66     46     63     31
D16V7, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              1               66
  CLUS_2              2               46
  CLUS_3              1               63
  CLUS_4              0               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        0      2      0
  ZNF236 WILD-TYPE     70     38     51
D16V8, multiclass
[1] "Remove cluster labels:" "ZNF236 MUTATED"        
clus
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               2              159 
      TCGA-04-1348       TCGA-04-1362       TCGA-04-1364       TCGA-04-1365 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-04-1514       TCGA-09-0366       TCGA-09-0369       TCGA-09-1662 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-09-1666       TCGA-09-1669       TCGA-09-2044       TCGA-09-2045 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-09-2051       TCGA-09-2056       TCGA-10-0928       TCGA-13-0730 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0800       TCGA-13-0890       TCGA-13-0893       TCGA-13-0897 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0899       TCGA-13-0913       TCGA-13-0916       TCGA-13-0920 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0924       TCGA-13-1403       TCGA-13-1405       TCGA-13-1410 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-1481       TCGA-13-1497       TCGA-13-1498       TCGA-13-1505 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-1506       TCGA-13-1507       TCGA-13-1512       TCGA-13-2060 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-23-1023       TCGA-23-1026       TCGA-23-1027       TCGA-23-1120 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-23-1122       TCGA-23-1123       TCGA-23-2077       TCGA-23-2081 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-0975       TCGA-24-1103       TCGA-24-1413       TCGA-24-1416 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1417       TCGA-24-1418       TCGA-24-1419       TCGA-24-1423 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1424       TCGA-24-1427       TCGA-24-1428       TCGA-24-1436 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1469       TCGA-24-1474       TCGA-24-1544       TCGA-24-1548 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1549       TCGA-24-1551       TCGA-24-1552       TCGA-24-1553 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1555       TCGA-24-1556       TCGA-24-1557       TCGA-24-1558 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1560       TCGA-24-1562       TCGA-24-1563       TCGA-24-1564 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1567       TCGA-24-1603       TCGA-24-1604       TCGA-24-1616 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2019       TCGA-24-2024       TCGA-24-2035       TCGA-24-2038 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2254       TCGA-24-2261       TCGA-24-2262       TCGA-24-2267 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2271       TCGA-24-2281       TCGA-24-2288       TCGA-24-2290 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2298       TCGA-25-1313       TCGA-25-1315       TCGA-25-1316 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1317       TCGA-25-1318       TCGA-25-1319       TCGA-25-1321 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1322       TCGA-25-1324       TCGA-25-1326       TCGA-25-1328 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1329       TCGA-25-1623       TCGA-25-1625       TCGA-25-1627 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1630       TCGA-25-1631       TCGA-25-1632       TCGA-25-1633 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1634       TCGA-25-1635       TCGA-25-2391       TCGA-25-2392 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-2393       TCGA-25-2396       TCGA-25-2399       TCGA-25-2400 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-2404       TCGA-25-2409       TCGA-29-2427       TCGA-30-1862 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-30-1891       TCGA-31-1953       TCGA-36-1568       TCGA-36-1570 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-36-1571       TCGA-36-1574       TCGA-36-1575       TCGA-36-1577 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-36-1578       TCGA-36-1580       TCGA-57-1582       TCGA-57-1583 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-57-1584       TCGA-57-1993       TCGA-59-2348       TCGA-59-2350 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-59-2351       TCGA-59-2352       TCGA-59-2355       TCGA-59-2363 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-1728       TCGA-61-1919       TCGA-61-1995       TCGA-61-1998 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2000       TCGA-61-2008       TCGA-61-2009       TCGA-61-2012 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2016       TCGA-61-2088       TCGA-61-2092       TCGA-61-2094 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2097       TCGA-61-2102       TCGA-61-2104       TCGA-61-2109 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2110       TCGA-61-2111       TCGA-61-2113 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        1      1      0
  ZNF236 WILD-TYPE     65     75     19
D16V9, multiclass
[1] "Remove cluster labels:" "ZNF236 MUTATED"        
clus
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               2              159 
      TCGA-04-1348       TCGA-04-1362       TCGA-04-1364       TCGA-04-1365 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-04-1514       TCGA-09-0366       TCGA-09-0369       TCGA-09-1662 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-09-1666       TCGA-09-1669       TCGA-09-2044       TCGA-09-2045 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-09-2051       TCGA-09-2056       TCGA-10-0928       TCGA-13-0730 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0800       TCGA-13-0890       TCGA-13-0893       TCGA-13-0897 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0899       TCGA-13-0913       TCGA-13-0916       TCGA-13-0920 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-0924       TCGA-13-1403       TCGA-13-1405       TCGA-13-1410 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-1481       TCGA-13-1497       TCGA-13-1498       TCGA-13-1505 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-13-1506       TCGA-13-1507       TCGA-13-1512       TCGA-13-2060 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-23-1023       TCGA-23-1026       TCGA-23-1027       TCGA-23-1120 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-23-1122       TCGA-23-1123       TCGA-23-2077       TCGA-23-2081 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-0975       TCGA-24-1103       TCGA-24-1413       TCGA-24-1416 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1417       TCGA-24-1418       TCGA-24-1419       TCGA-24-1423 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1424       TCGA-24-1427       TCGA-24-1428       TCGA-24-1436 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1469       TCGA-24-1474       TCGA-24-1544       TCGA-24-1548 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1549       TCGA-24-1551       TCGA-24-1552       TCGA-24-1553 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1555       TCGA-24-1556       TCGA-24-1557       TCGA-24-1558 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1560       TCGA-24-1562       TCGA-24-1563       TCGA-24-1564 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-1567       TCGA-24-1603       TCGA-24-1604       TCGA-24-1616 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2019       TCGA-24-2024       TCGA-24-2035       TCGA-24-2038 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2254       TCGA-24-2261       TCGA-24-2262       TCGA-24-2267 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2271       TCGA-24-2281       TCGA-24-2288       TCGA-24-2290 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-24-2298       TCGA-25-1313       TCGA-25-1315       TCGA-25-1316 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1317       TCGA-25-1318       TCGA-25-1319       TCGA-25-1321 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1322       TCGA-25-1324       TCGA-25-1326       TCGA-25-1328 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1329       TCGA-25-1623       TCGA-25-1625       TCGA-25-1627 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1630       TCGA-25-1631       TCGA-25-1632       TCGA-25-1633 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-1634       TCGA-25-1635       TCGA-25-2391       TCGA-25-2392 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-2393       TCGA-25-2396       TCGA-25-2399       TCGA-25-2400 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-25-2404       TCGA-25-2409       TCGA-29-2427       TCGA-30-1862 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-30-1891       TCGA-31-1953       TCGA-36-1568       TCGA-36-1570 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-36-1571       TCGA-36-1574       TCGA-36-1575       TCGA-36-1577 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-36-1578       TCGA-36-1580       TCGA-57-1582       TCGA-57-1583 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-57-1584       TCGA-57-1993       TCGA-59-2348       TCGA-59-2350 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-59-2351       TCGA-59-2352       TCGA-59-2355       TCGA-59-2363 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-1728       TCGA-61-1919       TCGA-61-1995       TCGA-61-1998 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2000       TCGA-61-2008       TCGA-61-2009       TCGA-61-2012 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2016       TCGA-61-2088       TCGA-61-2092       TCGA-61-2094 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2097       TCGA-61-2102       TCGA-61-2104       TCGA-61-2109 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
      TCGA-61-2110       TCGA-61-2111       TCGA-61-2113 
"ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" "ZNF236 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        1      1      4
  ZNF236 WILD-TYPE     78    118     85
D16V10, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              1               78
  CLUS_2              1              118
  CLUS_3              4               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
  ZNF236 MUTATED        2      0      0      4
  ZNF236 WILD-TYPE     72     46     99     64
D16V11, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              2               72
  CLUS_2              0               46
  CLUS_3              0               99
  CLUS_4              4               64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF236 MUTATED        1      1      4
  ZNF236 WILD-TYPE     63    123     95
D16V12, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              1               63
  CLUS_2              1              123
  CLUS_3              4               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
  ZNF236 MUTATED        1      5      0
  ZNF236 WILD-TYPE    110    108     63
D16V13, multiclass
        clus
vv       ZNF236 MUTATED ZNF236 WILD-TYPE
  CLUS_1              1              110
  CLUS_2              5              108
  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"

Clustering(17) Variable = NBPF16 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF16 MUTATED        1      1      2
  NBPF16 WILD-TYPE    118    114     80
D17V1, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              1              118
  CLUS_2              1              114
  CLUS_3              2               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
  NBPF16 MUTATED        3      1      0
  NBPF16 WILD-TYPE    170     93     49
D17V2, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              3              170
  CLUS_2              1               93
  CLUS_3              0               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
  NBPF16 MUTATED        2      2      0
  NBPF16 WILD-TYPE     90     94    128
D17V3, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              2               90
  CLUS_2              2               94
  CLUS_3              0              128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NBPF16 MUTATED        0       0      1      0      2      1      0      0
  NBPF16 WILD-TYPE     51      28     32     53     18     43     20     16
                  vv
clus               CLUS_8 CLUS_9
  NBPF16 MUTATED        0      0
  NBPF16 WILD-TYPE     21     30
D17V4, multiclass
         clus
vv        NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1               0               51
  CLUS_10              0               28
  CLUS_2               1               32
  CLUS_3               0               53
  CLUS_4               2               18
  CLUS_5               1               43
  CLUS_6               0               20
  CLUS_7               0               16
  CLUS_8               0               21
  CLUS_9               0               30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF16 MUTATED        3      0      1
  NBPF16 WILD-TYPE    109    103     95
D17V5, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              3              109
  CLUS_2              0              103
  CLUS_3              1               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
  NBPF16 MUTATED        0      2      1
  NBPF16 WILD-TYPE     76     94     37
D17V6, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              0               76
  CLUS_2              2               94
  CLUS_3              1               37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NBPF16 MUTATED        1      2      0      0
  NBPF16 WILD-TYPE     66     46     64     31
D17V7, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              1               66
  CLUS_2              2               46
  CLUS_3              0               64
  CLUS_4              0               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF16 MUTATED        0      1      2
  NBPF16 WILD-TYPE     70     39     49
D17V8, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              0               70
  CLUS_2              1               39
  CLUS_3              2               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
  NBPF16 MUTATED        1      2      0
  NBPF16 WILD-TYPE     65     74     19
D17V9, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              2               74
  CLUS_3              0               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF16 MUTATED        0      1      3
  NBPF16 WILD-TYPE     79    118     86
D17V10, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              0               79
  CLUS_2              1              118
  CLUS_3              3               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 CLUS_4
  NBPF16 MUTATED        1      1      0      2
  NBPF16 WILD-TYPE     73     45     99     66
D17V11, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              1               73
  CLUS_2              1               45
  CLUS_3              0               99
  CLUS_4              2               66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NBPF16 MUTATED        0      1      3
  NBPF16 WILD-TYPE     64    123     96
D17V12, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              0               64
  CLUS_2              1              123
  CLUS_3              3               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
  NBPF16 MUTATED        0      3      1
  NBPF16 WILD-TYPE    111    110     62
D17V13, multiclass
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  CLUS_1              0              111
  CLUS_2              3              110
  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"

Clustering(18) Variable = CYP11B1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        1      6      0
  CYP11B1 WILD-TYPE    118    109     82
D18V1, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               1               118
  CLUS_2               6               109
  CLUS_3               0                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
  CYP11B1 MUTATED        6      1      0
  CYP11B1 WILD-TYPE    167     93     49
D18V2, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               6               167
  CLUS_2               1                93
  CLUS_3               0                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
  CYP11B1 MUTATED        2      1      4
  CYP11B1 WILD-TYPE     90     95    124
D18V3, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                90
  CLUS_2               1                95
  CLUS_3               4               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CYP11B1 MUTATED        1       0      0      1      0      1      0      1
  CYP11B1 WILD-TYPE     50      28     33     52     20     43     20     15
                   vv
clus                CLUS_8 CLUS_9
  CYP11B1 MUTATED        0      3
  CYP11B1 WILD-TYPE     21     27
D18V4, multiclass
         clus
vv        CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1                1                50
  CLUS_10               0                28
  CLUS_2                0                33
  CLUS_3                1                52
  CLUS_4                0                20
  CLUS_5                1                43
  CLUS_6                0                20
  CLUS_7                1                15
  CLUS_8                0                21
  CLUS_9                3                27
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        2      3      2
  CYP11B1 WILD-TYPE    110    100     94
D18V5, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2               110
  CLUS_2               3               100
  CLUS_3               2                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
  CYP11B1 MUTATED        2      1      0
  CYP11B1 WILD-TYPE     74     95     38
D18V6, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                74
  CLUS_2               1                95
  CLUS_3               0                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        3      0      0      0
  CYP11B1 WILD-TYPE     64     48     64     31
D18V7, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                64
  CLUS_2               0                48
  CLUS_3               0                64
  CLUS_4               0                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        2      2      1
  CYP11B1 WILD-TYPE     68     38     50
D18V8, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                68
  CLUS_2               2                38
  CLUS_3               1                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
  CYP11B1 MUTATED        2      3      0
  CYP11B1 WILD-TYPE     64     73     19
D18V9, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                64
  CLUS_2               3                73
  CLUS_3               0                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        1      5      1
  CYP11B1 WILD-TYPE     78    114     88
D18V10, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               1                78
  CLUS_2               5               114
  CLUS_3               1                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        3      1      2      1
  CYP11B1 WILD-TYPE     71     45     97     67
D18V11, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                71
  CLUS_2               1                45
  CLUS_3               2                97
  CLUS_4               1                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        1      4      2
  CYP11B1 WILD-TYPE     63    120     97
D18V12, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               1                63
  CLUS_2               4               120
  CLUS_3               2                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
  CYP11B1 MUTATED        2      3      2
  CYP11B1 WILD-TYPE    109    110     61
D18V13, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2               109
  CLUS_2               3               110
  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"

Clustering(19) Variable = SON MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        4      1      3
  SON WILD-TYPE    115    114     79
D19V1, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           4           115
  CLUS_2           1           114
  CLUS_3           3            79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        3      3      2
  SON WILD-TYPE    170     91     47
D19V2, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           3           170
  CLUS_2           3            91
  CLUS_3           2            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
  SON MUTATED        2      3      3
  SON WILD-TYPE     90     93    125
D19V3, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           2            90
  CLUS_2           3            93
  CLUS_3           3           125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SON MUTATED        2       0      1      1      0      2      2      0      0
  SON WILD-TYPE     49      28     32     52     20     42     18     16     21
               vv
clus            CLUS_9
  SON MUTATED        0
  SON WILD-TYPE     30
D19V4, multiclass
         clus
vv        SON MUTATED SON WILD-TYPE
  CLUS_1            2            49
  CLUS_10           0            28
  CLUS_2            1            32
  CLUS_3            1            52
  CLUS_4            0            20
  CLUS_5            2            42
  CLUS_6            2            18
  CLUS_7            0            16
  CLUS_8            0            21
  CLUS_9            0            30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        6      1      1
  SON WILD-TYPE    106    102     95
D19V5, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           6           106
  CLUS_2           1           102
  CLUS_3           1            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
  SON MUTATED        0      2      2
  SON WILD-TYPE     76     94     36
D19V6, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           0            76
  CLUS_2           2            94
  CLUS_3           2            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 CLUS_4
  SON MUTATED        1      0      1      2
  SON WILD-TYPE     66     48     63     29
D19V7, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           1            66
  CLUS_2           0            48
  CLUS_3           1            63
  CLUS_4           2            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        1      2      1
  SON WILD-TYPE     69     38     50
D19V8, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           1            69
  CLUS_2           2            38
  CLUS_3           1            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
  SON MUTATED        1      3      0
  SON WILD-TYPE     65     73     19
D19V9, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           1            65
  CLUS_2           3            73
  CLUS_3           0            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        2      3      1
  SON WILD-TYPE     77    116     88
D19V10, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           2            77
  CLUS_2           3           116
  CLUS_3           1            88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SON MUTATED        3      0      2      1
  SON WILD-TYPE     71     46     97     67
D19V11, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           3            71
  CLUS_2           0            46
  CLUS_3           2            97
  CLUS_4           1            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SON MUTATED        1      4      1
  SON WILD-TYPE     63    120     98
D19V12, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           1            63
  CLUS_2           4           120
  CLUS_3           1            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
  SON MUTATED        3      1      2
  SON WILD-TYPE    108    112     61
D19V13, multiclass
        clus
vv       SON MUTATED SON WILD-TYPE
  CLUS_1           3           108
  CLUS_2           1           112
  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"
