[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"        "-oTTHCA-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/THCA-TP/10667977/THCA-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/10685823/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=401, common to both=401
[1] "Reduce the number of clustering variables from 12 to 11."
[1]  11 401
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           240            161 
  BRAF MUTATED BRAF WILD-TYPE 
           240            161 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            34            367 
  NRAS MUTATED NRAS WILD-TYPE 
            34            367 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14            387 
  HRAS MUTATED HRAS WILD-TYPE 
            14            387 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              395 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              395 
[1] "NUP93 MUTATION ANALYSIS"
[1] 3
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             397 
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             397 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             396 
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             396 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              398 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              398 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             4            397 
  KRAS MUTATED KRAS WILD-TYPE 
             4            397 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            397 
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            397 
[1] "ITGAL MUTATION ANALYSIS"
[1] 3
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             397 
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             397 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             398 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             398 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 401 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 401 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        8    203     29
  BRAF WILD-TYPE     18    110     31
D1V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            8             18
  CLUS_2          203            110
  CLUS_3           29             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED      185     19     36
  BRAF WILD-TYPE     28    108     25
D1V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1          185             28
  CLUS_2           19            108
  CLUS_3           36             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED       21     57     43
  BRAF WILD-TYPE     39     19     34
D1V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           21             39
  CLUS_2           57             19
  CLUS_3           43             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BRAF MUTATED        6     23     29      6     36     12      9
  BRAF WILD-TYPE     40      4      2     20     11     15      0
D1V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            6             40
  CLUS_2           23              4
  CLUS_3           29              2
  CLUS_4            6             20
  CLUS_5           36             11
  CLUS_6           12             15
  CLUS_7            9              0
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED       13     27     78    122
  BRAF WILD-TYPE    117     16     15     11
D1V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           13            117
  CLUS_2           27             16
  CLUS_3           78             15
  CLUS_4          122             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        4     36     59     86     55
  BRAF WILD-TYPE    103     41      2      6      7
D1V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4            103
  CLUS_2           36             41
  CLUS_3           59              2
  CLUS_4           86              6
  CLUS_5           55              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED       15    122    102
  BRAF WILD-TYPE    115     18     28
D1V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           15            115
  CLUS_2          122             18
  CLUS_3          102             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        4    137     98
  BRAF WILD-TYPE    104     32     25
D1V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4            104
  CLUS_2          137             32
  CLUS_3           98             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED       23    117     99
  BRAF WILD-TYPE    119     14     28
D1V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           23            119
  CLUS_2          117             14
  CLUS_3           99             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        4    127     52     56
  BRAF WILD-TYPE    102     26     29      4
D1V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4            102
  CLUS_2          127             26
  CLUS_3           52             29
  CLUS_4           56              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        1     20     11
  NRAS WILD-TYPE     25    293     49
D2V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             25
  CLUS_2           20            293
  CLUS_3           11             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
  NRAS MUTATED        0     34      0
  NRAS WILD-TYPE    213     93     61
D2V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0            213
  CLUS_2           34             93
  CLUS_3            0             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        4      5      5
  NRAS WILD-TYPE     56     71     72
D2V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4             56
  CLUS_2            5             71
  CLUS_3            5             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NRAS MUTATED        5      1      0      3      0      5      0
  NRAS WILD-TYPE     41     26     31     23     47     22      9
D2V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             41
  CLUS_2            1             26
  CLUS_3            0             31
  CLUS_4            3             23
  CLUS_5            0             47
  CLUS_6            5             22
  CLUS_7            0              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED       34      0      0      0
  NRAS WILD-TYPE     96     43     93    133
D2V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           34             96
  CLUS_2            0             43
  CLUS_3            0             93
  CLUS_4            0            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED       33      1      0      0      0
  NRAS WILD-TYPE     74     76     61     92     62
D2V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           33             74
  CLUS_2            1             76
  CLUS_3            0             61
  CLUS_4            0             92
  CLUS_5            0             62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED       33      0      1
  NRAS WILD-TYPE     97    140    129
D2V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           33             97
  CLUS_2            0            140
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED       33      0      1
  NRAS WILD-TYPE     75    169    122
D2V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           33             75
  CLUS_2            0            169
  CLUS_3            1            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_2 CLUS_3
  NRAS MUTATED       33      0      1
  NRAS WILD-TYPE    109    131    126
D2V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           33            109
  CLUS_2            0            131
  CLUS_3            1            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_2 CLUS_3 CLUS_4
  NRAS MUTATED       32      0      2      0
  NRAS WILD-TYPE     74    153     79     60
D2V10, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           32             74
  CLUS_2            0            153
  CLUS_3            2             79
  CLUS_4            0             60
[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"

Clustering(3) Variable = HRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        0      4     10
  HRAS WILD-TYPE     26    309     50
D3V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             26
  CLUS_2            4            309
  CLUS_3           10             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
  HRAS MUTATED        0     14      0
  HRAS WILD-TYPE    213    113     61
D3V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0            213
  CLUS_2           14            113
  CLUS_3            0             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        9      1      0
  HRAS WILD-TYPE     51     75     77
D3V3, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            9             51
  CLUS_2            1             75
  CLUS_3            0             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  HRAS MUTATED        7      0      0      2      0      1      0
  HRAS WILD-TYPE     39     27     31     24     47     26      9
D3V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            7             39
  CLUS_2            0             27
  CLUS_3            0             31
  CLUS_4            2             24
  CLUS_5            0             47
  CLUS_6            1             26
  CLUS_7            0              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED       14      0      0      0
  HRAS WILD-TYPE    116     43     93    133
D3V5, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14            116
  CLUS_2            0             43
  CLUS_3            0             93
  CLUS_4            0            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HRAS MUTATED       14      0      0      0      0
  HRAS WILD-TYPE     93     77     61     92     62
D3V6, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14             93
  CLUS_2            0             77
  CLUS_3            0             61
  CLUS_4            0             92
  CLUS_5            0             62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED       14      0      0
  HRAS WILD-TYPE    116    140    130
D3V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14            116
  CLUS_2            0            140
  CLUS_3            0            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED       14      0      0
  HRAS WILD-TYPE     94    169    123
D3V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14             94
  CLUS_2            0            169
  CLUS_3            0            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_2 CLUS_3
  HRAS MUTATED       14      0      0
  HRAS WILD-TYPE    128    131    127
D3V9, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14            128
  CLUS_2            0            131
  CLUS_3            0            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_2 CLUS_3 CLUS_4
  HRAS MUTATED       14      0      0      0
  HRAS WILD-TYPE     92    153     81     60
D3V10, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14             92
  CLUS_2            0            153
  CLUS_3            0             81
  CLUS_4            0             60
[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"

Clustering(4) Variable = EIF1AX MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      6      0
  EIF1AX WILD-TYPE     26    307     60
D4V1, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               26
  CLUS_2              6              307
  CLUS_3              0               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        1      4      1
  EIF1AX WILD-TYPE    212    123     60
D4V2, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              1              212
  CLUS_2              4              123
  CLUS_3              1               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        3      1      1
  EIF1AX WILD-TYPE     57     75     76
D4V3, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3               57
  CLUS_2              1               75
  CLUS_3              1               76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  EIF1AX MUTATED        3      0      0      1      0      1      0
  EIF1AX WILD-TYPE     43     27     31     25     47     26      9
D4V4, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3               43
  CLUS_2              0               27
  CLUS_3              0               31
  CLUS_4              1               25
  CLUS_5              0               47
  CLUS_6              1               26
  CLUS_7              0                9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        5      0      1      0
  EIF1AX WILD-TYPE    125     43     92    133
D4V5, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              5              125
  CLUS_2              0               43
  CLUS_3              1               92
  CLUS_4              0              133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EIF1AX MUTATED        4      2      0      0      0
  EIF1AX WILD-TYPE    103     75     61     92     62
D4V6, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              4              103
  CLUS_2              2               75
  CLUS_3              0               61
  CLUS_4              0               92
  CLUS_5              0               62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        4      1      1
  EIF1AX WILD-TYPE    126    139    129
D4V7, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              4              126
  CLUS_2              1              139
  CLUS_3              1              129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        3      1      2
  EIF1AX WILD-TYPE    105    168    121
D4V8, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3              105
  CLUS_2              1              168
  CLUS_3              2              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        4      1      1
  EIF1AX WILD-TYPE    138    130    126
D4V9, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              4              138
  CLUS_2              1              130
  CLUS_3              1              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_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        3      1      2      0
  EIF1AX WILD-TYPE    103    152     79     60
D4V10, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3              103
  CLUS_2              1              152
  CLUS_3              2               79
  CLUS_4              0               60
[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"

Clustering(5) Variable = NUP93 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUP93 MUTATED        0      4      0
  NUP93 WILD-TYPE     26    309     60
D5V1, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             4             309
  CLUS_3             0              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUP93 MUTATED        3      1      0
  NUP93 WILD-TYPE    210    126     61
D5V2, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             3             210
  CLUS_2             1             126
  CLUS_3             0              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUP93 MUTATED        0      0      2
  NUP93 WILD-TYPE     60     76     75
D5V3, multiclass
[1] "Remove cluster labels:" "NUP93 MUTATED"         
clus
  NUP93 MUTATED NUP93 WILD-TYPE 
              2             211 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A0ZE      TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K      TCGA-CE-A27D 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2      TCGA-DE-A2OL 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM      TCGA-DJ-A1QN 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PU 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY      TCGA-DJ-A2PZ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q5 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8      TCGA-DJ-A2Q9 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A2QC      TCGA-DO-A1JZ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DO-A1K0      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A2EA 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CL      TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CP      TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GY      TCGA-EL-A3GZ      TCGA-EL-A3H1      TCGA-EL-A3H2 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MY 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3N3      TCGA-EM-A1CT 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YA 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22L      TCGA-EM-A22M 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A22O      TCGA-EM-A22Q      TCGA-EM-A2CJ      TCGA-EM-A2CK 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO      TCGA-EM-A2CP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CU      TCGA-EM-A2OV 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2OY      TCGA-EM-A2P1      TCGA-EM-A3AI      TCGA-EM-A3AJ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AO      TCGA-EM-A3AP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FL      TCGA-EM-A3FN      TCGA-EM-A3FO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O      TCGA-ET-A2MY 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J      TCGA-ET-A39L 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P      TCGA-ET-A39R 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP      TCGA-ET-A3BS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP      TCGA-ET-A3DS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-FE-A22Z 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL      TCGA-FY-A3ON 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB      TCGA-IM-A3ED 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NUP93 MUTATED        0      0      0      0      2      0      0
  NUP93 WILD-TYPE     46     27     31     26     45     27      9
D5V4, multiclass
[1] "Remove cluster labels:" "NUP93 MUTATED"         
clus
  NUP93 MUTATED NUP93 WILD-TYPE 
              2             211 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A0ZE      TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K      TCGA-CE-A27D 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2      TCGA-DE-A2OL 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM      TCGA-DJ-A1QN 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PU 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY      TCGA-DJ-A2PZ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q5 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8      TCGA-DJ-A2Q9 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A2QC      TCGA-DO-A1JZ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-DO-A1K0      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A2EA 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CL      TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CP      TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3GY      TCGA-EL-A3GZ      TCGA-EL-A3H1      TCGA-EL-A3H2 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MY 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3N3      TCGA-EM-A1CT 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YA 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22L      TCGA-EM-A22M 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A22O      TCGA-EM-A22Q      TCGA-EM-A2CJ      TCGA-EM-A2CK 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO      TCGA-EM-A2CP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CU      TCGA-EM-A2OV 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A2OY      TCGA-EM-A2P1      TCGA-EM-A3AI      TCGA-EM-A3AJ 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AO      TCGA-EM-A3AP 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FL      TCGA-EM-A3FN      TCGA-EM-A3FO 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O      TCGA-ET-A2MY 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J      TCGA-ET-A39L 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P      TCGA-ET-A39R 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP      TCGA-ET-A3BS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP      TCGA-ET-A3DS 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-FE-A22Z 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL      TCGA-FY-A3ON 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB      TCGA-IM-A3ED 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
     TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"NUP93 WILD-TYPE" "NUP93 WILD-TYPE" "NUP93 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUP93 MUTATED        1      0      0      3
  NUP93 WILD-TYPE    129     43     93    130
D5V5, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             129
  CLUS_2             0              43
  CLUS_3             0              93
  CLUS_4             3             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NUP93 MUTATED        1      0      0      2      1
  NUP93 WILD-TYPE    106     77     61     90     61
D5V6, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             106
  CLUS_2             0              77
  CLUS_3             0              61
  CLUS_4             2              90
  CLUS_5             1              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUP93 MUTATED        1      2      1
  NUP93 WILD-TYPE    129    138    129
D5V7, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             129
  CLUS_2             2             138
  CLUS_3             1             129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUP93 MUTATED        1      2      1
  NUP93 WILD-TYPE    107    167    122
D5V8, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             107
  CLUS_2             2             167
  CLUS_3             1             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_2 CLUS_3
  NUP93 MUTATED        1      2      1
  NUP93 WILD-TYPE    141    129    126
D5V9, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             141
  CLUS_2             2             129
  CLUS_3             1             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_2 CLUS_3 CLUS_4
  NUP93 MUTATED        1      2      0      1
  NUP93 WILD-TYPE    105    151     81     59
D5V10, multiclass
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  CLUS_1             1             105
  CLUS_2             2             151
  CLUS_3             0              81
  CLUS_4             1              59
[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"

Clustering(6) Variable = PPM1D MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PPM1D MUTATED        0      5      0
  PPM1D WILD-TYPE     26    308     60
D6V1, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             0              26
  CLUS_2             5             308
  CLUS_3             0              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PPM1D MUTATED        3      2      0
  PPM1D WILD-TYPE    210    125     61
D6V2, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             3             210
  CLUS_2             2             125
  CLUS_3             0              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PPM1D MUTATED        0      0      3
  PPM1D WILD-TYPE     60     76     74
D6V3, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             0              60
  CLUS_2             0              76
  CLUS_3             3              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PPM1D MUTATED        1      0      0      0      2      0      0
  PPM1D WILD-TYPE     45     27     31     26     45     27      9
D6V4, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             1              45
  CLUS_2             0              27
  CLUS_3             0              31
  CLUS_4             0              26
  CLUS_5             2              45
  CLUS_6             0              27
  CLUS_7             0               9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PPM1D MUTATED        1      0      2      2
  PPM1D WILD-TYPE    129     43     91    131
D6V5, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             1             129
  CLUS_2             0              43
  CLUS_3             2              91
  CLUS_4             2             131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PPM1D MUTATED        1      0      3      0      1
  PPM1D WILD-TYPE    106     77     58     92     61
D6V6, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             1             106
  CLUS_2             0              77
  CLUS_3             3              58
  CLUS_4             0              92
  CLUS_5             1              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PPM1D MUTATED        2      3      0
  PPM1D WILD-TYPE    128    137    130
D6V7, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             2             128
  CLUS_2             3             137
  CLUS_3             0             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PPM1D MUTATED        1      4      0
  PPM1D WILD-TYPE    107    165    123
D6V8, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             1             107
  CLUS_2             4             165
  CLUS_3             0             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_2 CLUS_3
  PPM1D MUTATED        2      3      0
  PPM1D WILD-TYPE    140    128    127
D6V9, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             2             140
  CLUS_2             3             128
  CLUS_3             0             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_2 CLUS_3 CLUS_4
  PPM1D MUTATED        1      4      0      0
  PPM1D WILD-TYPE    105    149     81     60
D6V10, multiclass
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  CLUS_1             1             105
  CLUS_2             4             149
  CLUS_3             0              81
  CLUS_4             0              60
[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"

Clustering(7) Variable = DNMT3A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        1      2      0
  DNMT3A WILD-TYPE     25    311     60
D7V1, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              1               25
  CLUS_2              2              311
  CLUS_3              0               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        1      2      0
  DNMT3A WILD-TYPE    212    125     61
D7V2, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              1              212
  CLUS_2              2              125
  CLUS_3              0               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        1      0      1
  DNMT3A WILD-TYPE     59     76     76
D7V3, multiclass
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2              211 
      TCGA-BJ-A0YZ       TCGA-BJ-A0Z0       TCGA-BJ-A0Z2       TCGA-BJ-A0Z3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0Z9       TCGA-BJ-A0ZA       TCGA-BJ-A0ZB       TCGA-BJ-A0ZC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZE       TCGA-BJ-A0ZG       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A18Z       TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A28S       TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A290       TCGA-BJ-A2N7       TCGA-BJ-A2N9       TCGA-BJ-A2NA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A2P4       TCGA-BJ-A3EZ       TCGA-BJ-A3F0       TCGA-CE-A13K 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CE-A27D       TCGA-CE-A3MD       TCGA-CE-A3ME       TCGA-DE-A0Y2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A2OL       TCGA-DE-A3KN       TCGA-DJ-A13M       TCGA-DJ-A13O 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13R       TCGA-DJ-A13S       TCGA-DJ-A13V       TCGA-DJ-A13W 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13X       TCGA-DJ-A1QD       TCGA-DJ-A1QE       TCGA-DJ-A1QF 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QG       TCGA-DJ-A1QI       TCGA-DJ-A1QL       TCGA-DJ-A1QM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QN       TCGA-DJ-A1QO       TCGA-DJ-A2PN       TCGA-DJ-A2PO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PP       TCGA-DJ-A2PQ       TCGA-DJ-A2PR       TCGA-DJ-A2PS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PU       TCGA-DJ-A2PV       TCGA-DJ-A2PW       TCGA-DJ-A2PY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PZ       TCGA-DJ-A2Q0       TCGA-DJ-A2Q1       TCGA-DJ-A2Q4 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q5       TCGA-DJ-A2Q6       TCGA-DJ-A2Q7       TCGA-DJ-A2Q8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q9       TCGA-DJ-A2QA       TCGA-DJ-A2QB       TCGA-DJ-A2QC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-E3-A3DY       TCGA-E3-A3DZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E3-A3E0       TCGA-E3-A3E1       TCGA-E3-A3E3       TCGA-E3-A3E5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E8-A2EA       TCGA-EL-A3CL       TCGA-EL-A3CM       TCGA-EL-A3CN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CO       TCGA-EL-A3CP       TCGA-EL-A3CS       TCGA-EL-A3CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW       TCGA-EL-A3CX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0       TCGA-EL-A3D1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6       TCGA-EL-A3GO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR       TCGA-EL-A3GS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW       TCGA-EL-A3GX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H1       TCGA-EL-A3H2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5       TCGA-EL-A3H7 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX       TCGA-EL-A3MY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3       TCGA-EM-A1CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1CU       TCGA-EM-A1CV       TCGA-EM-A1CW       TCGA-EM-A1YA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1YB       TCGA-EM-A1YC       TCGA-EM-A1YD       TCGA-EM-A1YE 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22I       TCGA-EM-A22J       TCGA-EM-A22L       TCGA-EM-A22M 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22O       TCGA-EM-A22Q       TCGA-EM-A2CJ       TCGA-EM-A2CK 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CL       TCGA-EM-A2CN       TCGA-EM-A2CO       TCGA-EM-A2CP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CQ       TCGA-EM-A2CR       TCGA-EM-A2CU       TCGA-EM-A2OV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2OY       TCGA-EM-A2P1       TCGA-EM-A3AI       TCGA-EM-A3AJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AL       TCGA-EM-A3AN       TCGA-EM-A3AO       TCGA-EM-A3AP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FJ       TCGA-EM-A3FL       TCGA-EM-A3FN       TCGA-EM-A3FO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FP       TCGA-ET-A25G       TCGA-ET-A25O       TCGA-ET-A2MY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2MZ       TCGA-ET-A2N0       TCGA-ET-A2N1       TCGA-ET-A2N4 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2N5       TCGA-ET-A39I       TCGA-ET-A39J       TCGA-ET-A39L 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39M       TCGA-ET-A39N       TCGA-ET-A39P       TCGA-ET-A39R 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BP       TCGA-ET-A3BS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BT       TCGA-ET-A3BU       TCGA-ET-A3BV       TCGA-ET-A3BW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BX       TCGA-ET-A3DO       TCGA-ET-A3DP       TCGA-ET-A3DS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3DT       TCGA-ET-A3DV       TCGA-ET-A3DW       TCGA-FE-A22Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A230       TCGA-FE-A231       TCGA-FE-A232       TCGA-FE-A233 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A234       TCGA-FE-A235       TCGA-FE-A236       TCGA-FE-A237 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A23A       TCGA-FY-A2QD       TCGA-FY-A3BL       TCGA-FY-A3ON 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-GE-A2C6       TCGA-H2-A2K9       TCGA-IM-A3EB       TCGA-IM-A3ED 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-J8-A3NZ       TCGA-J8-A3O0       TCGA-J8-A3O1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DNMT3A MUTATED        1      0      0      1      0      0      0
  DNMT3A WILD-TYPE     45     27     31     25     47     27      9
D7V4, multiclass
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2              211 
      TCGA-BJ-A0YZ       TCGA-BJ-A0Z0       TCGA-BJ-A0Z2       TCGA-BJ-A0Z3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0Z9       TCGA-BJ-A0ZA       TCGA-BJ-A0ZB       TCGA-BJ-A0ZC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZE       TCGA-BJ-A0ZG       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A18Z       TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A28S       TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A290       TCGA-BJ-A2N7       TCGA-BJ-A2N9       TCGA-BJ-A2NA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A2P4       TCGA-BJ-A3EZ       TCGA-BJ-A3F0       TCGA-CE-A13K 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CE-A27D       TCGA-CE-A3MD       TCGA-CE-A3ME       TCGA-DE-A0Y2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A2OL       TCGA-DE-A3KN       TCGA-DJ-A13M       TCGA-DJ-A13O 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13R       TCGA-DJ-A13S       TCGA-DJ-A13V       TCGA-DJ-A13W 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13X       TCGA-DJ-A1QD       TCGA-DJ-A1QE       TCGA-DJ-A1QF 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QG       TCGA-DJ-A1QI       TCGA-DJ-A1QL       TCGA-DJ-A1QM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QN       TCGA-DJ-A1QO       TCGA-DJ-A2PN       TCGA-DJ-A2PO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PP       TCGA-DJ-A2PQ       TCGA-DJ-A2PR       TCGA-DJ-A2PS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PU       TCGA-DJ-A2PV       TCGA-DJ-A2PW       TCGA-DJ-A2PY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PZ       TCGA-DJ-A2Q0       TCGA-DJ-A2Q1       TCGA-DJ-A2Q4 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q5       TCGA-DJ-A2Q6       TCGA-DJ-A2Q7       TCGA-DJ-A2Q8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q9       TCGA-DJ-A2QA       TCGA-DJ-A2QB       TCGA-DJ-A2QC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-E3-A3DY       TCGA-E3-A3DZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E3-A3E0       TCGA-E3-A3E1       TCGA-E3-A3E3       TCGA-E3-A3E5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E8-A2EA       TCGA-EL-A3CL       TCGA-EL-A3CM       TCGA-EL-A3CN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CO       TCGA-EL-A3CP       TCGA-EL-A3CS       TCGA-EL-A3CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW       TCGA-EL-A3CX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0       TCGA-EL-A3D1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6       TCGA-EL-A3GO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR       TCGA-EL-A3GS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW       TCGA-EL-A3GX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H1       TCGA-EL-A3H2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5       TCGA-EL-A3H7 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX       TCGA-EL-A3MY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3       TCGA-EM-A1CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1CU       TCGA-EM-A1CV       TCGA-EM-A1CW       TCGA-EM-A1YA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1YB       TCGA-EM-A1YC       TCGA-EM-A1YD       TCGA-EM-A1YE 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22I       TCGA-EM-A22J       TCGA-EM-A22L       TCGA-EM-A22M 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22O       TCGA-EM-A22Q       TCGA-EM-A2CJ       TCGA-EM-A2CK 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CL       TCGA-EM-A2CN       TCGA-EM-A2CO       TCGA-EM-A2CP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CQ       TCGA-EM-A2CR       TCGA-EM-A2CU       TCGA-EM-A2OV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2OY       TCGA-EM-A2P1       TCGA-EM-A3AI       TCGA-EM-A3AJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AL       TCGA-EM-A3AN       TCGA-EM-A3AO       TCGA-EM-A3AP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FJ       TCGA-EM-A3FL       TCGA-EM-A3FN       TCGA-EM-A3FO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FP       TCGA-ET-A25G       TCGA-ET-A25O       TCGA-ET-A2MY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2MZ       TCGA-ET-A2N0       TCGA-ET-A2N1       TCGA-ET-A2N4 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2N5       TCGA-ET-A39I       TCGA-ET-A39J       TCGA-ET-A39L 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39M       TCGA-ET-A39N       TCGA-ET-A39P       TCGA-ET-A39R 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BP       TCGA-ET-A3BS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BT       TCGA-ET-A3BU       TCGA-ET-A3BV       TCGA-ET-A3BW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BX       TCGA-ET-A3DO       TCGA-ET-A3DP       TCGA-ET-A3DS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3DT       TCGA-ET-A3DV       TCGA-ET-A3DW       TCGA-FE-A22Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A230       TCGA-FE-A231       TCGA-FE-A232       TCGA-FE-A233 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A234       TCGA-FE-A235       TCGA-FE-A236       TCGA-FE-A237 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A23A       TCGA-FY-A2QD       TCGA-FY-A3BL       TCGA-FY-A3ON 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-GE-A2C6       TCGA-H2-A2K9       TCGA-IM-A3EB       TCGA-IM-A3ED 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-J8-A3NZ       TCGA-J8-A3O0       TCGA-J8-A3O1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT3A MUTATED        2      0      0      1
  DNMT3A WILD-TYPE    128     43     93    132
D7V5, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              128
  CLUS_2              0               43
  CLUS_3              0               93
  CLUS_4              1              132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DNMT3A MUTATED        2      0      0      1      0
  DNMT3A WILD-TYPE    105     77     61     91     62
D7V6, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              105
  CLUS_2              0               77
  CLUS_3              0               61
  CLUS_4              1               91
  CLUS_5              0               62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        2      0      1
  DNMT3A WILD-TYPE    128    140    129
D7V7, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              128
  CLUS_2              0              140
  CLUS_3              1              129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        2      0      1
  DNMT3A WILD-TYPE    106    169    122
D7V8, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              106
  CLUS_2              0              169
  CLUS_3              1              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_2 CLUS_3
  DNMT3A MUTATED        2      0      1
  DNMT3A WILD-TYPE    140    131    126
D7V9, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              140
  CLUS_2              0              131
  CLUS_3              1              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_2 CLUS_3 CLUS_4
  DNMT3A MUTATED        2      0      0      1
  DNMT3A WILD-TYPE    104    153     81     59
D7V10, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2              104
  CLUS_2              0              153
  CLUS_3              0               81
  CLUS_4              1               59
[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"

Clustering(8) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        0      4      0
  KRAS WILD-TYPE     26    309     60
D8V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             26
  CLUS_2            4            309
  CLUS_3            0             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        1      3      0
  KRAS WILD-TYPE    212    124     61
D8V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1            212
  CLUS_2            3            124
  CLUS_3            0             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        2      0      0
  KRAS WILD-TYPE     58     76     77
D8V3, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            211 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z0     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0Z9     TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZG     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y     TCGA-BJ-A18Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R     TCGA-BJ-A28S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28Z     TCGA-BJ-A290 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A2N7     TCGA-BJ-A2N9     TCGA-BJ-A2NA     TCGA-BJ-A2P4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A3EZ     TCGA-BJ-A3F0     TCGA-CE-A13K     TCGA-CE-A27D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A3MD     TCGA-CE-A3ME     TCGA-DE-A0Y2     TCGA-DE-A2OL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A3KN     TCGA-DJ-A13M     TCGA-DJ-A13O     TCGA-DJ-A13R 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13S     TCGA-DJ-A13V     TCGA-DJ-A13W     TCGA-DJ-A13X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QD     TCGA-DJ-A1QE     TCGA-DJ-A1QF     TCGA-DJ-A1QG 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QI     TCGA-DJ-A1QL     TCGA-DJ-A1QM     TCGA-DJ-A1QN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QO     TCGA-DJ-A2PN     TCGA-DJ-A2PO     TCGA-DJ-A2PP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PS     TCGA-DJ-A2PU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PY     TCGA-DJ-A2PZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2     TCGA-DJ-A2Q4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7     TCGA-DJ-A2Q8 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB     TCGA-DJ-A2QC 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-E3-A3DY     TCGA-E3-A3DZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3E0     TCGA-E3-A3E1     TCGA-E3-A3E3     TCGA-E3-A3E5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A2EA     TCGA-EL-A3CL     TCGA-EL-A3CM     TCGA-EL-A3CN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CR     TCGA-EL-A3CS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV     TCGA-EL-A3GW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ     TCGA-EL-A3H1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N2     TCGA-EL-A3N3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1CT     TCGA-EM-A1CU     TCGA-EM-A1CV     TCGA-EM-A1CW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1YA     TCGA-EM-A1YB     TCGA-EM-A1YC     TCGA-EM-A1YD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1YE     TCGA-EM-A22I     TCGA-EM-A22J     TCGA-EM-A22L 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A22M     TCGA-EM-A22O     TCGA-EM-A22Q     TCGA-EM-A2CJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2CK     TCGA-EM-A2CL     TCGA-EM-A2CN     TCGA-EM-A2CO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2CP     TCGA-EM-A2CR     TCGA-EM-A2CU     TCGA-EM-A2OV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2OY     TCGA-EM-A2P1     TCGA-EM-A3AI     TCGA-EM-A3AJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO     TCGA-EM-A3AP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3FJ     TCGA-EM-A3FL     TCGA-EM-A3FN     TCGA-EM-A3FO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3FP     TCGA-ET-A25G     TCGA-ET-A25O     TCGA-ET-A2MY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39L 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39P     TCGA-ET-A39R 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39T     TCGA-ET-A3BN     TCGA-ET-A3BP     TCGA-ET-A3BS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BX     TCGA-ET-A3DO     TCGA-ET-A3DP     TCGA-ET-A3DS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DT     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-FE-A22Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A23A     TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3ON 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GE-A2C6     TCGA-H2-A2K9     TCGA-IM-A3EB     TCGA-IM-A3ED 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KRAS MUTATED        1      0      0      1      0      0      0
  KRAS WILD-TYPE     45     27     31     25     47     27      9
D8V4, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            211 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z0     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0Z9     TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZG     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y     TCGA-BJ-A18Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R     TCGA-BJ-A28S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28Z     TCGA-BJ-A290 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A2N7     TCGA-BJ-A2N9     TCGA-BJ-A2NA     TCGA-BJ-A2P4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A3EZ     TCGA-BJ-A3F0     TCGA-CE-A13K     TCGA-CE-A27D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A3MD     TCGA-CE-A3ME     TCGA-DE-A0Y2     TCGA-DE-A2OL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A3KN     TCGA-DJ-A13M     TCGA-DJ-A13O     TCGA-DJ-A13R 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13S     TCGA-DJ-A13V     TCGA-DJ-A13W     TCGA-DJ-A13X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QD     TCGA-DJ-A1QE     TCGA-DJ-A1QF     TCGA-DJ-A1QG 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QI     TCGA-DJ-A1QL     TCGA-DJ-A1QM     TCGA-DJ-A1QN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QO     TCGA-DJ-A2PN     TCGA-DJ-A2PO     TCGA-DJ-A2PP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PS     TCGA-DJ-A2PU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PY     TCGA-DJ-A2PZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2     TCGA-DJ-A2Q4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7     TCGA-DJ-A2Q8 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB     TCGA-DJ-A2QC 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-E3-A3DY     TCGA-E3-A3DZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3E0     TCGA-E3-A3E1     TCGA-E3-A3E3     TCGA-E3-A3E5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A2EA     TCGA-EL-A3CL     TCGA-EL-A3CM     TCGA-EL-A3CN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CR     TCGA-EL-A3CS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV     TCGA-EL-A3GW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ     TCGA-EL-A3H1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N2     TCGA-EL-A3N3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1CT     TCGA-EM-A1CU     TCGA-EM-A1CV     TCGA-EM-A1CW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1YA     TCGA-EM-A1YB     TCGA-EM-A1YC     TCGA-EM-A1YD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A1YE     TCGA-EM-A22I     TCGA-EM-A22J     TCGA-EM-A22L 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A22M     TCGA-EM-A22O     TCGA-EM-A22Q     TCGA-EM-A2CJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2CK     TCGA-EM-A2CL     TCGA-EM-A2CN     TCGA-EM-A2CO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2CP     TCGA-EM-A2CR     TCGA-EM-A2CU     TCGA-EM-A2OV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A2OY     TCGA-EM-A2P1     TCGA-EM-A3AI     TCGA-EM-A3AJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO     TCGA-EM-A3AP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3FJ     TCGA-EM-A3FL     TCGA-EM-A3FN     TCGA-EM-A3FO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3FP     TCGA-ET-A25G     TCGA-ET-A25O     TCGA-ET-A2MY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39L 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39P     TCGA-ET-A39R 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39T     TCGA-ET-A3BN     TCGA-ET-A3BP     TCGA-ET-A3BS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BX     TCGA-ET-A3DO     TCGA-ET-A3DP     TCGA-ET-A3DS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DT     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-FE-A22Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A23A     TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3ON 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GE-A2C6     TCGA-H2-A2K9     TCGA-IM-A3EB     TCGA-IM-A3ED 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        3      0      1      0
  KRAS WILD-TYPE    127     43     92    133
D8V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            127
  CLUS_2            0             43
  CLUS_3            1             92
  CLUS_4            0            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        3      1      0      0      0
  KRAS WILD-TYPE    104     76     61     92     62
D8V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            104
  CLUS_2            1             76
  CLUS_3            0             61
  CLUS_4            0             92
  CLUS_5            0             62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        3      1      0
  KRAS WILD-TYPE    127    139    130
D8V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            127
  CLUS_2            1            139
  CLUS_3            0            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        3      1      0
  KRAS WILD-TYPE    105    168    123
D8V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            105
  CLUS_2            1            168
  CLUS_3            0            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_2 CLUS_3
  KRAS MUTATED        3      1      0
  KRAS WILD-TYPE    139    130    127
D8V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            139
  CLUS_2            1            130
  CLUS_3            0            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_2 CLUS_3 CLUS_4
  KRAS MUTATED        3      1      0      0
  KRAS WILD-TYPE    103    152     81     60
D8V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3            103
  CLUS_2            1            152
  CLUS_3            0             81
  CLUS_4            0             60
[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"

Clustering(9) Variable = DLC1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLC1 MUTATED        0      4      0
  DLC1 WILD-TYPE     26    309     60
D9V1, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            4            309
  CLUS_3            0             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLC1 MUTATED        3      1      0
  DLC1 WILD-TYPE    210    126     61
D9V2, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            3            210
  CLUS_2            1            126
  CLUS_3            0             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLC1 MUTATED        0      1      1
  DLC1 WILD-TYPE     60     75     76
D9V3, multiclass
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2            211 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z0     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A0Z9     TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A0ZE     TCGA-BJ-A0ZG     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A18Z     TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A28S     TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A290     TCGA-BJ-A2N7     TCGA-BJ-A2N9     TCGA-BJ-A2NA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A2P4     TCGA-BJ-A3EZ     TCGA-BJ-A3F0     TCGA-CE-A13K 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CE-A27D     TCGA-CE-A3MD     TCGA-CE-A3ME     TCGA-DE-A0Y2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DE-A2OL     TCGA-DE-A3KN     TCGA-DJ-A13M     TCGA-DJ-A13O 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13R     TCGA-DJ-A13S     TCGA-DJ-A13V     TCGA-DJ-A13W 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13X     TCGA-DJ-A1QD     TCGA-DJ-A1QE     TCGA-DJ-A1QF 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A1QG     TCGA-DJ-A1QI     TCGA-DJ-A1QL     TCGA-DJ-A1QM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A1QN     TCGA-DJ-A1QO     TCGA-DJ-A2PN     TCGA-DJ-A2PO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PP     TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PU     TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PZ     TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q4     TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q8     TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2QC     TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-E3-A3DY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1     TCGA-E3-A3E3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3E5     TCGA-E8-A2EA     TCGA-EL-A3CL     TCGA-EL-A3CM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CN     TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV     TCGA-EL-A3GW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ     TCGA-EL-A3H1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N3     TCGA-EM-A1CT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1CU     TCGA-EM-A1CV     TCGA-EM-A1CW     TCGA-EM-A1YA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1YB     TCGA-EM-A1YC     TCGA-EM-A1YD     TCGA-EM-A1YE 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22I     TCGA-EM-A22J     TCGA-EM-A22L     TCGA-EM-A22M 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22O     TCGA-EM-A22Q     TCGA-EM-A2CJ     TCGA-EM-A2CK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CL     TCGA-EM-A2CN     TCGA-EM-A2CO     TCGA-EM-A2CP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CQ     TCGA-EM-A2CR     TCGA-EM-A2CU     TCGA-EM-A2OV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2OY     TCGA-EM-A2P1     TCGA-EM-A3AI     TCGA-EM-A3AJ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO     TCGA-EM-A3AP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FJ     TCGA-EM-A3FL     TCGA-EM-A3FN     TCGA-EM-A3FO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FP     TCGA-ET-A25G     TCGA-ET-A25O     TCGA-ET-A2MY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39L 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39P     TCGA-ET-A39R 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39T     TCGA-ET-A3BN     TCGA-ET-A3BP     TCGA-ET-A3BS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BX     TCGA-ET-A3DO     TCGA-ET-A3DP     TCGA-ET-A3DS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DT     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-FE-A22Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A23A     TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3ON 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-GE-A2C6     TCGA-H2-A2K9     TCGA-IM-A3EB     TCGA-IM-A3ED 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DLC1 MUTATED        0      0      1      1      0      0      0
  DLC1 WILD-TYPE     46     27     30     25     47     27      9
D9V4, multiclass
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2            211 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z0     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A0Z9     TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A0ZE     TCGA-BJ-A0ZG     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A18Z     TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A28S     TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A290     TCGA-BJ-A2N7     TCGA-BJ-A2N9     TCGA-BJ-A2NA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A2P4     TCGA-BJ-A3EZ     TCGA-BJ-A3F0     TCGA-CE-A13K 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CE-A27D     TCGA-CE-A3MD     TCGA-CE-A3ME     TCGA-DE-A0Y2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DE-A2OL     TCGA-DE-A3KN     TCGA-DJ-A13M     TCGA-DJ-A13O 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13R     TCGA-DJ-A13S     TCGA-DJ-A13V     TCGA-DJ-A13W 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13X     TCGA-DJ-A1QD     TCGA-DJ-A1QE     TCGA-DJ-A1QF 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A1QG     TCGA-DJ-A1QI     TCGA-DJ-A1QL     TCGA-DJ-A1QM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A1QN     TCGA-DJ-A1QO     TCGA-DJ-A2PN     TCGA-DJ-A2PO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PP     TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PU     TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PZ     TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q4     TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q8     TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2QC     TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-E3-A3DY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1     TCGA-E3-A3E3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3E5     TCGA-E8-A2EA     TCGA-EL-A3CL     TCGA-EL-A3CM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CN     TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV     TCGA-EL-A3GW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ     TCGA-EL-A3H1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N3     TCGA-EM-A1CT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1CU     TCGA-EM-A1CV     TCGA-EM-A1CW     TCGA-EM-A1YA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1YB     TCGA-EM-A1YC     TCGA-EM-A1YD     TCGA-EM-A1YE 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22I     TCGA-EM-A22J     TCGA-EM-A22L     TCGA-EM-A22M 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22O     TCGA-EM-A22Q     TCGA-EM-A2CJ     TCGA-EM-A2CK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CL     TCGA-EM-A2CN     TCGA-EM-A2CO     TCGA-EM-A2CP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CQ     TCGA-EM-A2CR     TCGA-EM-A2CU     TCGA-EM-A2OV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2OY     TCGA-EM-A2P1     TCGA-EM-A3AI     TCGA-EM-A3AJ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO     TCGA-EM-A3AP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FJ     TCGA-EM-A3FL     TCGA-EM-A3FN     TCGA-EM-A3FO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FP     TCGA-ET-A25G     TCGA-ET-A25O     TCGA-ET-A2MY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39L 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39P     TCGA-ET-A39R 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39T     TCGA-ET-A3BN     TCGA-ET-A3BP     TCGA-ET-A3BS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BX     TCGA-ET-A3DO     TCGA-ET-A3DP     TCGA-ET-A3DS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DT     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-FE-A22Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A23A     TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3ON 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-GE-A2C6     TCGA-H2-A2K9     TCGA-IM-A3EB     TCGA-IM-A3ED 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DLC1 MUTATED        1      0      0      3
  DLC1 WILD-TYPE    129     43     93    130
D9V5, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            129
  CLUS_2            0             43
  CLUS_3            0             93
  CLUS_4            3            130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DLC1 MUTATED        1      0      0      2      1
  DLC1 WILD-TYPE    106     77     61     90     61
D9V6, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            106
  CLUS_2            0             77
  CLUS_3            0             61
  CLUS_4            2             90
  CLUS_5            1             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLC1 MUTATED        1      2      1
  DLC1 WILD-TYPE    129    138    129
D9V7, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            129
  CLUS_2            2            138
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLC1 MUTATED        1      2      1
  DLC1 WILD-TYPE    107    167    122
D9V8, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            107
  CLUS_2            2            167
  CLUS_3            1            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_2 CLUS_3
  DLC1 MUTATED        1      2      1
  DLC1 WILD-TYPE    141    129    126
D9V9, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            141
  CLUS_2            2            129
  CLUS_3            1            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_2 CLUS_3 CLUS_4
  DLC1 MUTATED        1      2      0      1
  DLC1 WILD-TYPE    105    151     81     59
D9V10, multiclass
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  CLUS_1            1            105
  CLUS_2            2            151
  CLUS_3            0             81
  CLUS_4            1             59
[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"

Clustering(10) Variable = ITGAL MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGAL MUTATED        1      3      0
  ITGAL WILD-TYPE     25    310     60
D10V1, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             1              25
  CLUS_2             3             310
  CLUS_3             0              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGAL MUTATED        3      0      1
  ITGAL WILD-TYPE    210    127     60
D10V2, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             3             210
  CLUS_2             0             127
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGAL MUTATED        0      1      1
  ITGAL WILD-TYPE     60     75     76
D10V3, multiclass
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2             211 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K      TCGA-CE-A27D 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2      TCGA-DE-A2OL 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM      TCGA-DJ-A1QN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY      TCGA-DJ-A2PZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A2QC 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-E3-A3DY      TCGA-E3-A3DZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E3      TCGA-E3-A3E5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A2EA      TCGA-EL-A3CL      TCGA-EL-A3CM      TCGA-EL-A3CN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CO      TCGA-EL-A3CP      TCGA-EL-A3CR      TCGA-EL-A3CS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ      TCGA-EL-A3H1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3N3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22O      TCGA-EM-A22Q      TCGA-EM-A2CJ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CK      TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OY      TCGA-EM-A2P1      TCGA-EM-A3AI 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AJ      TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FL      TCGA-EM-A3FN      TCGA-EM-A3FO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O      TCGA-ET-A2MY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J      TCGA-ET-A39L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P      TCGA-ET-A39R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP      TCGA-ET-A3BS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP      TCGA-ET-A3DS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-FE-A22Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL      TCGA-FY-A3ON 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB      TCGA-IM-A3ED 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ITGAL MUTATED        0      0      1      0      1      0      0
  ITGAL WILD-TYPE     46     27     30     26     46     27      9
D10V4, multiclass
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2             211 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K      TCGA-CE-A27D 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2      TCGA-DE-A2OL 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM      TCGA-DJ-A1QN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY      TCGA-DJ-A2PZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A2QC 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-E3-A3DY      TCGA-E3-A3DZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E3      TCGA-E3-A3E5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A2EA      TCGA-EL-A3CL      TCGA-EL-A3CM      TCGA-EL-A3CN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CO      TCGA-EL-A3CP      TCGA-EL-A3CR      TCGA-EL-A3CS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ      TCGA-EL-A3H1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3N3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22O      TCGA-EM-A22Q      TCGA-EM-A2CJ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CK      TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OY      TCGA-EM-A2P1      TCGA-EM-A3AI 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AJ      TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FL      TCGA-EM-A3FN      TCGA-EM-A3FO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O      TCGA-ET-A2MY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J      TCGA-ET-A39L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P      TCGA-ET-A39R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP      TCGA-ET-A3BS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP      TCGA-ET-A3DS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-FE-A22Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL      TCGA-FY-A3ON 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB      TCGA-IM-A3ED 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ITGAL MUTATED        0      0      1      3
  ITGAL WILD-TYPE    130     43     92    130
D10V5, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             130
  CLUS_2             0              43
  CLUS_3             1              92
  CLUS_4             3             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ITGAL MUTATED        0      1      0      2      1
  ITGAL WILD-TYPE    107     76     61     90     61
D10V6, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             107
  CLUS_2             1              76
  CLUS_3             0              61
  CLUS_4             2              90
  CLUS_5             1              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGAL MUTATED        0      2      2
  ITGAL WILD-TYPE    130    138    128
D10V7, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             130
  CLUS_2             2             138
  CLUS_3             2             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_2 CLUS_3
  ITGAL MUTATED        0      2      2
  ITGAL WILD-TYPE    108    167    121
D10V8, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             108
  CLUS_2             2             167
  CLUS_3             2             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ITGAL MUTATED        0      2      2
  ITGAL WILD-TYPE    142    129    125
D10V9, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             142
  CLUS_2             2             129
  CLUS_3             2             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_2 CLUS_3 CLUS_4
  ITGAL MUTATED        0      2      1      1
  ITGAL WILD-TYPE    106    151     80     59
D10V10, multiclass
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  CLUS_1             0             106
  CLUS_2             2             151
  CLUS_3             1              80
  CLUS_4             1              59
[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"

Clustering(11) Variable = NLRP6 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRP6 MUTATED        0      2      1
  NLRP6 WILD-TYPE     26    311     59
D11V1, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             2             311
  CLUS_3             1              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRP6 MUTATED        3      0      0
  NLRP6 WILD-TYPE    210    127     61
D11V2, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             3             210
  CLUS_2             0             127
  CLUS_3             0              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRP6 MUTATED        0      0      1
  NLRP6 WILD-TYPE     60     76     76
D11V3, multiclass
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              1             212 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZE      TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28S      TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A290      TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2P4      TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A27D      TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A2OL      TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13R      TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13X      TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QG      TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QN      TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q4      TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q8      TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2QC      TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-E3-A3DY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E5      TCGA-E8-A2EA      TCGA-EL-A3CL      TCGA-EL-A3CM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CP      TCGA-EL-A3CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H1      TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N3      TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CW      TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YD      TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22L      TCGA-EM-A22M      TCGA-EM-A22O      TCGA-EM-A22Q 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CJ      TCGA-EM-A2CK      TCGA-EM-A2CL      TCGA-EM-A2CN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CO      TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CU      TCGA-EM-A2OV      TCGA-EM-A2OY      TCGA-EM-A2P1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AI      TCGA-EM-A3AJ      TCGA-EM-A3AL      TCGA-EM-A3AN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AO      TCGA-EM-A3AP      TCGA-EM-A3FJ      TCGA-EM-A3FL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FN      TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N4      TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39L      TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39R      TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BW      TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A237      TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3ED      TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NLRP6 MUTATED        0      0      0      0      1      0      0
  NLRP6 WILD-TYPE     46     27     31     26     46     27      9
D11V4, multiclass
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              1             212 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z0      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0Z9      TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZE      TCGA-BJ-A0ZG      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28S      TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A290      TCGA-BJ-A2N7      TCGA-BJ-A2N9      TCGA-BJ-A2NA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2P4      TCGA-BJ-A3EZ      TCGA-BJ-A3F0      TCGA-CE-A13K 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A27D      TCGA-CE-A3MD      TCGA-CE-A3ME      TCGA-DE-A0Y2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A2OL      TCGA-DE-A3KN      TCGA-DJ-A13M      TCGA-DJ-A13O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13R      TCGA-DJ-A13S      TCGA-DJ-A13V      TCGA-DJ-A13W 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13X      TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QG      TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QN      TCGA-DJ-A1QO      TCGA-DJ-A2PN      TCGA-DJ-A2PO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q4      TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q8      TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2QC      TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-E3-A3DY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E5      TCGA-E8-A2EA      TCGA-EL-A3CL      TCGA-EL-A3CM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CP      TCGA-EL-A3CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H1      TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N3      TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CW      TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YD      TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22L      TCGA-EM-A22M      TCGA-EM-A22O      TCGA-EM-A22Q 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CJ      TCGA-EM-A2CK      TCGA-EM-A2CL      TCGA-EM-A2CN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CO      TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CU      TCGA-EM-A2OV      TCGA-EM-A2OY      TCGA-EM-A2P1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AI      TCGA-EM-A3AJ      TCGA-EM-A3AL      TCGA-EM-A3AN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AO      TCGA-EM-A3AP      TCGA-EM-A3FJ      TCGA-EM-A3FL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FN      TCGA-EM-A3FP      TCGA-ET-A25G      TCGA-ET-A25O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N4      TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39L      TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39P 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39R      TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BW      TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DV      TCGA-ET-A3DW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A237      TCGA-FE-A23A      TCGA-FY-A2QD      TCGA-FY-A3BL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-GE-A2C6      TCGA-H2-A2K9      TCGA-IM-A3EB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3ED      TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NLRP6 MUTATED        0      0      2      1
  NLRP6 WILD-TYPE    130     43     91    132
D11V5, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             0             130
  CLUS_2             0              43
  CLUS_3             2              91
  CLUS_4             1             132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NLRP6 MUTATED        0      1      1      0      1
  NLRP6 WILD-TYPE    107     76     60     92     61
D11V6, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             0             107
  CLUS_2             1              76
  CLUS_3             1              60
  CLUS_4             0              92
  CLUS_5             1              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRP6 MUTATED        1      2      0
  NLRP6 WILD-TYPE    129    138    130
D11V7, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             1             129
  CLUS_2             2             138
  CLUS_3             0             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRP6 MUTATED        0      3      0
  NLRP6 WILD-TYPE    108    166    123
D11V8, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             0             108
  CLUS_2             3             166
  CLUS_3             0             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_2 CLUS_3
  NLRP6 MUTATED        1      2      0
  NLRP6 WILD-TYPE    141    129    127
D11V9, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             1             141
  CLUS_2             2             129
  CLUS_3             0             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_2 CLUS_3 CLUS_4
  NLRP6 MUTATED        0      3      0      0
  NLRP6 WILD-TYPE    106    150     81     60
D11V10, multiclass
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  CLUS_1             0             106
  CLUS_2             3             150
  CLUS_3             0              81
  CLUS_4             0              60
[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"
