[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"        "-oTLUSC-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/LUSC-TP/10668108/LUSC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/10686857/transformed.cor.cli.txt"

nPatients in clinical file=493, in cluster file=178, common to both=178
[1]  17 178
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           141             37 
  TP53 MUTATED TP53 WILD-TYPE 
           141             37 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            35            143 
  MLL2 MUTATED MLL2 WILD-TYPE 
            35            143 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
             5            173 
  IBTK MUTATED IBTK WILD-TYPE 
             5            173 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
[1] "SLC28A1 MUTATION ANALYSIS"
[1] 3
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            25            153 
  CPS1 MUTATED CPS1 WILD-TYPE 
            25            153 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              166 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              166 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             10             168 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             10             168 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 178 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 178 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
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=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, 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=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       29     43     10     14
  TP53 WILD-TYPE      8      5      7      5
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           29              8
  CLUS_2           43              5
  CLUS_3           10              7
  CLUS_4           14              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       30     47     19
  TP53 WILD-TYPE     11      5      9
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30             11
  CLUS_2           47              5
  CLUS_3           19              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       38     63     40
  TP53 WILD-TYPE     24      6      7
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           38             24
  CLUS_2           63              6
  CLUS_3           40              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       16     28     15
  TP53 WILD-TYPE     11      1      3
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           16             11
  CLUS_2           28              1
  CLUS_3           15              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       26     37     24
  TP53 WILD-TYPE      8     10      7
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           26              8
  CLUS_2           37             10
  CLUS_3           24              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       21     16     28     22
  TP53 WILD-TYPE      8      6      6      5
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           21              8
  CLUS_2           16              6
  CLUS_3           28              6
  CLUS_4           22              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       30     55     42     14
  TP53 WILD-TYPE      9      6      9     13
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30              9
  CLUS_2           55              6
  CLUS_3           42              9
  CLUS_4           14             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       58     55     28
  TP53 WILD-TYPE     23      7      7
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           58             23
  CLUS_2           55              7
  CLUS_3           28              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       83     14     15     21
  TP53 WILD-TYPE     17      2      8      2
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           83             17
  CLUS_2           14              2
  CLUS_3           15              8
  CLUS_4           21              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       27     57     49
  TP53 WILD-TYPE      4     17      8
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           27              4
  CLUS_2           57             17
  CLUS_3           49              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       13     14     15
  TP53 WILD-TYPE      2      4      4
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           13              2
  CLUS_2           14              4
  CLUS_3           15              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  TP53 MUTATED        4      3      1      9      9      5      5      2      4
  TP53 WILD-TYPE      1      0      2      4      1      2      0      0      0
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4              1
  CLUS_2            3              0
  CLUS_3            1              2
  CLUS_4            9              4
  CLUS_5            9              1
  CLUS_6            5              2
  CLUS_7            5              0
  CLUS_8            2              0
  CLUS_9            4              0
[1] 9 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 = NFE2L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED        0     14      1      1
  NFE2L2 WILD-TYPE     37     34     16     18
D2V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               37
  CLUS_2             14               34
  CLUS_3              1               16
  CLUS_4              1               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0     14      2
  NFE2L2 WILD-TYPE     41     38     26
D2V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               41
  CLUS_2             14               38
  CLUS_3              2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        7     17      3
  NFE2L2 WILD-TYPE     55     52     44
D2V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              7               55
  CLUS_2             17               52
  CLUS_3              3               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        4      8      0
  NFE2L2 WILD-TYPE     23     21     18
D2V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               23
  CLUS_2              8               21
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        8      5      6
  NFE2L2 WILD-TYPE     26     42     25
D2V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              8               26
  CLUS_2              5               42
  CLUS_3              6               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 CLUS_4
  NFE2L2 MUTATED        5      5      4      5
  NFE2L2 WILD-TYPE     24     17     30     22
D2V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              5               24
  CLUS_2              5               17
  CLUS_3              4               30
  CLUS_4              5               22
[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
  NFE2L2 MUTATED        2     21      1      3
  NFE2L2 WILD-TYPE     37     40     50     24
D2V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               37
  CLUS_2             21               40
  CLUS_3              1               50
  CLUS_4              3               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        4     22      1
  NFE2L2 WILD-TYPE     77     40     34
D2V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               77
  CLUS_2             22               40
  CLUS_3              1               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
  NFE2L2 MUTATED       15      0      3      8
  NFE2L2 WILD-TYPE     85     16     20     15
D2V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1             15               85
  CLUS_2              0               16
  CLUS_3              3               20
  CLUS_4              8               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED       15      9      2
  NFE2L2 WILD-TYPE     16     65     55
D2V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1             15               16
  CLUS_2              9               65
  CLUS_3              2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        4      2      3
  NFE2L2 WILD-TYPE     11     16     16
D2V11, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               11
  CLUS_2              2               16
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NFE2L2 MUTATED        2      0      0      2      0      2      3      0
  NFE2L2 WILD-TYPE      3      3      3     11     10      5      2      2
                  vv
clus               CLUS_9
  NFE2L2 MUTATED        0
  NFE2L2 WILD-TYPE      4
D2V12, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2                3
  CLUS_2              0                3
  CLUS_3              0                3
  CLUS_4              2               11
  CLUS_5              0               10
  CLUS_6              2                5
  CLUS_7              3                2
  CLUS_8              0                2
  CLUS_9              0                4
[1] 9 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 = CDKN2A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        0     13      3      2
  CDKN2A WILD-TYPE     37     35     14     17
D3V1, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              0               37
  CLUS_2             13               35
  CLUS_3              3               14
  CLUS_4              2               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        1     13      4
  CDKN2A WILD-TYPE     40     39     24
D3V2, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               40
  CLUS_2             13               39
  CLUS_3              4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3     14      9
  CDKN2A WILD-TYPE     59     55     38
D3V3, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               59
  CLUS_2             14               55
  CLUS_3              9               38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      4      3
  CDKN2A WILD-TYPE     25     25     15
D3V4, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               25
  CLUS_2              4               25
  CLUS_3              3               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      8      3
  CDKN2A WILD-TYPE     32     39     28
D3V5, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               32
  CLUS_2              8               39
  CLUS_3              3               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
  CDKN2A MUTATED        2      5      5      1
  CDKN2A WILD-TYPE     27     17     29     26
D3V6, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               27
  CLUS_2              5               17
  CLUS_3              5               29
  CLUS_4              1               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        4     12      5      5
  CDKN2A WILD-TYPE     35     49     46     22
D3V7, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              4               35
  CLUS_2             12               49
  CLUS_3              5               46
  CLUS_4              5               22
[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
  CDKN2A MUTATED       10     12      4
  CDKN2A WILD-TYPE     71     50     31
D3V8, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1             10               71
  CLUS_2             12               50
  CLUS_3              4               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 CLUS_4
  CDKN2A MUTATED       15      3      2      4
  CDKN2A WILD-TYPE     85     13     21     19
D3V9, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1             15               85
  CLUS_2              3               13
  CLUS_3              2               21
  CLUS_4              4               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        4      9     11
  CDKN2A WILD-TYPE     27     65     46
D3V10, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              4               27
  CLUS_2              9               65
  CLUS_3             11               46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      2      3
  CDKN2A WILD-TYPE     13     16     16
D3V11, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               13
  CLUS_2              2               16
  CLUS_3              3               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDKN2A MUTATED        1      0      0      1      2      1      1      0
  CDKN2A WILD-TYPE      4      3      3     12      8      6      4      2
                  vv
clus               CLUS_9
  CDKN2A MUTATED        1
  CDKN2A WILD-TYPE      3
D3V12, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1                4
  CLUS_2              0                3
  CLUS_3              0                3
  CLUS_4              1               12
  CLUS_5              2                8
  CLUS_6              1                6
  CLUS_7              1                4
  CLUS_8              0                2
  CLUS_9              1                3
[1] 9 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 = KEAP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        0     12      1      4
  KEAP1 WILD-TYPE     37     36     16     15
D4V1, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              37
  CLUS_2            12              36
  CLUS_3             1              16
  CLUS_4             4              15
[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
  KEAP1 MUTATED        0     13      4
  KEAP1 WILD-TYPE     41     39     24
D4V2, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2            13              39
  CLUS_3             4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        4     12      6
  KEAP1 WILD-TYPE     58     57     41
D4V3, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              58
  CLUS_2            12              57
  CLUS_3             6              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        0      4      3
  KEAP1 WILD-TYPE     27     25     15
D4V4, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              27
  CLUS_2             4              25
  CLUS_3             3              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        5      2      4
  KEAP1 WILD-TYPE     29     45     27
D4V5, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             5              29
  CLUS_2             2              45
  CLUS_3             4              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        4      1      1      5
  KEAP1 WILD-TYPE     25     21     33     22
D4V6, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              25
  CLUS_2             1              21
  CLUS_3             1              33
  CLUS_4             5              22
[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
  KEAP1 MUTATED        1     12      6      3
  KEAP1 WILD-TYPE     38     49     45     24
D4V7, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             1              38
  CLUS_2            12              49
  CLUS_3             6              45
  CLUS_4             3              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        4     11      7
  KEAP1 WILD-TYPE     77     51     28
D4V8, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              77
  CLUS_2            11              51
  CLUS_3             7              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
  KEAP1 MUTATED       13      1      1      3
  KEAP1 WILD-TYPE     87     15     22     20
D4V9, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1            13              87
  CLUS_2             1              15
  CLUS_3             1              22
  CLUS_4             3              20
[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
  KEAP1 MUTATED        4      5      9
  KEAP1 WILD-TYPE     27     69     48
D4V10, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              27
  CLUS_2             5              69
  CLUS_3             9              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        4      0      0
  KEAP1 WILD-TYPE     11     18     19
D4V11, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              11
  CLUS_2             0              18
  CLUS_3             0              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KEAP1 MUTATED        1      0      0      1      2      0      0      0
  KEAP1 WILD-TYPE      4      3      3     12      8      7      5      2
                 vv
clus              CLUS_9
  KEAP1 MUTATED        0
  KEAP1 WILD-TYPE      4
D4V12, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             1               4
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             1              12
  CLUS_5             2               8
  CLUS_6             0               7
  CLUS_7             0               5
  CLUS_8             0               2
  CLUS_9             0               4
[1] 9 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 = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        4      2      0      2
  PTEN WILD-TYPE     33     46     17     17
D5V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             33
  CLUS_2            2             46
  CLUS_3            0             17
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        5      2      1
  PTEN WILD-TYPE     36     50     27
D5V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             36
  CLUS_2            2             50
  CLUS_3            1             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      4      3
  PTEN WILD-TYPE     55     65     44
D5V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             55
  CLUS_2            4             65
  CLUS_3            3             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        5      3      0
  PTEN WILD-TYPE     22     26     18
D5V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             22
  CLUS_2            3             26
  CLUS_3            0             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      4      1
  PTEN WILD-TYPE     31     43     30
D5V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             31
  CLUS_2            4             43
  CLUS_3            1             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        2      2      2      2
  PTEN WILD-TYPE     27     20     32     25
D5V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             27
  CLUS_2            2             20
  CLUS_3            2             32
  CLUS_4            2             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        4      3      4      3
  PTEN WILD-TYPE     35     58     47     24
D5V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             35
  CLUS_2            3             58
  CLUS_3            4             47
  CLUS_4            3             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      3      4
  PTEN WILD-TYPE     74     59     31
D5V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             74
  CLUS_2            3             59
  CLUS_3            4             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 CLUS_4
  PTEN MUTATED        9      1      2      0
  PTEN WILD-TYPE     91     15     21     23
D5V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            9             91
  CLUS_2            1             15
  CLUS_3            2             21
  CLUS_4            0             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      5      6
  PTEN WILD-TYPE     30     69     51
D5V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             30
  CLUS_2            5             69
  CLUS_3            6             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      2      3
  PTEN WILD-TYPE     15     16     16
D5V11, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             15
  CLUS_2            2             16
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  PTEN MUTATED        0      0      0      1      2      2      0      0      0
  PTEN WILD-TYPE      5      3      3     12      8      5      5      2      4
D5V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              5
  CLUS_2            0              3
  CLUS_3            0              3
  CLUS_4            1             12
  CLUS_5            2              8
  CLUS_6            2              5
  CLUS_7            0              5
  CLUS_8            0              2
  CLUS_9            0              4
[1] 9 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 = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        4      6      3      4
  PIK3CA WILD-TYPE     33     42     14     15
D6V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               33
  CLUS_2              6               42
  CLUS_3              3               14
  CLUS_4              4               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        7      6      4
  PIK3CA WILD-TYPE     34     46     24
D6V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               34
  CLUS_2              6               46
  CLUS_3              4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       12      8      7
  PIK3CA WILD-TYPE     50     61     40
D6V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             12               50
  CLUS_2              8               61
  CLUS_3              7               40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        4      3      4
  PIK3CA WILD-TYPE     23     26     14
D6V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               23
  CLUS_2              3               26
  CLUS_3              4               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        5      7      5
  PIK3CA WILD-TYPE     29     40     26
D6V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               29
  CLUS_2              7               40
  CLUS_3              5               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        5      2      7      3
  PIK3CA WILD-TYPE     24     20     27     24
D6V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               24
  CLUS_2              2               20
  CLUS_3              7               27
  CLUS_4              3               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        8      7     10      2
  PIK3CA WILD-TYPE     31     54     41     25
D6V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               31
  CLUS_2              7               54
  CLUS_3             10               41
  CLUS_4              2               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       11      8      8
  PIK3CA WILD-TYPE     70     54     27
D6V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               70
  CLUS_2              8               54
  CLUS_3              8               27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED       18      2      2      2
  PIK3CA WILD-TYPE     82     14     21     21
D6V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             18               82
  CLUS_2              2               14
  CLUS_3              2               21
  CLUS_4              2               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        3     13      8
  PIK3CA WILD-TYPE     28     61     49
D6V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               28
  CLUS_2             13               61
  CLUS_3              8               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
  PIK3CA MUTATED        4      4      2
  PIK3CA WILD-TYPE     11     14     17
D6V11, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               11
  CLUS_2              4               14
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PIK3CA MUTATED        1      1      0      2      2      1      1      1
  PIK3CA WILD-TYPE      4      2      3     11      8      6      4      1
                  vv
clus               CLUS_9
  PIK3CA MUTATED        1
  PIK3CA WILD-TYPE      3
D6V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                4
  CLUS_2              1                2
  CLUS_3              0                3
  CLUS_4              2               11
  CLUS_5              2                8
  CLUS_6              1                6
  CLUS_7              1                4
  CLUS_8              1                1
  CLUS_9              1                3
[1] 9 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 = MLL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        4     10      6      5
  MLL2 WILD-TYPE     33     38     11     14
D7V1, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             33
  CLUS_2           10             38
  CLUS_3            6             11
  CLUS_4            5             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6     13      6
  MLL2 WILD-TYPE     35     39     22
D7V2, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             35
  CLUS_2           13             39
  CLUS_3            6             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        8     16     11
  MLL2 WILD-TYPE     54     53     36
D7V3, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            8             54
  CLUS_2           16             53
  CLUS_3           11             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6      6      1
  MLL2 WILD-TYPE     21     23     17
D7V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             21
  CLUS_2            6             23
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6      9      8
  MLL2 WILD-TYPE     28     38     23
D7V5, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             28
  CLUS_2            9             38
  CLUS_3            8             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        6      7      7      3
  MLL2 WILD-TYPE     23     15     27     24
D7V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             23
  CLUS_2            7             15
  CLUS_3            7             27
  CLUS_4            3             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        4     15     11      5
  MLL2 WILD-TYPE     35     46     40     22
D7V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             35
  CLUS_2           15             46
  CLUS_3           11             40
  CLUS_4            5             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED       12     15      8
  MLL2 WILD-TYPE     69     47     27
D7V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           12             69
  CLUS_2           15             47
  CLUS_3            8             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED       17      3      4      5
  MLL2 WILD-TYPE     83     13     19     18
D7V9, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           17             83
  CLUS_2            3             13
  CLUS_3            4             19
  CLUS_4            5             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        5     14     10
  MLL2 WILD-TYPE     26     60     47
D7V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             26
  CLUS_2           14             60
  CLUS_3           10             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        2      5      3
  MLL2 WILD-TYPE     13     13     16
D7V11, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            5             13
  CLUS_3            3             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  MLL2 MUTATED        0      2      0      3      1      1      3      0      0
  MLL2 WILD-TYPE      5      1      3     10      9      6      2      2      4
D7V12, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            0              5
  CLUS_2            2              1
  CLUS_3            0              3
  CLUS_4            3             10
  CLUS_5            1              9
  CLUS_6            1              6
  CLUS_7            3              2
  CLUS_8            0              2
  CLUS_9            0              4
[1] 9 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 = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      5      0      3
  RB1 WILD-TYPE     35     43     17     16
D8V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            35
  CLUS_2           5            43
  CLUS_3           0            17
  CLUS_4           3            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      5      3
  RB1 WILD-TYPE     39     47     25
D8V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            39
  CLUS_2           5            47
  CLUS_3           3            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
  RB1 MUTATED        4      3      5
  RB1 WILD-TYPE     58     66     42
D8V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4            58
  CLUS_2           3            66
  CLUS_3           5            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        0      4      1
  RB1 WILD-TYPE     27     25     17
D8V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            27
  CLUS_2           4            25
  CLUS_3           1            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        3      2      1
  RB1 WILD-TYPE     31     45     30
D8V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            31
  CLUS_2           2            45
  CLUS_3           1            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        1      0      2      3
  RB1 WILD-TYPE     28     22     32     24
D8V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            28
  CLUS_2           0            22
  CLUS_3           2            32
  CLUS_4           3            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        1      4      4      3
  RB1 WILD-TYPE     38     57     47     24
D8V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            38
  CLUS_2           4            57
  CLUS_3           4            47
  CLUS_4           3            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        4      4      4
  RB1 WILD-TYPE     77     58     31
D8V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4            77
  CLUS_2           4            58
  CLUS_3           4            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 CLUS_4
  RB1 MUTATED        9      1      0      2
  RB1 WILD-TYPE     91     15     23     21
D8V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           9            91
  CLUS_2           1            15
  CLUS_3           0            23
  CLUS_4           2            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      4      6
  RB1 WILD-TYPE     29     70     51
D8V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            29
  CLUS_2           4            70
  CLUS_3           6            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      0      0
  RB1 WILD-TYPE     14     18     19
D8V11, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            51 
   TCGA-18-5592    TCGA-18-5595    TCGA-21-5782    TCGA-21-5784    TCGA-21-5786 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-21-5787    TCGA-22-4593    TCGA-22-5471    TCGA-22-5472    TCGA-22-5473 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5474    TCGA-22-5477    TCGA-22-5478    TCGA-22-5480    TCGA-22-5482 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5485    TCGA-22-5489    TCGA-22-5491    TCGA-22-5492    TCGA-33-6737 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5231    TCGA-34-5232    TCGA-34-5234    TCGA-34-5236    TCGA-34-5239 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5927    TCGA-34-5928    TCGA-34-5929    TCGA-37-3783    TCGA-37-5819 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-39-5019    TCGA-39-5022    TCGA-39-5024    TCGA-39-5027    TCGA-43-5668 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-43-6647    TCGA-43-6770    TCGA-43-6771    TCGA-46-6025    TCGA-46-6026 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-56-5897    TCGA-56-5898    TCGA-56-6545    TCGA-56-6546    TCGA-60-2709 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-63-6202    TCGA-70-6722    TCGA-70-6723    TCGA-85-6175    TCGA-85-6560 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-85-6561 
"RB1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  RB1 MUTATED        0      0      0      0      1      0      0      0      0
  RB1 WILD-TYPE      5      3      3     13      9      7      5      2      4
D8V12, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            51 
   TCGA-18-5592    TCGA-18-5595    TCGA-21-5782    TCGA-21-5784    TCGA-21-5786 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-21-5787    TCGA-22-4593    TCGA-22-5471    TCGA-22-5472    TCGA-22-5473 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5474    TCGA-22-5477    TCGA-22-5478    TCGA-22-5480    TCGA-22-5482 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5485    TCGA-22-5489    TCGA-22-5491    TCGA-22-5492    TCGA-33-6737 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5231    TCGA-34-5232    TCGA-34-5234    TCGA-34-5236    TCGA-34-5239 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5927    TCGA-34-5928    TCGA-34-5929    TCGA-37-3783    TCGA-37-5819 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-39-5019    TCGA-39-5022    TCGA-39-5024    TCGA-39-5027    TCGA-43-5668 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-43-6647    TCGA-43-6770    TCGA-43-6771    TCGA-46-6025    TCGA-46-6026 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-56-5897    TCGA-56-5898    TCGA-56-6545    TCGA-56-6546    TCGA-60-2709 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-63-6202    TCGA-70-6722    TCGA-70-6723    TCGA-85-6175    TCGA-85-6560 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-85-6561 
"RB1 WILD-TYPE" 

Clustering(9) Variable = IBTK MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IBTK MUTATED        1      2      0      2
  IBTK WILD-TYPE     36     46     17     17
D9V1, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             36
  CLUS_2            2             46
  CLUS_3            0             17
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        1      3      1
  IBTK WILD-TYPE     40     49     27
D9V2, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             40
  CLUS_2            3             49
  CLUS_3            1             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        1      3      1
  IBTK WILD-TYPE     61     66     46
D9V3, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             61
  CLUS_2            3             66
  CLUS_3            1             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        0      0      0
  IBTK WILD-TYPE     27     29     18
D9V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        1      0      0
  IBTK WILD-TYPE     33     47     31
D9V5, multiclass
[1] "Remove cluster labels:" "IBTK MUTATED"          
clus
  IBTK MUTATED IBTK WILD-TYPE 
             1            111 
    TCGA-18-4721     TCGA-18-5592     TCGA-18-5595     TCGA-21-1070 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-21-1071     TCGA-21-1076     TCGA-21-1078     TCGA-21-1081 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-21-5787 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-1011     TCGA-22-4591     TCGA-22-4607     TCGA-22-5471 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-4532 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-33-4547     TCGA-33-4566     TCGA-33-4582     TCGA-33-4586 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-33-6737     TCGA-34-2596     TCGA-34-2608     TCGA-34-5231 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-34-5241     TCGA-34-5927     TCGA-34-5928     TCGA-34-5929 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-37-3789     TCGA-37-4135     TCGA-37-4141     TCGA-37-5819 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5016     TCGA-39-5019     TCGA-39-5021     TCGA-39-5022 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5024     TCGA-39-5027     TCGA-39-5028     TCGA-39-5029 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5030     TCGA-39-5031     TCGA-39-5035     TCGA-39-5037 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-43-2578     TCGA-43-3394     TCGA-43-5668     TCGA-43-6143 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2698     TCGA-60-2708     TCGA-60-2709     TCGA-60-2710 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2711     TCGA-60-2712     TCGA-60-2713     TCGA-60-2719 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2720     TCGA-60-2721     TCGA-60-2724     TCGA-60-2725 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5128     TCGA-63-5131     TCGA-63-6202 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2727     TCGA-66-2758     TCGA-66-2766     TCGA-66-2767 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2768     TCGA-66-2770     TCGA-66-2773     TCGA-66-2777 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2778     TCGA-66-2781     TCGA-66-2782     TCGA-66-2783 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2785     TCGA-66-2788     TCGA-66-2791     TCGA-66-2794 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2795     TCGA-66-2800     TCGA-70-6722     TCGA-70-6723 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IBTK MUTATED        1      0      0      0
  IBTK WILD-TYPE     28     22     34     27
D9V6, multiclass
[1] "Remove cluster labels:" "IBTK MUTATED"          
clus
  IBTK MUTATED IBTK WILD-TYPE 
             1            111 
    TCGA-18-4721     TCGA-18-5592     TCGA-18-5595     TCGA-21-1070 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-21-1071     TCGA-21-1076     TCGA-21-1078     TCGA-21-1081 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-21-5787 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-1011     TCGA-22-4591     TCGA-22-4607     TCGA-22-5471 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-4532 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-33-4547     TCGA-33-4566     TCGA-33-4582     TCGA-33-4586 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-33-6737     TCGA-34-2596     TCGA-34-2608     TCGA-34-5231 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-34-5241     TCGA-34-5927     TCGA-34-5928     TCGA-34-5929 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-37-3789     TCGA-37-4135     TCGA-37-4141     TCGA-37-5819 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5016     TCGA-39-5019     TCGA-39-5021     TCGA-39-5022 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5024     TCGA-39-5027     TCGA-39-5028     TCGA-39-5029 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-39-5030     TCGA-39-5031     TCGA-39-5035     TCGA-39-5037 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-43-2578     TCGA-43-3394     TCGA-43-5668     TCGA-43-6143 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2698     TCGA-60-2708     TCGA-60-2709     TCGA-60-2710 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2711     TCGA-60-2712     TCGA-60-2713     TCGA-60-2719 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2720     TCGA-60-2721     TCGA-60-2724     TCGA-60-2725 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5128     TCGA-63-5131     TCGA-63-6202 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2727     TCGA-66-2758     TCGA-66-2766     TCGA-66-2767 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2768     TCGA-66-2770     TCGA-66-2773     TCGA-66-2777 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2778     TCGA-66-2781     TCGA-66-2782     TCGA-66-2783 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2785     TCGA-66-2788     TCGA-66-2791     TCGA-66-2794 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-66-2795     TCGA-66-2800     TCGA-70-6722     TCGA-70-6723 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IBTK MUTATED        1      3      1      0
  IBTK WILD-TYPE     38     58     50     27
D9V7, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             38
  CLUS_2            3             58
  CLUS_3            1             50
  CLUS_4            0             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        1      3      1
  IBTK WILD-TYPE     80     59     34
D9V8, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             80
  CLUS_2            3             59
  CLUS_3            1             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
  IBTK MUTATED        4      0      0      1
  IBTK WILD-TYPE     96     16     23     22
D9V9, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            4             96
  CLUS_2            0             16
  CLUS_3            0             23
  CLUS_4            1             22
[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
  IBTK MUTATED        1      3      1
  IBTK WILD-TYPE     30     71     56
D9V10, multiclass
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  CLUS_1            1             30
  CLUS_2            3             71
  CLUS_3            1             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IBTK MUTATED        0      0      0
  IBTK WILD-TYPE     15     18     19
D9V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  IBTK MUTATED        0      0      0      0      0      0      0      0      0
  IBTK WILD-TYPE      5      3      3     13     10      7      5      2      4
D9V12, multiclass

Clustering(10) Variable = CYP11B1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        3      5      3      1
  CYP11B1 WILD-TYPE     34     43     14     18
D10V1, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                34
  CLUS_2               5                43
  CLUS_3               3                14
  CLUS_4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        3      5      4
  CYP11B1 WILD-TYPE     38     47     24
D10V2, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                38
  CLUS_2               5                47
  CLUS_3               4                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        5      6      4
  CYP11B1 WILD-TYPE     57     63     43
D10V3, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               5                57
  CLUS_2               6                63
  CLUS_3               4                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        3      0      1
  CYP11B1 WILD-TYPE     24     29     17
D10V4, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                29
  CLUS_3               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        5      2      2
  CYP11B1 WILD-TYPE     29     45     29
D10V5, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               5                29
  CLUS_2               2                45
  CLUS_3               2                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        4      0      1      4
  CYP11B1 WILD-TYPE     25     22     33     23
D10V6, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               4                25
  CLUS_2               0                22
  CLUS_3               1                33
  CLUS_4               4                23
[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
  CYP11B1 MUTATED        2      4      6      3
  CYP11B1 WILD-TYPE     37     57     45     24
D10V7, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                37
  CLUS_2               4                57
  CLUS_3               6                45
  CLUS_4               3                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        6      4      5
  CYP11B1 WILD-TYPE     75     58     30
D10V8, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               6                75
  CLUS_2               4                58
  CLUS_3               5                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        7      2      1      3
  CYP11B1 WILD-TYPE     93     14     22     20
D10V9, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               7                93
  CLUS_2               2                14
  CLUS_3               1                22
  CLUS_4               3                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        3      5      5
  CYP11B1 WILD-TYPE     28     69     52
D10V10, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                28
  CLUS_2               5                69
  CLUS_3               5                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        2      1      0
  CYP11B1 WILD-TYPE     13     17     19
D10V11, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                17
  CLUS_3               0                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CYP11B1 MUTATED        1      0      0      1      0      0      0      0
  CYP11B1 WILD-TYPE      4      3      3     12     10      7      5      2
                   vv
clus                CLUS_9
  CYP11B1 MUTATED        1
  CYP11B1 WILD-TYPE      3
D10V12, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               0                 3
  CLUS_3               0                 3
  CLUS_4               1                12
  CLUS_5               0                10
  CLUS_6               0                 7
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 3
[1] 9 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 = NOTCH1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH1 MUTATED        1      4      1      1
  NOTCH1 WILD-TYPE     36     44     16     18
D11V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               36
  CLUS_2              4               44
  CLUS_3              1               16
  CLUS_4              1               18
[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
  NOTCH1 MUTATED        1      4      2
  NOTCH1 WILD-TYPE     40     48     26
D11V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               40
  CLUS_2              4               48
  CLUS_3              2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        3      7      4
  NOTCH1 WILD-TYPE     59     62     43
D11V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               59
  CLUS_2              7               62
  CLUS_3              4               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        0      4      4
  NOTCH1 WILD-TYPE     27     25     14
D11V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0               27
  CLUS_2              4               25
  CLUS_3              4               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        1      4      3
  NOTCH1 WILD-TYPE     33     43     28
D11V5, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               33
  CLUS_2              4               43
  CLUS_3              3               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
  NOTCH1 MUTATED        2      3      2      1
  NOTCH1 WILD-TYPE     27     19     32     26
D11V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               27
  CLUS_2              3               19
  CLUS_3              2               32
  CLUS_4              1               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH1 MUTATED        2      6      5      1
  NOTCH1 WILD-TYPE     37     55     46     26
D11V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               37
  CLUS_2              6               55
  CLUS_3              5               46
  CLUS_4              1               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        4      7      3
  NOTCH1 WILD-TYPE     77     55     32
D11V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              4               77
  CLUS_2              7               55
  CLUS_3              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH1 MUTATED        8      3      0      2
  NOTCH1 WILD-TYPE     92     13     23     21
D11V9, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              8               92
  CLUS_2              3               13
  CLUS_3              0               23
  CLUS_4              2               21
[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
  NOTCH1 MUTATED        4      3      6
  NOTCH1 WILD-TYPE     27     71     51
D11V10, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              4               27
  CLUS_2              3               71
  CLUS_3              6               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        3      1      2
  NOTCH1 WILD-TYPE     12     17     17
D11V11, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              1               17
  CLUS_3              2               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NOTCH1 MUTATED        2      1      0      0      1      0      0      0
  NOTCH1 WILD-TYPE      3      2      3     13      9      7      5      2
                  vv
clus               CLUS_9
  NOTCH1 MUTATED        2
  NOTCH1 WILD-TYPE      2
D11V12, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2                3
  CLUS_2              1                2
  CLUS_3              0                3
  CLUS_4              0               13
  CLUS_5              1                9
  CLUS_6              0                7
  CLUS_7              0                5
  CLUS_8              0                2
  CLUS_9              2                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = SLC28A1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC28A1 MUTATED        0      1      3      0
  SLC28A1 WILD-TYPE     37     47     14     19
D12V1, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                37
  CLUS_2               1                47
  CLUS_3               3                14
  CLUS_4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        0      1      3
  SLC28A1 WILD-TYPE     41     51     25
D12V2, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                41
  CLUS_2               1                51
  CLUS_3               3                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
  SLC28A1 MUTATED        7      1      1
  SLC28A1 WILD-TYPE     55     68     46
D12V3, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               7                55
  CLUS_2               1                68
  CLUS_3               1                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        3      0      2
  SLC28A1 WILD-TYPE     24     29     16
D12V4, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                29
  CLUS_3               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        2      4      0
  SLC28A1 WILD-TYPE     32     43     31
D12V5, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               2                32
  CLUS_2               4                43
  CLUS_3               0                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 CLUS_4
  SLC28A1 MUTATED        2      1      3      0
  SLC28A1 WILD-TYPE     27     21     31     27
D12V6, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               2                27
  CLUS_2               1                21
  CLUS_3               3                31
  CLUS_4               0                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC28A1 MUTATED        3      0      5      1
  SLC28A1 WILD-TYPE     36     61     46     26
D12V7, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                36
  CLUS_2               0                61
  CLUS_3               5                46
  CLUS_4               1                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        4      0      5
  SLC28A1 WILD-TYPE     77     62     30
D12V8, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               4                77
  CLUS_2               0                62
  CLUS_3               5                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC28A1 MUTATED        3      1      3      1
  SLC28A1 WILD-TYPE     97     15     20     22
D12V9, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                97
  CLUS_2               1                15
  CLUS_3               3                20
  CLUS_4               1                22
[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
  SLC28A1 MUTATED        0      5      3
  SLC28A1 WILD-TYPE     31     69     54
D12V10, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                31
  CLUS_2               5                69
  CLUS_3               3                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        0      2      2
  SLC28A1 WILD-TYPE     15     16     17
D12V11, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                15
  CLUS_2               2                16
  CLUS_3               2                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SLC28A1 MUTATED        0      1      1      2      0      0      0      0
  SLC28A1 WILD-TYPE      5      2      2     11     10      7      5      2
                   vv
clus                CLUS_9
  SLC28A1 MUTATED        0
  SLC28A1 WILD-TYPE      4
D12V12, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 2
  CLUS_3               1                 2
  CLUS_4               2                11
  CLUS_5               0                10
  CLUS_6               0                 7
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = ASB5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        1      4      2      2
  ASB5 WILD-TYPE     36     44     15     17
D13V1, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             36
  CLUS_2            4             44
  CLUS_3            2             15
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        2      4      3
  ASB5 WILD-TYPE     39     48     25
D13V2, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             39
  CLUS_2            4             48
  CLUS_3            3             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
  ASB5 MUTATED        2      6      1
  ASB5 WILD-TYPE     60     63     46
D13V3, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             60
  CLUS_2            6             63
  CLUS_3            1             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        0      2      0
  ASB5 WILD-TYPE     27     27     18
D13V4, multiclass
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             2             72 
    TCGA-18-3417     TCGA-18-4721     TCGA-18-5592     TCGA-18-5595 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-21-5787 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4599     TCGA-22-4601     TCGA-22-5471 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-4566 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-33-4582     TCGA-33-4583     TCGA-33-4586     TCGA-33-6737 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5231     TCGA-34-5232     TCGA-34-5234     TCGA-34-5236 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5239     TCGA-34-5240     TCGA-34-5241     TCGA-34-5927 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5928     TCGA-34-5929     TCGA-37-5819     TCGA-39-5019 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5021     TCGA-39-5022     TCGA-39-5024     TCGA-39-5027 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5028     TCGA-39-5029     TCGA-39-5030     TCGA-39-5031 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5035     TCGA-39-5036     TCGA-39-5037     TCGA-39-5039 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-43-5668     TCGA-43-6143     TCGA-43-6647     TCGA-43-6770 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-43-6771     TCGA-46-6025     TCGA-46-6026     TCGA-56-5897 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-56-5898     TCGA-56-6545     TCGA-56-6546     TCGA-60-2709 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-63-5128     TCGA-63-5131     TCGA-63-6202     TCGA-70-6722 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-70-6723     TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        2      1      0
  ASB5 WILD-TYPE     32     46     31
D13V5, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             32
  CLUS_2            1             46
  CLUS_3            0             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 CLUS_4
  ASB5 MUTATED        1      0      1      1
  ASB5 WILD-TYPE     28     22     33     26
D13V6, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             28
  CLUS_2            0             22
  CLUS_3            1             33
  CLUS_4            1             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        1      4      4      0
  ASB5 WILD-TYPE     38     57     47     27
D13V7, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             38
  CLUS_2            4             57
  CLUS_3            4             47
  CLUS_4            0             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        4      2      3
  ASB5 WILD-TYPE     77     60     32
D13V8, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            4             77
  CLUS_2            2             60
  CLUS_3            3             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        7      0      0      0
  ASB5 WILD-TYPE     93     16     23     23
D13V9, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            7             93
  CLUS_2            0             16
  CLUS_3            0             23
  CLUS_4            0             23
[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
  ASB5 MUTATED        0      5      2
  ASB5 WILD-TYPE     31     69     55
D13V10, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            0             31
  CLUS_2            5             69
  CLUS_3            2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        0      0      0
  ASB5 WILD-TYPE     15     18     19
D13V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  ASB5 MUTATED        0      0      0      0      0      0      0      0      0
  ASB5 WILD-TYPE      5      3      3     13     10      7      5      2      4
D13V12, multiclass

Clustering(14) Variable = CPS1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CPS1 MUTATED        5      8      4      2
  CPS1 WILD-TYPE     32     40     13     17
D14V1, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            5             32
  CLUS_2            8             40
  CLUS_3            4             13
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        4      8      7
  CPS1 WILD-TYPE     37     44     21
D14V2, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             37
  CLUS_2            8             44
  CLUS_3            7             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        7      9      9
  CPS1 WILD-TYPE     55     60     38
D14V3, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            7             55
  CLUS_2            9             60
  CLUS_3            9             38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        3      3      1
  CPS1 WILD-TYPE     24     26     17
D14V4, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            3             24
  CLUS_2            3             26
  CLUS_3            1             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        4      8      3
  CPS1 WILD-TYPE     30     39     28
D14V5, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             30
  CLUS_2            8             39
  CLUS_3            3             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
  CPS1 MUTATED        4      2      7      2
  CPS1 WILD-TYPE     25     20     27     25
D14V6, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             25
  CLUS_2            2             20
  CLUS_3            7             27
  CLUS_4            2             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CPS1 MUTATED        5      9      7      4
  CPS1 WILD-TYPE     34     52     44     23
D14V7, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            5             34
  CLUS_2            9             52
  CLUS_3            7             44
  CLUS_4            4             23
[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
  CPS1 MUTATED       10     10      5
  CPS1 WILD-TYPE     71     52     30
D14V8, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1           10             71
  CLUS_2           10             52
  CLUS_3            5             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CPS1 MUTATED        7      3      4      5
  CPS1 WILD-TYPE     93     13     19     18
D14V9, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            7             93
  CLUS_2            3             13
  CLUS_3            4             19
  CLUS_4            5             18
[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
  CPS1 MUTATED        6      7      6
  CPS1 WILD-TYPE     25     67     51
D14V10, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            6             25
  CLUS_2            7             67
  CLUS_3            6             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        2      2      2
  CPS1 WILD-TYPE     13     16     17
D14V11, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            2             16
  CLUS_3            2             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  CPS1 MUTATED        1      0      1      1      0      2      1      0      0
  CPS1 WILD-TYPE      4      3      2     12     10      5      4      2      4
D14V12, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            0              3
  CLUS_3            1              2
  CLUS_4            1             12
  CLUS_5            0             10
  CLUS_6            2              5
  CLUS_7            1              4
  CLUS_8            0              2
  CLUS_9            0              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = EP300 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        5      2      0      0
  EP300 WILD-TYPE     32     46     17     19
D15V1, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              32
  CLUS_2             2              46
  CLUS_3             0              17
  CLUS_4             0              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        5      2      0
  EP300 WILD-TYPE     36     50     28
D15V2, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              36
  CLUS_2             2              50
  CLUS_3             0              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
  EP300 MUTATED        2      2      4
  EP300 WILD-TYPE     60     67     43
D15V3, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              60
  CLUS_2             2              67
  CLUS_3             4              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        0      1      0
  EP300 WILD-TYPE     27     28     18
D15V4, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              1              73 
     TCGA-18-3417      TCGA-18-4721      TCGA-18-5592      TCGA-18-5595 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-21-5782      TCGA-21-5784      TCGA-21-5787      TCGA-22-4593 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-4599      TCGA-22-4601      TCGA-22-4613      TCGA-22-5471 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5472      TCGA-22-5473      TCGA-22-5474      TCGA-22-5477 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5478      TCGA-22-5480      TCGA-22-5482      TCGA-22-5485 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5489      TCGA-22-5491      TCGA-22-5492      TCGA-33-4566 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-33-4582      TCGA-33-4583      TCGA-33-4586      TCGA-33-6737 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5231      TCGA-34-5232      TCGA-34-5234      TCGA-34-5236 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5239      TCGA-34-5240      TCGA-34-5241      TCGA-34-5927 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5928      TCGA-34-5929      TCGA-37-5819      TCGA-39-5016 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5021      TCGA-39-5022      TCGA-39-5024 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5027      TCGA-39-5028      TCGA-39-5029      TCGA-39-5030 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5031      TCGA-39-5035      TCGA-39-5036      TCGA-39-5037 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5039      TCGA-43-5668      TCGA-43-6143      TCGA-43-6647 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6770      TCGA-43-6771      TCGA-46-6025      TCGA-46-6026 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5897      TCGA-56-5898      TCGA-56-6545      TCGA-56-6546 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-60-2709      TCGA-63-5128      TCGA-63-5131      TCGA-63-6202 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-70-6722      TCGA-70-6723      TCGA-85-6175      TCGA-85-6560 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6561 
"EP300 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        0      1      2
  EP300 WILD-TYPE     34     46     29
D15V5, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             0              34
  CLUS_2             1              46
  CLUS_3             2              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        1      0      1      1
  EP300 WILD-TYPE     28     22     33     26
D15V6, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             0              22
  CLUS_3             1              33
  CLUS_4             1              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        3      0      3      2
  EP300 WILD-TYPE     36     61     48     25
D15V7, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             3              36
  CLUS_2             0              61
  CLUS_3             3              48
  CLUS_4             2              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        5      1      2
  EP300 WILD-TYPE     76     61     33
D15V8, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              76
  CLUS_2             1              61
  CLUS_3             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        7      0      0      0
  EP300 WILD-TYPE     93     16     23     23
D15V9, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             7              93
  CLUS_2             0              16
  CLUS_3             0              23
  CLUS_4             0              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        0      3      4
  EP300 WILD-TYPE     31     71     53
D15V10, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             0              31
  CLUS_2             3              71
  CLUS_3             4              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        0      2      0
  EP300 WILD-TYPE     15     16     19
D15V11, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              50 
     TCGA-18-5592      TCGA-18-5595      TCGA-21-5782      TCGA-21-5784 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-21-5787      TCGA-22-4593      TCGA-22-5471      TCGA-22-5472 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-5819 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5022      TCGA-39-5024      TCGA-39-5027 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-5668      TCGA-43-6143      TCGA-43-6647      TCGA-43-6770 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6771      TCGA-46-6025      TCGA-46-6026      TCGA-56-5897 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5898      TCGA-56-6545      TCGA-56-6546      TCGA-60-2709 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-63-6202      TCGA-70-6722      TCGA-70-6723      TCGA-85-6175 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6560      TCGA-85-6561 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  EP300 MUTATED        0      0      0      1      0      0      0      1
  EP300 WILD-TYPE      5      3      3     12     10      7      5      1
                 vv
clus              CLUS_9
  EP300 MUTATED        0
  EP300 WILD-TYPE      4
D15V12, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              50 
     TCGA-18-5592      TCGA-18-5595      TCGA-21-5782      TCGA-21-5784 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-21-5787      TCGA-22-4593      TCGA-22-5471      TCGA-22-5472 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-5819 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5022      TCGA-39-5024      TCGA-39-5027 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-5668      TCGA-43-6143      TCGA-43-6647      TCGA-43-6770 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6771      TCGA-46-6025      TCGA-46-6026      TCGA-56-5897 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5898      TCGA-56-6545      TCGA-56-6546      TCGA-60-2709 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-63-6202      TCGA-70-6722      TCGA-70-6723      TCGA-85-6175 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6560      TCGA-85-6561 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 

Clustering(16) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      4      1      3
  ARID1A WILD-TYPE     36     44     16     16
D16V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               36
  CLUS_2              4               44
  CLUS_3              1               16
  CLUS_4              3               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        2      4      3
  ARID1A WILD-TYPE     39     48     25
D16V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               39
  CLUS_2              4               48
  CLUS_3              3               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
  ARID1A MUTATED        5      5      2
  ARID1A WILD-TYPE     57     64     45
D16V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               57
  CLUS_2              5               64
  CLUS_3              2               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      1      0
  ARID1A WILD-TYPE     24     28     18
D16V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               24
  CLUS_2              1               28
  CLUS_3              0               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      2      3
  ARID1A WILD-TYPE     33     45     28
D16V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               33
  CLUS_2              2               45
  CLUS_3              3               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
  ARID1A MUTATED        1      1      1      3
  ARID1A WILD-TYPE     28     21     33     24
D16V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               28
  CLUS_2              1               21
  CLUS_3              1               33
  CLUS_4              3               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      4      6      2
  ARID1A WILD-TYPE     39     57     45     25
D16V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               39
  CLUS_2              4               57
  CLUS_3              6               45
  CLUS_4              2               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        4      5      3
  ARID1A WILD-TYPE     77     57     32
D16V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               77
  CLUS_2              5               57
  CLUS_3              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        4      2      3      1
  ARID1A WILD-TYPE     96     14     20     22
D16V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               96
  CLUS_2              2               14
  CLUS_3              3               20
  CLUS_4              1               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      4      3
  ARID1A WILD-TYPE     28     70     54
D16V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               28
  CLUS_2              4               70
  CLUS_3              3               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      0      2
  ARID1A WILD-TYPE     15     18     17
D16V11, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               50 
      TCGA-18-5592       TCGA-18-5595       TCGA-21-5782       TCGA-21-5784 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-21-5786       TCGA-21-5787       TCGA-22-4593       TCGA-22-5471 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5472       TCGA-22-5473       TCGA-22-5474       TCGA-22-5477 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5478       TCGA-22-5480       TCGA-22-5482       TCGA-22-5485 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5489       TCGA-22-5491       TCGA-22-5492       TCGA-33-6737 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5231       TCGA-34-5232       TCGA-34-5234       TCGA-34-5236 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5239       TCGA-34-5927       TCGA-34-5928       TCGA-34-5929 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-37-3783       TCGA-37-5819       TCGA-39-5019       TCGA-39-5024 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-39-5027       TCGA-43-5668       TCGA-43-6143       TCGA-43-6647 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-43-6770       TCGA-43-6771       TCGA-46-6025       TCGA-46-6026 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-56-5897       TCGA-56-5898       TCGA-56-6545       TCGA-56-6546 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2709       TCGA-70-6722       TCGA-70-6723       TCGA-85-6175 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-85-6560       TCGA-85-6561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARID1A MUTATED        0      0      0      1      0      1      0      0
  ARID1A WILD-TYPE      5      3      3     12     10      6      5      2
                  vv
clus               CLUS_9
  ARID1A MUTATED        0
  ARID1A WILD-TYPE      4
D16V12, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               50 
      TCGA-18-5592       TCGA-18-5595       TCGA-21-5782       TCGA-21-5784 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-21-5786       TCGA-21-5787       TCGA-22-4593       TCGA-22-5471 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5472       TCGA-22-5473       TCGA-22-5474       TCGA-22-5477 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5478       TCGA-22-5480       TCGA-22-5482       TCGA-22-5485 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5489       TCGA-22-5491       TCGA-22-5492       TCGA-33-6737 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5231       TCGA-34-5232       TCGA-34-5234       TCGA-34-5236 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5239       TCGA-34-5927       TCGA-34-5928       TCGA-34-5929 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-37-3783       TCGA-37-5819       TCGA-39-5019       TCGA-39-5024 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-39-5027       TCGA-43-5668       TCGA-43-6143       TCGA-43-6647 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-43-6770       TCGA-43-6771       TCGA-46-6025       TCGA-46-6026 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-56-5897       TCGA-56-5898       TCGA-56-6545       TCGA-56-6546 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2709       TCGA-70-6722       TCGA-70-6723       TCGA-85-6175 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-85-6560       TCGA-85-6561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 

Clustering(17) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        1      4      2      2
  FBXW7 WILD-TYPE     36     44     15     17
D17V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1              36
  CLUS_2             4              44
  CLUS_3             2              15
  CLUS_4             2              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        2      5      2
  FBXW7 WILD-TYPE     39     47     26
D17V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              39
  CLUS_2             5              47
  CLUS_3             2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        4      5      1
  FBXW7 WILD-TYPE     58     64     46
D17V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              58
  CLUS_2             5              64
  CLUS_3             1              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        0      0      1
  FBXW7 WILD-TYPE     27     29     17
D17V4, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              1              73 
     TCGA-18-3417      TCGA-18-4721      TCGA-18-5592      TCGA-21-5782 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-21-5784      TCGA-21-5786      TCGA-21-5787      TCGA-22-4593 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-4599      TCGA-22-4601      TCGA-22-4613      TCGA-22-5471 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5472      TCGA-22-5473      TCGA-22-5474      TCGA-22-5477 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5478      TCGA-22-5480      TCGA-22-5482      TCGA-22-5485 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5489      TCGA-22-5491      TCGA-22-5492      TCGA-33-4566 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-33-4582      TCGA-33-4583      TCGA-33-4586      TCGA-33-6737 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5231      TCGA-34-5232      TCGA-34-5234      TCGA-34-5236 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5239      TCGA-34-5240      TCGA-34-5241      TCGA-34-5927 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5928      TCGA-34-5929      TCGA-37-5819      TCGA-39-5016 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5021      TCGA-39-5022      TCGA-39-5024 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5027      TCGA-39-5028      TCGA-39-5029      TCGA-39-5030 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5031      TCGA-39-5035      TCGA-39-5036      TCGA-39-5037 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5039      TCGA-43-5668      TCGA-43-6143      TCGA-43-6647 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-43-6770      TCGA-43-6771      TCGA-46-6025      TCGA-46-6026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-56-5897      TCGA-56-5898      TCGA-56-6545      TCGA-56-6546 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-60-2709      TCGA-63-5128      TCGA-63-5131      TCGA-63-6202 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-70-6722      TCGA-70-6723      TCGA-85-6175      TCGA-85-6560 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-85-6561 
"FBXW7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        0      2      1
  FBXW7 WILD-TYPE     34     45     30
D17V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0              34
  CLUS_2             2              45
  CLUS_3             1              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        0      1      1      1
  FBXW7 WILD-TYPE     29     21     33     26
D17V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             1              21
  CLUS_3             1              33
  CLUS_4             1              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        2      5      2      1
  FBXW7 WILD-TYPE     37     56     49     26
D17V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              37
  CLUS_2             5              56
  CLUS_3             2              49
  CLUS_4             1              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        4      5      1
  FBXW7 WILD-TYPE     77     57     34
D17V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              77
  CLUS_2             5              57
  CLUS_3             1              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
  FBXW7 MUTATED        6      0      1      1
  FBXW7 WILD-TYPE     94     16     22     22
D17V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              94
  CLUS_2             0              16
  CLUS_3             1              22
  CLUS_4             1              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        2      5      1
  FBXW7 WILD-TYPE     29     69     56
D17V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              29
  CLUS_2             5              69
  CLUS_3             1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        1      0      0
  FBXW7 WILD-TYPE     14     18     19
D17V11, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              1              51 
     TCGA-18-5592      TCGA-21-5782      TCGA-21-5784      TCGA-21-5786 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-21-5787      TCGA-22-4593      TCGA-22-5471      TCGA-22-5472 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-3783 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-37-5819      TCGA-39-5019      TCGA-39-5022      TCGA-39-5024 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5027      TCGA-43-5668      TCGA-43-6143      TCGA-43-6647 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-43-6770      TCGA-43-6771      TCGA-46-6025      TCGA-46-6026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-56-5897      TCGA-56-5898      TCGA-56-6545      TCGA-56-6546 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-60-2709      TCGA-63-6202      TCGA-70-6722      TCGA-70-6723 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-85-6175      TCGA-85-6560      TCGA-85-6561 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FBXW7 MUTATED        1      0      0      0      0      0      0      0
  FBXW7 WILD-TYPE      4      3      3     13     10      7      5      2
                 vv
clus              CLUS_9
  FBXW7 MUTATED        0
  FBXW7 WILD-TYPE      4
D17V12, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              1              51 
     TCGA-18-5592      TCGA-21-5782      TCGA-21-5784      TCGA-21-5786 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-21-5787      TCGA-22-4593      TCGA-22-5471      TCGA-22-5472 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-3783 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-37-5819      TCGA-39-5019      TCGA-39-5022      TCGA-39-5024 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-39-5027      TCGA-43-5668      TCGA-43-6143      TCGA-43-6647 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-43-6770      TCGA-43-6771      TCGA-46-6025      TCGA-46-6026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-56-5897      TCGA-56-5898      TCGA-56-6545      TCGA-56-6546 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-60-2709      TCGA-63-6202      TCGA-70-6722      TCGA-70-6723 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-85-6175      TCGA-85-6560      TCGA-85-6561 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
