[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"        "-oTREAD-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/READ-TP/10703786/READ-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/10686211/transformed.cor.cli.txt"

nPatients in clinical file=169, in cluster file=69, common to both=69
[1] 12 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           56            13 
  APC MUTATED APC WILD-TYPE 
           56            13 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            44             25 
  TP53 MUTATED TP53 WILD-TYPE 
            44             25 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               64 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               64 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              65 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              65 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
[1] "CCDC88C MUTATION ANALYSIS"
[1] 3
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                3                66 
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                3                66 
[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 69 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[7] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 69 columns, 0 survival variables, and 9 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       19     16     16
  APC WILD-TYPE      5      5      3
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             5
  CLUS_2          16             5
  CLUS_3          16             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 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  APC MUTATED        4     10      8      8      5      7      7      2
  APC WILD-TYPE      2      2      4      1      1      2      1      0
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           4             2
  CLUS_2          10             2
  CLUS_3           8             4
  CLUS_4           8             1
  CLUS_5           5             1
  CLUS_6           7             2
  CLUS_7           7             1
  CLUS_8           2             0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APC MUTATED       11     16     15      9      4
  APC WILD-TYPE      6      2      2      2      1
D1V3, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_2          11             6
  CLUS_3          16             2
  CLUS_4          15             2
  CLUS_5           9             2
  CLUS_6           4             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       11     12     20
  APC WILD-TYPE      5      2      3
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             5
  CLUS_2          12             2
  CLUS_3          20             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 CLUS_4 CLUS_5
  APC MUTATED       15      7     12      1      8
  APC WILD-TYPE      5      2      2      1      0
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          15             5
  CLUS_2           7             2
  CLUS_3          12             2
  CLUS_4           1             1
  CLUS_5           8             0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APC MUTATED        0      4      2     50
  APC WILD-TYPE      1      0      0     11
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           0             1
  CLUS_2           4             0
  CLUS_3           2             0
  CLUS_4          50            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_2 CLUS_3 CLUS_4
  APC MUTATED        1     31     24
  APC WILD-TYPE      0      7      5
D1V7, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_2           1             0
  CLUS_3          31             7
  CLUS_4          24             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED        1      3      5     45
  APC WILD-TYPE      1      0      1      9
D1V8, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           1             1
  CLUS_3           3             0
  CLUS_4           5             1
  CLUS_5          45             9
[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
  APC MUTATED        8      2     44
  APC WILD-TYPE      1      1      9
D1V9, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           8             1
  CLUS_2           2             1
  CLUS_3          44             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"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        7     15     17
  TP53 WILD-TYPE     17      6      2
D2V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             17
  CLUS_2           15              6
  CLUS_3           17              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  TP53 MUTATED        2      8      4      9      5      6      5      0
  TP53 WILD-TYPE      4      4      8      0      1      3      3      2
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            8              4
  CLUS_3            4              8
  CLUS_4            9              0
  CLUS_5            5              1
  CLUS_6            6              3
  CLUS_7            5              3
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED       13      9     10      8      3
  TP53 WILD-TYPE      4      9      7      3      2
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_2           13              4
  CLUS_3            9              9
  CLUS_4           10              7
  CLUS_5            8              3
  CLUS_6            3              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       10     12     13
  TP53 WILD-TYPE      6      2     10
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              6
  CLUS_2           12              2
  CLUS_3           13             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       12      7      9      1      6
  TP53 WILD-TYPE      8      2      5      1      2
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12              8
  CLUS_2            7              2
  CLUS_3            9              5
  CLUS_4            1              1
  CLUS_5            6              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      2      1     40
  TP53 WILD-TYPE      1      2      1     21
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0              1
  CLUS_2            2              2
  CLUS_3            1              1
  CLUS_4           40             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_2 CLUS_3 CLUS_4
  TP53 MUTATED        1     22     20
  TP53 WILD-TYPE      0     16      9
D2V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_2            1              0
  CLUS_3           22             16
  CLUS_4           20              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_3 CLUS_4 CLUS_5
  TP53 MUTATED        1      2      4     34
  TP53 WILD-TYPE      1      1      2     20
D2V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            4              2
  CLUS_5           34             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
  TP53 MUTATED        8      1     32
  TP53 WILD-TYPE      1      2     21
D2V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            1              2
  CLUS_3           32             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"

Clustering(3) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       16     11      8
  KRAS WILD-TYPE      8     10     11
D3V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              8
  CLUS_2           11             10
  CLUS_3            8             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRAS MUTATED        3      9      9      3      3      6      0      2
  KRAS WILD-TYPE      3      3      3      6      3      3      8      0
D3V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3              3
  CLUS_2            9              3
  CLUS_3            9              3
  CLUS_4            3              6
  CLUS_5            3              3
  CLUS_6            6              3
  CLUS_7            0              8
  CLUS_8            2              0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        3     13      9      8      5
  KRAS WILD-TYPE     14      5      8      3      0
D3V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_2            3             14
  CLUS_3           13              5
  CLUS_4            9              8
  CLUS_5            8              3
  CLUS_6            5              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        7      8     12
  KRAS WILD-TYPE      9      6     11
D3V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7              9
  CLUS_2            8              6
  CLUS_3           12             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        9      4      9      1      4
  KRAS WILD-TYPE     11      5      5      1      4
D3V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             11
  CLUS_2            4              5
  CLUS_3            9              5
  CLUS_4            1              1
  CLUS_5            4              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        1      4      0     32
  KRAS WILD-TYPE      0      0      2     29
D3V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              0
  CLUS_2            4              0
  CLUS_3            0              2
  CLUS_4           32             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        1     28      8
  KRAS WILD-TYPE      0     10     21
D3V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_2            1              0
  CLUS_3           28             10
  CLUS_4            8             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_3 CLUS_4 CLUS_5
  KRAS MUTATED        1      2      1     30
  KRAS WILD-TYPE      1      1      5     24
D3V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            1              5
  CLUS_5           30             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
  KRAS MUTATED        1      3     30
  KRAS WILD-TYPE      8      0     23
D3V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              8
  CLUS_2            3              0
  CLUS_3           30             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"

Clustering(4) Variable = SMAD4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD4 MUTATED        5      0      2
  SMAD4 WILD-TYPE     19     21     17
D4V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             5              19
  CLUS_2             0              21
  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
  SMAD4 MUTATED        0      3      2      1      0      1      0      0
  SMAD4 WILD-TYPE      6      9     10      8      6      8      8      2
D4V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3               9
  CLUS_3             2              10
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             1               8
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SMAD4 MUTATED        1      3      2      1      1
  SMAD4 WILD-TYPE     16     15     15     10      4
D4V3, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_2             1              16
  CLUS_3             3              15
  CLUS_4             2              15
  CLUS_5             1              10
  CLUS_6             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD4 MUTATED        0      3      4
  SMAD4 WILD-TYPE     16     11     19
D4V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             3              11
  CLUS_3             4              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
  SMAD4 MUTATED        0      3      3      0      1
  SMAD4 WILD-TYPE     20      6     11      2      7
D4V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             3               6
  CLUS_3             3              11
  CLUS_4             0               2
  CLUS_5             1               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD4 MUTATED        1      0      0      7
  SMAD4 WILD-TYPE      0      4      2     54
D4V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1               0
  CLUS_2             0               4
  CLUS_3             0               2
  CLUS_4             7              54
[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_2 CLUS_3 CLUS_4
  SMAD4 MUTATED        0      7      1
  SMAD4 WILD-TYPE      1     31     28
D4V7, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_2             0               1
  CLUS_3             7              31
  CLUS_4             1              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_3 CLUS_4 CLUS_5
  SMAD4 MUTATED        1      0      0      7
  SMAD4 WILD-TYPE      1      3      6     47
D4V8, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1               1
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             7              47
[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
  SMAD4 MUTATED        0      1      7
  SMAD4 WILD-TYPE      9      2     46
D4V9, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1               2
  CLUS_3             7              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"

Clustering(5) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        2      5      1
  FBXW7 WILD-TYPE     22     16     18
D5V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             5              16
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FBXW7 MUTATED        0      3      1      1      0      3      0      0
  FBXW7 WILD-TYPE      6      9     11      8      6      6      8      2
D5V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3               9
  CLUS_3             1              11
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             3               6
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FBXW7 MUTATED        2      3      4      0      0
  FBXW7 WILD-TYPE     15     15     13     11      5
D5V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_2             2              15
  CLUS_3             3              15
  CLUS_4             4              13
  CLUS_5             0              11
  CLUS_6             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        3      2      2
  FBXW7 WILD-TYPE     13     12     21
D5V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             2              12
  CLUS_3             2              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 CLUS_4 CLUS_5
  FBXW7 MUTATED        2      2      1      0      2
  FBXW7 WILD-TYPE     18      7     13      2      6
D5V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             2               7
  CLUS_3             1              13
  CLUS_4             0               2
  CLUS_5             2               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        0      0      0      9
  FBXW7 WILD-TYPE      1      4      2     52
D5V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               1
  CLUS_2             0               4
  CLUS_3             0               2
  CLUS_4             9              52
[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_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        0      8      1
  FBXW7 WILD-TYPE      1     30     28
D5V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_2             0               1
  CLUS_3             8              30
  CLUS_4             1              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_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        0      0      0      9
  FBXW7 WILD-TYPE      2      3      6     45
D5V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             9              45
[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        0      0      9
  FBXW7 WILD-TYPE      9      3     44
D5V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0               3
  CLUS_3             9              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"

Clustering(6) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        2      2      1
  NRAS WILD-TYPE     22     19     18
D6V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             22
  CLUS_2            2             19
  CLUS_3            1             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NRAS MUTATED        1      2      1      1      0      0      0      0
  NRAS WILD-TYPE      5     10     11      8      6      9      8      2
D6V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2             10
  CLUS_3            1             11
  CLUS_4            1              8
  CLUS_5            0              6
  CLUS_6            0              9
  CLUS_7            0              8
  CLUS_8            0              2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NRAS MUTATED        0      3      0      2      0
  NRAS WILD-TYPE     17     15     17      9      5
D6V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_2            0             17
  CLUS_3            3             15
  CLUS_4            0             17
  CLUS_5            2              9
  CLUS_6            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        0      1      0
  NRAS WILD-TYPE     16     13     23
D6V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             52 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AG-3574     TCGA-AG-3578 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        1      0      0      0      0
  NRAS WILD-TYPE     19      9     14      2      8
D6V5, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             52 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AG-3574     TCGA-AG-3578 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        0      0      0      5
  NRAS WILD-TYPE      1      4      2     56
D6V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              1
  CLUS_2            0              4
  CLUS_3            0              2
  CLUS_4            5             56
[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_2 CLUS_3 CLUS_4
  NRAS MUTATED        0      3      2
  NRAS WILD-TYPE      1     35     27
D6V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_2            0              1
  CLUS_3            3             35
  CLUS_4            2             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_3 CLUS_4 CLUS_5
  NRAS MUTATED        1      0      1      3
  NRAS WILD-TYPE      1      3      5     51
D6V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            0              3
  CLUS_4            1              5
  CLUS_5            3             51
[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
  NRAS MUTATED        0      0      5
  NRAS WILD-TYPE      9      3     48
D6V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              9
  CLUS_2            0              3
  CLUS_3            5             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"

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      2      0
  ARID1A WILD-TYPE     21     19     19
D7V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               21
  CLUS_2              2               19
  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
  ARID1A MUTATED        1      1      1      0      0      1      0      1
  ARID1A WILD-TYPE      5     11     11      9      6      8      8      1
D7V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1                5
  CLUS_2              1               11
  CLUS_3              1               11
  CLUS_4              0                9
  CLUS_5              0                6
  CLUS_6              1                8
  CLUS_7              0                8
  CLUS_8              1                1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED        1      3      0      1      0
  ARID1A WILD-TYPE     16     15     17     10      5
D7V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_2              1               16
  CLUS_3              3               15
  CLUS_4              0               17
  CLUS_5              1               10
  CLUS_6              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        2      1      0
  ARID1A WILD-TYPE     14     13     23
D7V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               13
  CLUS_3              0               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 CLUS_5
  ARID1A MUTATED        2      0      0      0      1
  ARID1A WILD-TYPE     18      9     14      2      7
D7V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0                9
  CLUS_3              0               14
  CLUS_4              0                2
  CLUS_5              1                7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      0      0      5
  ARID1A WILD-TYPE      1      4      2     56
D7V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                1
  CLUS_2              0                4
  CLUS_3              0                2
  CLUS_4              5               56
[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_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      3      2
  ARID1A WILD-TYPE      1     35     27
D7V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_2              0                1
  CLUS_3              3               35
  CLUS_4              2               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_3 CLUS_4 CLUS_5
  ARID1A MUTATED        0      1      0      3
  ARID1A WILD-TYPE      2      2      6     51
D7V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                2
  CLUS_3              1                2
  CLUS_4              0                6
  CLUS_5              3               51
[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        0      1      3
  ARID1A WILD-TYPE      9      2     50
D7V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1                2
  CLUS_3              3               50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = RBM10 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RBM10 MUTATED        2      1      1
  RBM10 WILD-TYPE     22     20     18
D8V1, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             1              20
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RBM10 MUTATED        1      1      0      1      0      1      0      0
  RBM10 WILD-TYPE      5     11     12      8      6      8      8      2
D8V2, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              11
  CLUS_3             0              12
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             1               8
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RBM10 MUTATED        1      1      0      1      1
  RBM10 WILD-TYPE     16     17     17     10      4
D8V3, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_2             1              16
  CLUS_3             1              17
  CLUS_4             0              17
  CLUS_5             1              10
  CLUS_6             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RBM10 MUTATED        1      1      1
  RBM10 WILD-TYPE     15     13     22
D8V4, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              13
  CLUS_3             1              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 CLUS_4 CLUS_5
  RBM10 MUTATED        1      0      1      0      1
  RBM10 WILD-TYPE     19      9     13      2      7
D8V5, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             0               9
  CLUS_3             1              13
  CLUS_4             0               2
  CLUS_5             1               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBM10 MUTATED        0      2      0      1
  RBM10 WILD-TYPE      1      2      2     60
D8V6, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             0               1
  CLUS_2             2               2
  CLUS_3             0               2
  CLUS_4             1              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4
  RBM10 MUTATED        1      1      1
  RBM10 WILD-TYPE      0     37     28
D8V7, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_2             1               0
  CLUS_3             1              37
  CLUS_4             1              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_3 CLUS_4 CLUS_5
  RBM10 MUTATED        0      0      1      3
  RBM10 WILD-TYPE      2      3      5     51
D8V8, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             1               5
  CLUS_5             3              51
[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
  RBM10 MUTATED        1      0      3
  RBM10 WILD-TYPE      8      3     50
D8V9, multiclass
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0               3
  CLUS_3             3              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = TCF7L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        2      2      3
  TCF7L2 WILD-TYPE     22     19     16
D9V1, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               22
  CLUS_2              2               19
  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
  TCF7L2 MUTATED        1      0      1      1      1      0      3      0
  TCF7L2 WILD-TYPE      5     12     11      8      5      9      5      2
D9V2, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              0               12
  CLUS_3              1               11
  CLUS_4              1                8
  CLUS_5              1                5
  CLUS_6              0                9
  CLUS_7              3                5
  CLUS_8              0                2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TCF7L2 MUTATED        4      0      2      1      0
  TCF7L2 WILD-TYPE     13     18     15     10      5
D9V3, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_2              4               13
  CLUS_3              0               18
  CLUS_4              2               15
  CLUS_5              1               10
  CLUS_6              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        2      2      0
  TCF7L2 WILD-TYPE     14     12     23
D9V4, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               12
  CLUS_3              0               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 CLUS_5
  TCF7L2 MUTATED        2      0      0      0      2
  TCF7L2 WILD-TYPE     18      9     14      2      6
D9V5, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0                9
  CLUS_3              0               14
  CLUS_4              0                2
  CLUS_5              2                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        0      0      0      7
  TCF7L2 WILD-TYPE      1      4      2     54
D9V6, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                1
  CLUS_2              0                4
  CLUS_3              0                2
  CLUS_4              7               54
[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_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        0      2      5
  TCF7L2 WILD-TYPE      1     36     24
D9V7, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_2              0                1
  CLUS_3              2               36
  CLUS_4              5               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_3 CLUS_4 CLUS_5
  TCF7L2 MUTATED        0      0      0      6
  TCF7L2 WILD-TYPE      2      3      6     48
D9V8, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                2
  CLUS_3              0                3
  CLUS_4              0                6
  CLUS_5              6               48
[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
  TCF7L2 MUTATED        0      0      6
  TCF7L2 WILD-TYPE      9      3     47
D9V9, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              0                3
  CLUS_3              6               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"

Clustering(10) Variable = ERBB2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        2      1      1
  ERBB2 WILD-TYPE     22     20     18
D10V1, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             1              20
  CLUS_3             1              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ERBB2 MUTATED        0      1      2      1      0      0      0      0
  ERBB2 WILD-TYPE      6     11     10      8      6      9      8      2
D10V2, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1              11
  CLUS_3             2              10
  CLUS_4             1               8
  CLUS_5             0               6
  CLUS_6             0               9
  CLUS_7             0               8
  CLUS_8             0               2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ERBB2 MUTATED        1      1      0      1      1
  ERBB2 WILD-TYPE     16     17     17     10      4
D10V3, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_2             1              16
  CLUS_3             1              17
  CLUS_4             0              17
  CLUS_5             1              10
  CLUS_6             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        1      2      1
  ERBB2 WILD-TYPE     15     12     22
D10V4, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              12
  CLUS_3             1              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 CLUS_4 CLUS_5
  ERBB2 MUTATED        1      0      1      0      2
  ERBB2 WILD-TYPE     19      9     13      2      6
D10V5, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             0               9
  CLUS_3             1              13
  CLUS_4             0               2
  CLUS_5             2               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        0      2      0      2
  ERBB2 WILD-TYPE      1      2      2     59
D10V6, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               1
  CLUS_2             2               2
  CLUS_3             0               2
  CLUS_4             2              59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        1      1      2
  ERBB2 WILD-TYPE      0     37     27
D10V7, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_2             1               0
  CLUS_3             1              37
  CLUS_4             2              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_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        0      0      0      3
  ERBB2 WILD-TYPE      2      3      6     51
D10V8, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             3              51
[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
  ERBB2 MUTATED        0      0      3
  ERBB2 WILD-TYPE      9      3     50
D10V9, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0               3
  CLUS_3             3              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = KIAA1804 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1804 MUTATED        3      4      1
  KIAA1804 WILD-TYPE     21     17     18
D11V1, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                4                 17
  CLUS_3                1                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KIAA1804 MUTATED        0      1      3      1      0      2      1      0
  KIAA1804 WILD-TYPE      6     11      9      8      6      7      7      2
D11V2, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 11
  CLUS_3                3                  9
  CLUS_4                1                  8
  CLUS_5                0                  6
  CLUS_6                2                  7
  CLUS_7                1                  7
  CLUS_8                0                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KIAA1804 MUTATED        2      4      3      0      0
  KIAA1804 WILD-TYPE     15     14     14     11      5
D11V3, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_2                2                 15
  CLUS_3                4                 14
  CLUS_4                3                 14
  CLUS_5                0                 11
  CLUS_6                0                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1804 MUTATED        2      2      4
  KIAA1804 WILD-TYPE     14     12     19
D11V4, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 12
  CLUS_3                4                 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
  KIAA1804 MUTATED        3      0      3      0      2
  KIAA1804 WILD-TYPE     17      9     11      2      6
D11V5, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                0                  9
  CLUS_3                3                 11
  CLUS_4                0                  2
  CLUS_5                2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1804 MUTATED        0      0      0      9
  KIAA1804 WILD-TYPE      1      4      2     52
D11V6, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                0                  4
  CLUS_3                0                  2
  CLUS_4                9                 52
[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_2 CLUS_3 CLUS_4
  KIAA1804 MUTATED        0      6      3
  KIAA1804 WILD-TYPE      1     32     26
D11V7, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_2                0                  1
  CLUS_3                6                 32
  CLUS_4                3                 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_3 CLUS_4 CLUS_5
  KIAA1804 MUTATED        0      0      0      9
  KIAA1804 WILD-TYPE      2      3      6     45
D11V8, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  2
  CLUS_3                0                  3
  CLUS_4                0                  6
  CLUS_5                9                 45
[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
  KIAA1804 MUTATED        0      0      9
  KIAA1804 WILD-TYPE      9      3     44
D11V9, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                0                  3
  CLUS_3                9                 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"

Clustering(12) Variable = CCDC88C MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC88C MUTATED        1      1      0
  CCDC88C WILD-TYPE     23     20     19
D12V1, multiclass
[1] "Remove cluster labels:" "CCDC88C MUTATED"       
clus
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                2                62 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3727 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3887 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CCDC88C MUTATED        1      0      0      0      0      1      0      0
  CCDC88C WILD-TYPE      5     12     12      9      6      8      8      2
D12V2, multiclass
[1] "Remove cluster labels:" "CCDC88C MUTATED"       
clus
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                2                62 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3727 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3887 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
                   vv
clus                CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CCDC88C MUTATED        0      1      1      0      0
  CCDC88C WILD-TYPE     17     17     16     11      5
D12V3, multiclass
[1] "Remove cluster labels:" "CCDC88C MUTATED"       
clus
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                2                66 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3727 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3887 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC88C MUTATED        1      1      0
  CCDC88C WILD-TYPE     15     13     23
D12V4, multiclass
[1] "Remove cluster labels:" "CCDC88C MUTATED"       
clus
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                2                51 
       TCGA-AF-2689        TCGA-AF-3400        TCGA-AF-3913        TCGA-AG-3574 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3578        TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3612        TCGA-AG-3727        TCGA-AG-3881 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3893        TCGA-AG-3896        TCGA-AG-3898 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-4001        TCGA-AG-4005 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A026 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CCDC88C MUTATED        1      1      0      0      0
  CCDC88C WILD-TYPE     19      8     14      2      8
D12V5, multiclass
[1] "Remove cluster labels:" "CCDC88C MUTATED"       
clus
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                2                51 
       TCGA-AF-2689        TCGA-AF-3400        TCGA-AF-3913        TCGA-AG-3574 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3578        TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3612        TCGA-AG-3727        TCGA-AG-3881 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3893        TCGA-AG-3896        TCGA-AG-3898 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-4001        TCGA-AG-4005 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A026 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X 
"CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" "CCDC88C WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC88C MUTATED        0      0      0      3
  CCDC88C WILD-TYPE      1      4      2     58
D12V6, multiclass
        clus
vv       CCDC88C MUTATED CCDC88C WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                 4
  CLUS_3               0                 2
  CLUS_4               3                58
[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_2 CLUS_3 CLUS_4
  CCDC88C MUTATED        0      1      2
  CCDC88C WILD-TYPE      1     37     27
D12V7, multiclass
        clus
vv       CCDC88C MUTATED CCDC88C WILD-TYPE
  CLUS_2               0                 1
  CLUS_3               1                37
  CLUS_4               2                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_3 CLUS_4 CLUS_5
  CCDC88C MUTATED        0      0      1      2
  CCDC88C WILD-TYPE      2      3      5     52
D12V8, multiclass
        clus
vv       CCDC88C MUTATED CCDC88C WILD-TYPE
  CLUS_1               0                 2
  CLUS_3               0                 3
  CLUS_4               1                 5
  CLUS_5               2                52
[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
  CCDC88C MUTATED        1      0      2
  CCDC88C WILD-TYPE      8      3     51
D12V9, multiclass
        clus
vv       CCDC88C MUTATED CCDC88C WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                 3
  CLUS_3               2                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"
