[1] "ofn"        "-oTLIHC-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/LIHC-TP/15111045/LIHC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15165528/transformed.cor.cli.txt"

nPatients in clinical file=377, in cluster file=198, common to both=198
[1]  18 198
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            62            136 
  TP53 MUTATED TP53 WILD-TYPE 
            62            136 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              51              147 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              51              147 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           15           183 
  RB1 MUTATED RB1 WILD-TYPE 
           15           183 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             189 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             189 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            188 
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            188 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            189 
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            189 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              16              182 
  ARID1A MUTATED ARID1A WILD-TYPE 
              16              182 
[1] "IL6ST MUTATION ANALYSIS"
[1] 3
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             191 
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             191 
[1] "ALB MUTATION ANALYSIS"
[1] 3
  ALB MUTATED ALB WILD-TYPE 
           18           180 
  ALB MUTATED ALB WILD-TYPE 
           18           180 
[1] "HNF1A MUTATION ANALYSIS"
[1] 3
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             190 
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             190 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            24            174 
  APOB MUTATED APOB WILD-TYPE 
            24            174 
[1] "EEF1A1 MUTATION ANALYSIS"
[1] 3
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              193 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              193 
[1] "KIF19 MUTATION ANALYSIS"
[1] 3
  KIF19 MUTATED KIF19 WILD-TYPE 
             10             188 
  KIF19 MUTATED KIF19 WILD-TYPE 
             10             188 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             7            191 
  GNAS MUTATED GNAS WILD-TYPE 
             7            191 
[1] "F5 MUTATION ANALYSIS"
[1] 3
  F5 MUTATED F5 WILD-TYPE 
           4          194 
  F5 MUTATED F5 WILD-TYPE 
           4          194 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            191 
  PTEN MUTATED PTEN WILD-TYPE 
             7            191 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                193 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                193 
[1] "DLK2 MUTATION ANALYSIS"
[1] 3
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            194 
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            194 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 198 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 198 columns, 0 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        9     29     24
  TP53 WILD-TYPE     37     33     61
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             37
  CLUS_2           29             33
  CLUS_3           24             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       19     27     16
  TP53 WILD-TYPE     38     56     42
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           19             38
  CLUS_2           27             56
  CLUS_3           16             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 CLUS_4 CLUS_5
  TP53 MUTATED       30     16      3      5      7
  TP53 WILD-TYPE     13     39     26     31     25
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30             13
  CLUS_2           16             39
  CLUS_3            3             26
  CLUS_4            5             31
  CLUS_5            7             25
[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 CLUS_5
  TP53 MUTATED       18     10     20      6      7
  TP53 WILD-TYPE     16     19     47     30     22
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             16
  CLUS_2           10             19
  CLUS_3           20             47
  CLUS_4            6             30
  CLUS_5            7             22
[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       16     25     10     10
  TP53 WILD-TYPE     22     43     17     50
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           16             22
  CLUS_2           25             43
  CLUS_3           10             17
  CLUS_4           10             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       14     25      6     14      2
  TP53 WILD-TYPE     10     33     18     52     19
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           14             10
  CLUS_2           25             33
  CLUS_3            6             18
  CLUS_4           14             52
  CLUS_5            2             19
[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       22     10     17     10
  TP53 WILD-TYPE     35     31     39     11
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           22             35
  CLUS_2           10             31
  CLUS_3           17             39
  CLUS_4           10             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       13     23     10     10      3
  TP53 WILD-TYPE     19     30     40     10     17
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           13             19
  CLUS_2           23             30
  CLUS_3           10             40
  CLUS_4           10             10
  CLUS_5            3             17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED       19     13     19
  CTNNB1 WILD-TYPE     27     49     66
D2V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             19               27
  CLUS_2             13               49
  CLUS_3             19               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        9     33      9
  CTNNB1 WILD-TYPE     48     50     49
D2V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              9               48
  CLUS_2             33               50
  CLUS_3              9               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 CLUS_4 CLUS_5
  CTNNB1 MUTATED        9      8      1      5     28
  CTNNB1 WILD-TYPE     34     47     28     31      4
D2V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              9               34
  CLUS_2              8               47
  CLUS_3              1               28
  CLUS_4              5               31
  CLUS_5             28                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 CLUS_5
  CTNNB1 MUTATED        3      7      9      7     25
  CTNNB1 WILD-TYPE     31     22     58     29      4
D2V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               31
  CLUS_2              7               22
  CLUS_3              9               58
  CLUS_4              7               29
  CLUS_5             25                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
  CTNNB1 MUTATED        9     25      7      9
  CTNNB1 WILD-TYPE     29     43     20     51
D2V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              9               29
  CLUS_2             25               43
  CLUS_3              7               20
  CLUS_4              9               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 CLUS_4 CLUS_5
  CTNNB1 MUTATED        8     11      2     11     18
  CTNNB1 WILD-TYPE     16     47     22     55      3
D2V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              8               16
  CLUS_2             11               47
  CLUS_3              2               22
  CLUS_4             11               55
  CLUS_5             18                3
[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
  CTNNB1 MUTATED        8      5     25      5
  CTNNB1 WILD-TYPE     49     36     31     16
D2V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              8               49
  CLUS_2              5               36
  CLUS_3             25               31
  CLUS_4              5               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 CLUS_4 CLUS_5
  CTNNB1 MUTATED        3     10      7      7     16
  CTNNB1 WILD-TYPE     29     43     43     13      4
D2V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               29
  CLUS_2             10               43
  CLUS_3              7               43
  CLUS_4              7               13
  CLUS_5             16                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"

Clustering(3) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        3      6      5
  RB1 WILD-TYPE     43     56     80
D3V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            43
  CLUS_2           6            56
  CLUS_3           5            80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      3     11
  RB1 WILD-TYPE     56     80     47
D3V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            56
  CLUS_2           3            80
  CLUS_3          11            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 CLUS_4 CLUS_5
  RB1 MUTATED        3      6      6      0      0
  RB1 WILD-TYPE     40     49     23     36     32
D3V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            40
  CLUS_2           6            49
  CLUS_3           6            23
  CLUS_4           0            36
  CLUS_5           0            32
[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 CLUS_5
  RB1 MUTATED        3      1      8      3      0
  RB1 WILD-TYPE     31     28     59     33     29
D3V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            31
  CLUS_2           1            28
  CLUS_3           8            59
  CLUS_4           3            33
  CLUS_5           0            29
[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
  RB1 MUTATED        0      6      2      6
  RB1 WILD-TYPE     38     62     25     54
D3V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            38
  CLUS_2           6            62
  CLUS_3           2            25
  CLUS_4           6            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_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RB1 MUTATED        1      3      2      8      0
  RB1 WILD-TYPE     23     55     22     58     21
D3V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            23
  CLUS_2           3            55
  CLUS_3           2            22
  CLUS_4           8            58
  CLUS_5           0            21
[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
  RB1 MUTATED        6      4      1      1
  RB1 WILD-TYPE     51     37     55     20
D3V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           6            51
  CLUS_2           4            37
  CLUS_3           1            55
  CLUS_4           1            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 CLUS_4 CLUS_5
  RB1 MUTATED        5      3      3      1      0
  RB1 WILD-TYPE     27     50     47     19     20
D3V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           5            27
  CLUS_2           3            50
  CLUS_3           3            47
  CLUS_4           1            19
  CLUS_5           0            20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AXIN1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AXIN1 MUTATED        2      5      2
  AXIN1 WILD-TYPE     44     57     83
D4V1, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             2              44
  CLUS_2             5              57
  CLUS_3             2              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  AXIN1 MUTATED        1      4      4
  AXIN1 WILD-TYPE     56     79     54
D4V2, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             4              79
  CLUS_3             4              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 CLUS_4 CLUS_5
  AXIN1 MUTATED        1      3      5      0      0
  AXIN1 WILD-TYPE     42     52     24     36     32
D4V3, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             1              42
  CLUS_2             3              52
  CLUS_3             5              24
  CLUS_4             0              36
  CLUS_5             0              32
[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 CLUS_5
  AXIN1 MUTATED        1      0      4      4      0
  AXIN1 WILD-TYPE     33     29     63     32     29
D4V4, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             1              33
  CLUS_2             0              29
  CLUS_3             4              63
  CLUS_4             4              32
  CLUS_5             0              29
[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
  AXIN1 MUTATED        0      4      4      0
  AXIN1 WILD-TYPE     38     64     23     60
D4V5, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             0              38
  CLUS_2             4              64
  CLUS_3             4              23
  CLUS_4             0              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AXIN1 MUTATED        1      1      2      4      0
  AXIN1 WILD-TYPE     23     57     22     62     21
D4V6, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             1              23
  CLUS_2             1              57
  CLUS_3             2              22
  CLUS_4             4              62
  CLUS_5             0              21
[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
  AXIN1 MUTATED        1      0      2      4
  AXIN1 WILD-TYPE     56     41     54     17
D4V7, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             0              41
  CLUS_3             2              54
  CLUS_4             4              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 CLUS_4 CLUS_5
  AXIN1 MUTATED        0      2      3      1      1
  AXIN1 WILD-TYPE     32     51     47     19     19
D4V8, multiclass
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             2              51
  CLUS_3             3              47
  CLUS_4             1              19
  CLUS_5             1              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        2      2      6
  BAP1 WILD-TYPE     44     60     79
D5V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            2             44
  CLUS_2            2             60
  CLUS_3            6             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        5      0      5
  BAP1 WILD-TYPE     52     83     53
D5V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            5             52
  CLUS_2            0             83
  CLUS_3            5             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 CLUS_4 CLUS_5
  BAP1 MUTATED        1      0      4      5      0
  BAP1 WILD-TYPE     42     55     25     31     32
D5V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             42
  CLUS_2            0             55
  CLUS_3            4             25
  CLUS_4            5             31
  CLUS_5            0             32
[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 CLUS_5
  BAP1 MUTATED        5      0      0      5      0
  BAP1 WILD-TYPE     29     29     67     31     29
D5V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            5             29
  CLUS_2            0             29
  CLUS_3            0             67
  CLUS_4            5             31
  CLUS_5            0             29
[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
  BAP1 MUTATED        0      0      0     10
  BAP1 WILD-TYPE     38     68     27     50
D5V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             38
  CLUS_2            0             68
  CLUS_3            0             27
  CLUS_4           10             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BAP1 MUTATED        0      0      2      8      0
  BAP1 WILD-TYPE     24     58     22     58     21
D5V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             24
  CLUS_2            0             58
  CLUS_3            2             22
  CLUS_4            8             58
  CLUS_5            0             21
[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
  BAP1 MUTATED        4      5      0      1
  BAP1 WILD-TYPE     53     36     56     20
D5V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4             53
  CLUS_2            5             36
  CLUS_3            0             56
  CLUS_4            1             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 CLUS_4 CLUS_5
  BAP1 MUTATED        1      1      8      0      0
  BAP1 WILD-TYPE     31     52     42     20     20
D5V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             31
  CLUS_2            1             52
  CLUS_3            8             42
  CLUS_4            0             20
  CLUS_5            0             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = TSC2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC2 MUTATED        2      2      5
  TSC2 WILD-TYPE     44     60     80
D6V1, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            2             44
  CLUS_2            2             60
  CLUS_3            5             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC2 MUTATED        6      3      0
  TSC2 WILD-TYPE     51     80     58
D6V2, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            6             51
  CLUS_2            3             80
  CLUS_3            0             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  TSC2 MUTATED        5      1      2      1      0
  TSC2 WILD-TYPE     38     54     27     35     32
D6V3, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            5             38
  CLUS_2            1             54
  CLUS_3            2             27
  CLUS_4            1             35
  CLUS_5            0             32
[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 CLUS_5
  TSC2 MUTATED        5      0      4      0      0
  TSC2 WILD-TYPE     29     29     63     36     29
D6V4, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            5             29
  CLUS_2            0             29
  CLUS_3            4             63
  CLUS_4            0             36
  CLUS_5            0             29
[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
  TSC2 MUTATED        2      4      0      3
  TSC2 WILD-TYPE     36     64     27     57
D6V5, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            2             36
  CLUS_2            4             64
  CLUS_3            0             27
  CLUS_4            3             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TSC2 MUTATED        2      2      2      2      1
  TSC2 WILD-TYPE     22     56     22     64     20
D6V6, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            2             22
  CLUS_2            2             56
  CLUS_3            2             22
  CLUS_4            2             64
  CLUS_5            1             20
[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
  TSC2 MUTATED        4      2      3      0
  TSC2 WILD-TYPE     53     39     53     21
D6V7, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            4             53
  CLUS_2            2             39
  CLUS_3            3             53
  CLUS_4            0             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 CLUS_4 CLUS_5
  TSC2 MUTATED        4      1      1      1      2
  TSC2 WILD-TYPE     28     52     49     19     18
D6V8, multiclass
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  CLUS_1            4             28
  CLUS_2            1             52
  CLUS_3            1             49
  CLUS_4            1             19
  CLUS_5            2             18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      6      6
  ARID1A WILD-TYPE     43     56     79
D7V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               43
  CLUS_2              6               56
  CLUS_3              6               79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        5      4      7
  ARID1A WILD-TYPE     52     79     51
D7V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               52
  CLUS_2              4               79
  CLUS_3              7               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 CLUS_4 CLUS_5
  ARID1A MUTATED        2      2      6      2      4
  ARID1A WILD-TYPE     41     53     23     34     28
D7V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               41
  CLUS_2              2               53
  CLUS_3              6               23
  CLUS_4              2               34
  CLUS_5              4               28
[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 CLUS_5
  ARID1A MUTATED        1      2      2      7      4
  ARID1A WILD-TYPE     33     27     65     29     25
D7V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               33
  CLUS_2              2               27
  CLUS_3              2               65
  CLUS_4              7               29
  CLUS_5              4               25
[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        4      5      5      2
  ARID1A WILD-TYPE     34     63     22     58
D7V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               34
  CLUS_2              5               63
  CLUS_3              5               22
  CLUS_4              2               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_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        3      3      3      6      1
  ARID1A WILD-TYPE     21     55     21     60     20
D7V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               21
  CLUS_2              3               55
  CLUS_3              3               21
  CLUS_4              6               60
  CLUS_5              1               20
[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        4      3      2      6
  ARID1A WILD-TYPE     53     38     54     15
D7V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               53
  CLUS_2              3               38
  CLUS_3              2               54
  CLUS_4              6               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 CLUS_4 CLUS_5
  ARID1A MUTATED        2      3      6      3      1
  ARID1A WILD-TYPE     30     50     44     17     19
D7V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               30
  CLUS_2              3               50
  CLUS_3              6               44
  CLUS_4              3               17
  CLUS_5              1               19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = IL6ST MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IL6ST MUTATED        0      2      4
  IL6ST WILD-TYPE     46     60     81
D8V1, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             0              46
  CLUS_2             2              60
  CLUS_3             4              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IL6ST MUTATED        3      1      3
  IL6ST WILD-TYPE     54     82     55
D8V2, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             3              54
  CLUS_2             1              82
  CLUS_3             3              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 CLUS_4 CLUS_5
  IL6ST MUTATED        1      1      2      0      3
  IL6ST WILD-TYPE     42     54     27     36     29
D8V3, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             1              42
  CLUS_2             1              54
  CLUS_3             2              27
  CLUS_4             0              36
  CLUS_5             3              29
[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 CLUS_5
  IL6ST MUTATED        0      1      1      2      3
  IL6ST WILD-TYPE     34     28     66     34     26
D8V4, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             0              34
  CLUS_2             1              28
  CLUS_3             1              66
  CLUS_4             2              34
  CLUS_5             3              26
[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
  IL6ST MUTATED        0      3      2      2
  IL6ST WILD-TYPE     38     65     25     58
D8V5, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             0              38
  CLUS_2             3              65
  CLUS_3             2              25
  CLUS_4             2              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_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IL6ST MUTATED        0      0      1      4      2
  IL6ST WILD-TYPE     24     58     23     62     19
D8V6, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             0              24
  CLUS_2             0              58
  CLUS_3             1              23
  CLUS_4             4              62
  CLUS_5             2              19
[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
  IL6ST MUTATED        2      0      3      1
  IL6ST WILD-TYPE     55     41     53     20
D8V7, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             2              55
  CLUS_2             0              41
  CLUS_3             3              53
  CLUS_4             1              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 CLUS_4 CLUS_5
  IL6ST MUTATED        1      2      2      0      1
  IL6ST WILD-TYPE     31     51     48     20     19
D8V8, multiclass
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  CLUS_1             1              31
  CLUS_2             2              51
  CLUS_3             2              48
  CLUS_4             0              20
  CLUS_5             1              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = ALB MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ALB MUTATED        8      2      7
  ALB WILD-TYPE     38     60     78
D9V1, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           8            38
  CLUS_2           2            60
  CLUS_3           7            78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ALB MUTATED        5     12      1
  ALB WILD-TYPE     52     71     57
D9V2, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           5            52
  CLUS_2          12            71
  CLUS_3           1            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  ALB MUTATED        4      6      0      4      3
  ALB WILD-TYPE     39     49     29     32     29
D9V3, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           4            39
  CLUS_2           6            49
  CLUS_3           0            29
  CLUS_4           4            32
  CLUS_5           3            29
[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 CLUS_5
  ALB MUTATED        3      4      6      1      3
  ALB WILD-TYPE     31     25     61     35     26
D9V4, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           3            31
  CLUS_2           4            25
  CLUS_3           6            61
  CLUS_4           1            35
  CLUS_5           3            26
[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
  ALB MUTATED        4      6      1      5
  ALB WILD-TYPE     34     62     26     55
D9V5, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           4            34
  CLUS_2           6            62
  CLUS_3           1            26
  CLUS_4           5            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ALB MUTATED        3      5      2      4      2
  ALB WILD-TYPE     21     53     22     62     19
D9V6, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           3            21
  CLUS_2           5            53
  CLUS_3           2            22
  CLUS_4           4            62
  CLUS_5           2            19
[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
  ALB MUTATED        4      4      6      0
  ALB WILD-TYPE     53     37     50     21
D9V7, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           4            53
  CLUS_2           4            37
  CLUS_3           6            50
  CLUS_4           0            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 CLUS_4 CLUS_5
  ALB MUTATED        1      5      2      3      3
  ALB WILD-TYPE     31     48     48     17     17
D9V8, multiclass
        clus
vv       ALB MUTATED ALB WILD-TYPE
  CLUS_1           1            31
  CLUS_2           5            48
  CLUS_3           2            48
  CLUS_4           3            17
  CLUS_5           3            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = HNF1A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HNF1A MUTATED        0      2      6
  HNF1A WILD-TYPE     46     60     79
D10V1, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             0              46
  CLUS_2             2              60
  CLUS_3             6              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HNF1A MUTATED        3      4      1
  HNF1A WILD-TYPE     54     79     57
D10V2, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             3              54
  CLUS_2             4              79
  CLUS_3             1              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  HNF1A MUTATED        1      6      0      0      1
  HNF1A WILD-TYPE     42     49     29     36     31
D10V3, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             1              42
  CLUS_2             6              49
  CLUS_3             0              29
  CLUS_4             0              36
  CLUS_5             1              31
[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 CLUS_5
  HNF1A MUTATED        1      1      5      0      1
  HNF1A WILD-TYPE     33     28     62     36     28
D10V4, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             1              33
  CLUS_2             1              28
  CLUS_3             5              62
  CLUS_4             0              36
  CLUS_5             1              28
[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
  HNF1A MUTATED        1      5      2      0
  HNF1A WILD-TYPE     37     63     25     60
D10V5, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             1              37
  CLUS_2             5              63
  CLUS_3             2              25
  CLUS_4             0              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HNF1A MUTATED        0      6      0      2      0
  HNF1A WILD-TYPE     24     52     24     64     21
D10V6, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             0              24
  CLUS_2             6              52
  CLUS_3             0              24
  CLUS_4             2              64
  CLUS_5             0              21
[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
  HNF1A MUTATED        0      0      5      2
  HNF1A WILD-TYPE     57     41     51     19
D10V7, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             0              57
  CLUS_2             0              41
  CLUS_3             5              51
  CLUS_4             2              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 CLUS_4 CLUS_5
  HNF1A MUTATED        1      5      1      0      0
  HNF1A WILD-TYPE     31     48     49     20     20
D10V8, multiclass
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  CLUS_1             1              31
  CLUS_2             5              48
  CLUS_3             1              49
  CLUS_4             0              20
  CLUS_5             0              20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = APOB MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        5      7     10
  APOB WILD-TYPE     41     55     75
D11V1, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            5             41
  CLUS_2            7             55
  CLUS_3           10             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        6     10      8
  APOB WILD-TYPE     51     73     50
D11V2, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            6             51
  CLUS_2           10             73
  CLUS_3            8             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APOB MUTATED        3      6      4      2      8
  APOB WILD-TYPE     40     49     25     34     24
D11V3, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            3             40
  CLUS_2            6             49
  CLUS_3            4             25
  CLUS_4            2             34
  CLUS_5            8             24
[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 CLUS_5
  APOB MUTATED        4      2      7      2      8
  APOB WILD-TYPE     30     27     60     34     21
D11V4, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            4             30
  CLUS_2            2             27
  CLUS_3            7             60
  CLUS_4            2             34
  CLUS_5            8             21
[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
  APOB MUTATED        8      6      4      6
  APOB WILD-TYPE     30     62     23     54
D11V5, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            8             30
  CLUS_2            6             62
  CLUS_3            4             23
  CLUS_4            6             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_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APOB MUTATED        3      7      0      8      6
  APOB WILD-TYPE     21     51     24     58     15
D11V6, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            3             21
  CLUS_2            7             51
  CLUS_3            0             24
  CLUS_4            8             58
  CLUS_5            6             15
[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
  APOB MUTATED        6      3     11      1
  APOB WILD-TYPE     51     38     45     20
D11V7, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            6             51
  CLUS_2            3             38
  CLUS_3           11             45
  CLUS_4            1             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 CLUS_4 CLUS_5
  APOB MUTATED        1      5      5      3      7
  APOB WILD-TYPE     31     48     45     17     13
D11V8, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1             31
  CLUS_2            5             48
  CLUS_3            5             45
  CLUS_4            3             17
  CLUS_5            7             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = EEF1A1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EEF1A1 MUTATED        0      0      5
  EEF1A1 WILD-TYPE     46     62     80
D12V1, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              0               46
  CLUS_2              0               62
  CLUS_3              5               80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EEF1A1 MUTATED        1      3      1
  EEF1A1 WILD-TYPE     56     80     57
D12V2, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              1               56
  CLUS_2              3               80
  CLUS_3              1               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  EEF1A1 MUTATED        0      1      0      2      2
  EEF1A1 WILD-TYPE     43     54     29     34     30
D12V3, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              0               43
  CLUS_2              1               54
  CLUS_3              0               29
  CLUS_4              2               34
  CLUS_5              2               30
[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 CLUS_5
  EEF1A1 MUTATED        0      2      1      0      2
  EEF1A1 WILD-TYPE     34     27     66     36     27
D12V4, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              0               34
  CLUS_2              2               27
  CLUS_3              1               66
  CLUS_4              0               36
  CLUS_5              2               27
[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
  EEF1A1 MUTATED        1      1      0      3
  EEF1A1 WILD-TYPE     37     67     27     57
D12V5, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              1               37
  CLUS_2              1               67
  CLUS_3              0               27
  CLUS_4              3               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EEF1A1 MUTATED        1      2      1      0      1
  EEF1A1 WILD-TYPE     23     56     23     66     20
D12V6, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              1               23
  CLUS_2              2               56
  CLUS_3              1               23
  CLUS_4              0               66
  CLUS_5              1               20
[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
  EEF1A1 MUTATED        0      2      3      0
  EEF1A1 WILD-TYPE     57     39     53     21
D12V7, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              0               57
  CLUS_2              2               39
  CLUS_3              3               53
  CLUS_4              0               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 CLUS_4 CLUS_5
  EEF1A1 MUTATED        0      2      1      1      1
  EEF1A1 WILD-TYPE     32     51     49     19     19
D12V8, multiclass
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              2               51
  CLUS_3              1               49
  CLUS_4              1               19
  CLUS_5              1               19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = KIF19 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KIF19 MUTATED        2      4      4
  KIF19 WILD-TYPE     44     58     81
D13V1, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             2              44
  CLUS_2             4              58
  CLUS_3             4              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KIF19 MUTATED        0      6      4
  KIF19 WILD-TYPE     57     77     54
D13V2, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             0              57
  CLUS_2             6              77
  CLUS_3             4              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 CLUS_4 CLUS_5
  KIF19 MUTATED        4      3      0      0      2
  KIF19 WILD-TYPE     39     52     29     36     30
D13V3, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             4              39
  CLUS_2             3              52
  CLUS_3             0              29
  CLUS_4             0              36
  CLUS_5             2              30
[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 CLUS_5
  KIF19 MUTATED        3      0      4      0      2
  KIF19 WILD-TYPE     31     29     63     36     27
D13V4, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             3              31
  CLUS_2             0              29
  CLUS_3             4              63
  CLUS_4             0              36
  CLUS_5             2              27
[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
  KIF19 MUTATED        1      6      0      3
  KIF19 WILD-TYPE     37     62     27     57
D13V5, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             1              37
  CLUS_2             6              62
  CLUS_3             0              27
  CLUS_4             3              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIF19 MUTATED        2      3      0      4      1
  KIF19 WILD-TYPE     22     55     24     62     20
D13V6, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             3              55
  CLUS_3             0              24
  CLUS_4             4              62
  CLUS_5             1              20
[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
  KIF19 MUTATED        5      0      4      0
  KIF19 WILD-TYPE     52     41     52     21
D13V7, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             5              52
  CLUS_2             0              41
  CLUS_3             4              52
  CLUS_4             0              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 CLUS_4 CLUS_5
  KIF19 MUTATED        4      3      0      1      1
  KIF19 WILD-TYPE     28     50     50     19     19
D13V8, multiclass
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  CLUS_1             4              28
  CLUS_2             3              50
  CLUS_3             0              50
  CLUS_4             1              19
  CLUS_5             1              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = GNAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GNAS MUTATED        1      2      4
  GNAS WILD-TYPE     45     60     81
D14V1, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            1             45
  CLUS_2            2             60
  CLUS_3            4             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GNAS MUTATED        2      1      4
  GNAS WILD-TYPE     55     82     54
D14V2, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            2             55
  CLUS_2            1             82
  CLUS_3            4             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 CLUS_4 CLUS_5
  GNAS MUTATED        0      1      2      4      0
  GNAS WILD-TYPE     43     54     27     32     32
D14V3, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            0             43
  CLUS_2            1             54
  CLUS_3            2             27
  CLUS_4            4             32
  CLUS_5            0             32
[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 CLUS_5
  GNAS MUTATED        1      3      1      2      0
  GNAS WILD-TYPE     33     26     66     34     29
D14V4, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            1             33
  CLUS_2            3             26
  CLUS_3            1             66
  CLUS_4            2             34
  CLUS_5            0             29
[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
  GNAS MUTATED        0      1      0      5
  GNAS WILD-TYPE     38     67     27     55
D14V5, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            0             38
  CLUS_2            1             67
  CLUS_3            0             27
  CLUS_4            5             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GNAS MUTATED        0      1      2      3      0
  GNAS WILD-TYPE     24     57     22     63     21
D14V6, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            0             24
  CLUS_2            1             57
  CLUS_3            2             22
  CLUS_4            3             63
  CLUS_5            0             21
[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
  GNAS MUTATED        2      3      1      0
  GNAS WILD-TYPE     55     38     55     21
D14V7, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            2             55
  CLUS_2            3             38
  CLUS_3            1             55
  CLUS_4            0             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 CLUS_4 CLUS_5
  GNAS MUTATED        1      1      3      0      1
  GNAS WILD-TYPE     31     52     47     20     19
D14V8, multiclass
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  CLUS_1            1             31
  CLUS_2            1             52
  CLUS_3            3             47
  CLUS_4            0             20
  CLUS_5            1             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = F5 MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  F5 MUTATED        1      2      1
  F5 WILD-TYPE     45     60     84
D15V1, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          1           45
  CLUS_2          2           60
  CLUS_3          1           84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  F5 MUTATED        0      1      3
  F5 WILD-TYPE     57     82     55
D15V2, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          0           57
  CLUS_2          1           82
  CLUS_3          3           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 CLUS_4 CLUS_5
  F5 MUTATED        1      2      1      0      0
  F5 WILD-TYPE     42     53     28     36     32
D15V3, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          1           42
  CLUS_2          2           53
  CLUS_3          1           28
  CLUS_4          0           36
  CLUS_5          0           32
[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 CLUS_5
  F5 MUTATED        0      0      3      1      0
  F5 WILD-TYPE     34     29     64     35     29
D15V4, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          0           34
  CLUS_2          0           29
  CLUS_3          3           64
  CLUS_4          1           35
  CLUS_5          0           29
[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
  F5 MUTATED        0      4      0      0
  F5 WILD-TYPE     38     64     27     60
D15V5, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          0           38
  CLUS_2          4           64
  CLUS_3          0           27
  CLUS_4          0           60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  F5 MUTATED        0      1      1      2      0
  F5 WILD-TYPE     24     57     23     64     21
D15V6, multiclass
        clus
vv       F5 MUTATED F5 WILD-TYPE
  CLUS_1          0           24
  CLUS_2          1           57
  CLUS_3          1           23
  CLUS_4          2           64
  CLUS_5          0           21
[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
  F5 MUTATED        2      0      0      0
  F5 WILD-TYPE     55     41     56     21
D15V7, multiclass
[1] "Remove cluster labels:" "F5 MUTATED"            
clus
  F5 MUTATED F5 WILD-TYPE 
           2          173 
  TCGA-BC-4073   TCGA-BC-A10Q   TCGA-BC-A10R   TCGA-BC-A10T   TCGA-BC-A10U 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A10W   TCGA-BC-A10X   TCGA-BC-A10Y   TCGA-BC-A10Z   TCGA-BC-A110 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A112   TCGA-BC-A216   TCGA-BC-A217   TCGA-BC-A3KF   TCGA-BC-A3KG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A5W4   TCGA-BC-A69H   TCGA-BD-A2L6   TCGA-BD-A3EP   TCGA-BW-A5NO 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BW-A5NP   TCGA-BW-A5NQ   TCGA-CC-5258   TCGA-CC-5259   TCGA-CC-5260 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-5261   TCGA-CC-5262   TCGA-CC-5263   TCGA-CC-5264   TCGA-CC-A123 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A1HT   TCGA-CC-A3M9   TCGA-CC-A3MA   TCGA-CC-A3MB   TCGA-CC-A3MC 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A5UC   TCGA-CC-A5UD   TCGA-CC-A5UE   TCGA-CC-A7IF   TCGA-CC-A7IG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A7IH   TCGA-CC-A7II   TCGA-CC-A7IJ   TCGA-CC-A7IK   TCGA-DD-A113 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A114   TCGA-DD-A115   TCGA-DD-A116   TCGA-DD-A118   TCGA-DD-A119 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A11A   TCGA-DD-A11B   TCGA-DD-A11C   TCGA-DD-A11D   TCGA-DD-A1EA 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A1EB   TCGA-DD-A1EC   TCGA-DD-A1ED   TCGA-DD-A1EF   TCGA-DD-A1EG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A1EH   TCGA-DD-A1EI   TCGA-DD-A1EJ   TCGA-DD-A1EK   TCGA-DD-A1EL 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A39V   TCGA-DD-A39W   TCGA-DD-A39X   TCGA-DD-A39Y   TCGA-DD-A39Z 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A3A0   TCGA-DD-A3A1   TCGA-DD-A3A3   TCGA-DD-A3A5   TCGA-DD-A3A6 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A3A7   TCGA-DD-A3A9   TCGA-DD-A4NA   TCGA-DD-A4ND   TCGA-DD-A4NE 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A4NF   TCGA-DD-A4NG   TCGA-DD-A4NH   TCGA-DD-A4NI   TCGA-DD-A4NN 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A4NO   TCGA-DD-A4NP   TCGA-DD-A4NQ   TCGA-DD-A4NS   TCGA-DD-A73A 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A73B   TCGA-DD-A73C   TCGA-DD-A73D   TCGA-DD-A73F   TCGA-DD-A73G 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A4XI   TCGA-ED-A5KG   TCGA-ED-A627   TCGA-ED-A66X   TCGA-ED-A66Y 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A7PX   TCGA-ED-A7PY   TCGA-ED-A7PZ   TCGA-ED-A7XO   TCGA-ED-A7XP 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A82E   TCGA-EP-A12J   TCGA-EP-A26S   TCGA-EP-A2KA   TCGA-EP-A2KC 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-EP-A3JL   TCGA-EP-A3RK   TCGA-ES-A2HT   TCGA-FV-A23B   TCGA-FV-A2QQ 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-FV-A2QR   TCGA-FV-A3I0   TCGA-FV-A3I1   TCGA-FV-A495   TCGA-FV-A496 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-FV-A4ZP   TCGA-FV-A4ZQ   TCGA-G3-A25S   TCGA-G3-A25T   TCGA-G3-A25U 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A25V   TCGA-G3-A25W   TCGA-G3-A25Y   TCGA-G3-A25Z   TCGA-G3-A3CH 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A3CI   TCGA-G3-A3CJ   TCGA-G3-A3CK   TCGA-G3-A5SI   TCGA-G3-A5SJ 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A5SK   TCGA-G3-A5SL   TCGA-G3-A5SM   TCGA-G3-A7M6   TCGA-G3-A7M7 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A7M9   TCGA-GJ-A6C0   TCGA-HP-A5MZ   TCGA-HP-A5N0   TCGA-K7-A5RF 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-K7-A5RG   TCGA-KR-A7K0   TCGA-KR-A7K2   TCGA-KR-A7K7   TCGA-KR-A7K8 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-LG-A6GG   TCGA-MI-A75C   TCGA-MI-A75E   TCGA-MI-A75G   TCGA-MI-A75H 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-MI-A75I   TCGA-NI-A4U2   TCGA-O8-A75V   TCGA-PD-A5DF   TCGA-QA-A7B7 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-RC-A6M3   TCGA-RC-A6M4   TCGA-RC-A6M5   TCGA-RC-A6M6   TCGA-RC-A7SB 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-RC-A7SF   TCGA-RC-A7SK   TCGA-RG-A7D4   TCGA-T1-A6J8   TCGA-UB-A7MA 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-UB-A7MD   TCGA-UB-A7ME   TCGA-UB-A7MF 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  F5 MUTATED        2      0      0      0      0
  F5 WILD-TYPE     30     53     50     20     20
D15V8, multiclass
[1] "Remove cluster labels:" "F5 MUTATED"            
clus
  F5 MUTATED F5 WILD-TYPE 
           2          173 
  TCGA-BC-4073   TCGA-BC-A10Q   TCGA-BC-A10R   TCGA-BC-A10T   TCGA-BC-A10U 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A10W   TCGA-BC-A10X   TCGA-BC-A10Y   TCGA-BC-A10Z   TCGA-BC-A110 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A112   TCGA-BC-A216   TCGA-BC-A217   TCGA-BC-A3KF   TCGA-BC-A3KG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BC-A5W4   TCGA-BC-A69H   TCGA-BD-A2L6   TCGA-BD-A3EP   TCGA-BW-A5NO 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-BW-A5NP   TCGA-BW-A5NQ   TCGA-CC-5258   TCGA-CC-5259   TCGA-CC-5260 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-5261   TCGA-CC-5262   TCGA-CC-5263   TCGA-CC-5264   TCGA-CC-A123 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A1HT   TCGA-CC-A3M9   TCGA-CC-A3MA   TCGA-CC-A3MB   TCGA-CC-A3MC 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A5UC   TCGA-CC-A5UD   TCGA-CC-A5UE   TCGA-CC-A7IF   TCGA-CC-A7IG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-CC-A7IH   TCGA-CC-A7II   TCGA-CC-A7IJ   TCGA-CC-A7IK   TCGA-DD-A113 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A114   TCGA-DD-A115   TCGA-DD-A116   TCGA-DD-A118   TCGA-DD-A119 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A11A   TCGA-DD-A11B   TCGA-DD-A11C   TCGA-DD-A11D   TCGA-DD-A1EA 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A1EB   TCGA-DD-A1EC   TCGA-DD-A1ED   TCGA-DD-A1EF   TCGA-DD-A1EG 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A1EH   TCGA-DD-A1EI   TCGA-DD-A1EJ   TCGA-DD-A1EK   TCGA-DD-A1EL 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A39V   TCGA-DD-A39W   TCGA-DD-A39X   TCGA-DD-A39Y   TCGA-DD-A39Z 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A3A0   TCGA-DD-A3A1   TCGA-DD-A3A3   TCGA-DD-A3A5   TCGA-DD-A3A6 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A3A7   TCGA-DD-A3A9   TCGA-DD-A4NA   TCGA-DD-A4ND   TCGA-DD-A4NE 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A4NF   TCGA-DD-A4NG   TCGA-DD-A4NH   TCGA-DD-A4NI   TCGA-DD-A4NN 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A4NO   TCGA-DD-A4NP   TCGA-DD-A4NQ   TCGA-DD-A4NS   TCGA-DD-A73A 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-DD-A73B   TCGA-DD-A73C   TCGA-DD-A73D   TCGA-DD-A73F   TCGA-DD-A73G 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A4XI   TCGA-ED-A5KG   TCGA-ED-A627   TCGA-ED-A66X   TCGA-ED-A66Y 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A7PX   TCGA-ED-A7PY   TCGA-ED-A7PZ   TCGA-ED-A7XO   TCGA-ED-A7XP 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-ED-A82E   TCGA-EP-A12J   TCGA-EP-A26S   TCGA-EP-A2KA   TCGA-EP-A2KC 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-EP-A3JL   TCGA-EP-A3RK   TCGA-ES-A2HT   TCGA-FV-A23B   TCGA-FV-A2QQ 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-FV-A2QR   TCGA-FV-A3I0   TCGA-FV-A3I1   TCGA-FV-A495   TCGA-FV-A496 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-FV-A4ZP   TCGA-FV-A4ZQ   TCGA-G3-A25S   TCGA-G3-A25T   TCGA-G3-A25U 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A25V   TCGA-G3-A25W   TCGA-G3-A25Y   TCGA-G3-A25Z   TCGA-G3-A3CH 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A3CI   TCGA-G3-A3CJ   TCGA-G3-A3CK   TCGA-G3-A5SI   TCGA-G3-A5SJ 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A5SK   TCGA-G3-A5SL   TCGA-G3-A5SM   TCGA-G3-A7M6   TCGA-G3-A7M7 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-G3-A7M9   TCGA-GJ-A6C0   TCGA-HP-A5MZ   TCGA-HP-A5N0   TCGA-K7-A5RF 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-K7-A5RG   TCGA-KR-A7K0   TCGA-KR-A7K2   TCGA-KR-A7K7   TCGA-KR-A7K8 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-LG-A6GG   TCGA-MI-A75C   TCGA-MI-A75E   TCGA-MI-A75G   TCGA-MI-A75H 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-MI-A75I   TCGA-NI-A4U2   TCGA-O8-A75V   TCGA-PD-A5DF   TCGA-QA-A7B7 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-RC-A6M3   TCGA-RC-A6M4   TCGA-RC-A6M5   TCGA-RC-A6M6   TCGA-RC-A7SB 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-RC-A7SF   TCGA-RC-A7SK   TCGA-RG-A7D4   TCGA-T1-A6J8   TCGA-UB-A7MA 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 
  TCGA-UB-A7MD   TCGA-UB-A7ME   TCGA-UB-A7MF 
"F5 WILD-TYPE" "F5 WILD-TYPE" "F5 WILD-TYPE" 

Clustering(16) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      2      4
  PTEN WILD-TYPE     46     60     81
D16V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             46
  CLUS_2            2             60
  CLUS_3            4             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      4      3
  PTEN WILD-TYPE     57     79     55
D16V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             57
  CLUS_2            4             79
  CLUS_3            3             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 CLUS_4 CLUS_5
  PTEN MUTATED        1      4      0      0      1
  PTEN WILD-TYPE     42     51     29     36     31
D16V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             42
  CLUS_2            4             51
  CLUS_3            0             29
  CLUS_4            0             36
  CLUS_5            1             31
[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 CLUS_5
  PTEN MUTATED        1      0      4      0      1
  PTEN WILD-TYPE     33     29     63     36     28
D16V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             33
  CLUS_2            0             29
  CLUS_3            4             63
  CLUS_4            0             36
  CLUS_5            1             28
[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
  PTEN MUTATED        1      3      0      3
  PTEN WILD-TYPE     37     65     27     57
D16V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             37
  CLUS_2            3             65
  CLUS_3            0             27
  CLUS_4            3             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        0      5      0      2      0
  PTEN WILD-TYPE     24     53     24     64     21
D16V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             24
  CLUS_2            5             53
  CLUS_3            0             24
  CLUS_4            2             64
  CLUS_5            0             21
[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
  PTEN MUTATED        3      1      3      0
  PTEN WILD-TYPE     54     40     53     21
D16V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             54
  CLUS_2            1             40
  CLUS_3            3             53
  CLUS_4            0             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 CLUS_4 CLUS_5
  PTEN MUTATED        1      5      1      0      0
  PTEN WILD-TYPE     31     48     49     20     20
D16V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             31
  CLUS_2            5             48
  CLUS_3            1             49
  CLUS_4            0             20
  CLUS_5            0             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = HIST1H1C MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  HIST1H1C MUTATED        2      1      2
  HIST1H1C WILD-TYPE     44     61     83
D17V1, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                1                 61
  CLUS_3                2                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  HIST1H1C MUTATED        1      3      1
  HIST1H1C WILD-TYPE     56     80     57
D17V2, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                3                 80
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  HIST1H1C MUTATED        0      1      1      1      2
  HIST1H1C WILD-TYPE     43     54     28     35     30
D17V3, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                0                 43
  CLUS_2                1                 54
  CLUS_3                1                 28
  CLUS_4                1                 35
  CLUS_5                2                 30
[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 CLUS_5
  HIST1H1C MUTATED        1      1      1      0      2
  HIST1H1C WILD-TYPE     33     28     66     36     27
D17V4, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                1                 33
  CLUS_2                1                 28
  CLUS_3                1                 66
  CLUS_4                0                 36
  CLUS_5                2                 27
[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
  HIST1H1C MUTATED        1      3      0      1
  HIST1H1C WILD-TYPE     37     65     27     59
D17V5, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                3                 65
  CLUS_3                0                 27
  CLUS_4                1                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HIST1H1C MUTATED        0      1      1      1      2
  HIST1H1C WILD-TYPE     24     57     23     65     19
D17V6, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                0                 24
  CLUS_2                1                 57
  CLUS_3                1                 23
  CLUS_4                1                 65
  CLUS_5                2                 19
[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
  HIST1H1C MUTATED        1      1      3      0
  HIST1H1C WILD-TYPE     56     40     53     21
D17V7, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                1                 40
  CLUS_3                3                 53
  CLUS_4                0                 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 CLUS_4 CLUS_5
  HIST1H1C MUTATED        1      0      1      0      3
  HIST1H1C WILD-TYPE     31     53     49     20     17
D17V8, multiclass
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                0                 53
  CLUS_3                1                 49
  CLUS_4                0                 20
  CLUS_5                3                 17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = DLK2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLK2 MUTATED        1      2      1
  DLK2 WILD-TYPE     45     60     84
D18V1, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            1             45
  CLUS_2            2             60
  CLUS_3            1             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DLK2 MUTATED        2      1      1
  DLK2 WILD-TYPE     55     82     57
D18V2, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            2             55
  CLUS_2            1             82
  CLUS_3            1             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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
  DLK2 MUTATED        2      1      0      1      0
  DLK2 WILD-TYPE     41     54     29     35     32
D18V3, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            2             41
  CLUS_2            1             54
  CLUS_3            0             29
  CLUS_4            1             35
  CLUS_5            0             32
[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 CLUS_5
  DLK2 MUTATED        2      1      1      0      0
  DLK2 WILD-TYPE     32     28     66     36     29
D18V4, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            2             32
  CLUS_2            1             28
  CLUS_3            1             66
  CLUS_4            0             36
  CLUS_5            0             29
[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
  DLK2 MUTATED        1      0      1      2
  DLK2 WILD-TYPE     37     68     26     58
D18V5, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            1             37
  CLUS_2            0             68
  CLUS_3            1             26
  CLUS_4            2             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_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DLK2 MUTATED        1      1      0      2      0
  DLK2 WILD-TYPE     23     57     24     64     21
D18V6, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            1             23
  CLUS_2            1             57
  CLUS_3            0             24
  CLUS_4            2             64
  CLUS_5            0             21
[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
  DLK2 MUTATED        0      2      1      1
  DLK2 WILD-TYPE     57     39     55     20
D18V7, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            0             57
  CLUS_2            2             39
  CLUS_3            1             55
  CLUS_4            1             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 CLUS_4 CLUS_5
  DLK2 MUTATED        0      0      3      1      0
  DLK2 WILD-TYPE     32     53     47     19     20
D18V8, multiclass
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            0             53
  CLUS_3            3             47
  CLUS_4            1             19
  CLUS_5            0             20
[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"
