[1] "ofn"        "-oTKIRP-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/KIRP-TP/22542911/KIRP-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22574639/transformed.cor.cli.txt"

nPatients in clinical file=291, in cluster file=282, common to both=282
[1] "Reduce the number of clustering variables from 27 to 26."
[1]  26 282
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             16             266 
  SETD2 MUTATED SETD2 WILD-TYPE 
             16             266 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           10           272 
  NF2 MUTATED NF2 WILD-TYPE 
           10           272 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               9              273 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               9              273 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           21           261 
  MET MUTATED MET WILD-TYPE 
           21           261 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6            276 
  NEFH MUTATED NEFH WILD-TYPE 
             6            276 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             5            277 
  KRAS MUTATED KRAS WILD-TYPE 
             5            277 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            10            272 
  CUL3 MUTATED CUL3 WILD-TYPE 
            10            272 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
             11             271 
  PCF11 MUTATED PCF11 WILD-TYPE 
             11             271 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              276 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              276 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            3           279 
  PAM MUTATED PAM WILD-TYPE 
            3           279 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                6               276 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                6               276 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             272 
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             272 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
          13          269 
  AR MUTATED AR WILD-TYPE 
          13          269 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             7            275 
  TP53 MUTATED TP53 WILD-TYPE 
             7            275 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                277 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                277 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             4            278 
  BRAF MUTATED BRAF WILD-TYPE 
             4            278 
[1] "KIAA0922 MUTATION ANALYSIS"
[1] 3
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 5                277 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 5                277 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            277 
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            277 
[1] "ALMS1 MUTATION ANALYSIS"
[1] 3
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              8             274 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              8             274 
[1] "GXYLT1 MUTATION ANALYSIS"
[1] 3
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               4              278 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               4              278 
[1] "ATP1B1 MUTATION ANALYSIS"
[1] 3
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               7              275 
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               7              275 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             11             271 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             11             271 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            275 
  PTEN MUTATED PTEN WILD-TYPE 
             7            275 
[1] "SAV1 MUTATION ANALYSIS"
[1] 3
  SAV1 MUTATED SAV1 WILD-TYPE 
             6            276 
  SAV1 MUTATED SAV1 WILD-TYPE 
             6            276 
[1] "CALCR MUTATION ANALYSIS"
[1] 3
  CALCR MUTATED CALCR WILD-TYPE 
              3             279 
  CALCR MUTATED CALCR WILD-TYPE 
              3             279 
[1] "IGSF3 MUTATION ANALYSIS"
[1] 3
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              4             278 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              4             278 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 282 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	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 282 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SETD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        6      1      3      6
  SETD2 WILD-TYPE     96     70     45     53
D1V1, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             6              96
  CLUS_2             1              70
  CLUS_3             3              45
  CLUS_4             6              53
[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 CLUS_6
  SETD2 MUTATED        0      3      1      1     11      0
  SETD2 WILD-TYPE     56     39     57     57     15     27
D1V2, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             3              39
  CLUS_3             1              57
  CLUS_4             1              57
  CLUS_5            11              15
  CLUS_6             0              27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        2      4      7
  SETD2 WILD-TYPE     73     75     48
D1V3, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             4              75
  CLUS_3             7              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        0      4      3      6
  SETD2 WILD-TYPE     39     61     60     36
D1V4, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             4              61
  CLUS_3             3              60
  CLUS_4             6              36
[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
  SETD2 MUTATED        0      2      8      0      6
  SETD2 WILD-TYPE     32     86     61     31     55
D1V5, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             2              86
  CLUS_3             8              61
  CLUS_4             0              31
  CLUS_5             6              55
[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
  SETD2 MUTATED       13      2      1
  SETD2 WILD-TYPE    101    119     45
D1V6, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            13             101
  CLUS_2             2             119
  CLUS_3             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SETD2 MUTATED        1      4      1      6      3      1
  SETD2 WILD-TYPE     28     33     63     34     77     31
D1V7, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             4              33
  CLUS_3             1              63
  CLUS_4             6              34
  CLUS_5             3              77
  CLUS_6             1              31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED       13      1      2
  SETD2 WILD-TYPE    103     78     85
D1V8, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            13             103
  CLUS_2             1              78
  CLUS_3             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        5      3      5
  SETD2 WILD-TYPE     65     71     69
D1V9, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             5              65
  CLUS_2             3              71
  CLUS_3             5              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        6      6      1
  SETD2 WILD-TYPE     85     89     31
D1V10, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             6              85
  CLUS_2             6              89
  CLUS_3             1              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = NF2 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF2 MUTATED        4      1      4      1
  NF2 WILD-TYPE     98     70     44     58
D2V1, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           4            98
  CLUS_2           1            70
  CLUS_3           4            44
  CLUS_4           1            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 CLUS_6
  NF2 MUTATED        1      0      0      2      4      2
  NF2 WILD-TYPE     55     42     58     56     22     25
D2V2, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           1            55
  CLUS_2           0            42
  CLUS_3           0            58
  CLUS_4           2            56
  CLUS_5           4            22
  CLUS_6           2            25
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        4      2      2
  NF2 WILD-TYPE     71     77     53
D2V3, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           4            71
  CLUS_2           2            77
  CLUS_3           2            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
  NF2 MUTATED        1      2      4      1
  NF2 WILD-TYPE     38     63     59     41
D2V4, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           1            38
  CLUS_2           2            63
  CLUS_3           4            59
  CLUS_4           1            41
[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
  NF2 MUTATED        2      3      0      1      4
  NF2 WILD-TYPE     30     85     69     30     57
D2V5, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            30
  CLUS_2           3            85
  CLUS_3           0            69
  CLUS_4           1            30
  CLUS_5           4            57
[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
  NF2 MUTATED        2      4      4
  NF2 WILD-TYPE    112    117     42
D2V6, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2           112
  CLUS_2           4           117
  CLUS_3           4            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 CLUS_6
  NF2 MUTATED        0      1      3      2      4      0
  NF2 WILD-TYPE     29     36     61     38     76     32
D2V7, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           0            29
  CLUS_2           1            36
  CLUS_3           3            61
  CLUS_4           2            38
  CLUS_5           4            76
  CLUS_6           0            32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        4      2      4
  NF2 WILD-TYPE    112     77     83
D2V8, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           4           112
  CLUS_2           2            77
  CLUS_3           4            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
  NF2 MUTATED        1      2      3
  NF2 WILD-TYPE     69     72     71
D2V9, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           1            69
  CLUS_2           2            72
  CLUS_3           3            71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        3      3      0
  NF2 WILD-TYPE     88     92     32
D2V10, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           3            88
  CLUS_2           3            92
  CLUS_3           0            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = ZNF814 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        4      2      2      1
  ZNF814 WILD-TYPE     98     69     46     58
D3V1, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              4               98
  CLUS_2              2               69
  CLUS_3              2               46
  CLUS_4              1               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 CLUS_6
  ZNF814 MUTATED        2      1      3      1      2      0
  ZNF814 WILD-TYPE     54     41     55     57     24     27
D3V2, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              1               41
  CLUS_3              3               55
  CLUS_4              1               57
  CLUS_5              2               24
  CLUS_6              0               27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        2      3      2
  ZNF814 WILD-TYPE     73     76     53
D3V3, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               73
  CLUS_2              3               76
  CLUS_3              2               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
  ZNF814 MUTATED        0      3      3      1
  ZNF814 WILD-TYPE     39     62     60     41
D3V4, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               39
  CLUS_2              3               62
  CLUS_3              3               60
  CLUS_4              1               41
[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
  ZNF814 MUTATED        0      3      3      0      3
  ZNF814 WILD-TYPE     32     85     66     31     58
D3V5, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              3               85
  CLUS_3              3               66
  CLUS_4              0               31
  CLUS_5              3               58
[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
  ZNF814 MUTATED        4      4      1
  ZNF814 WILD-TYPE    110    117     45
D3V6, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              4              110
  CLUS_2              4              117
  CLUS_3              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZNF814 MUTATED        0      0      3      4      1      1
  ZNF814 WILD-TYPE     29     37     61     36     79     31
D3V7, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              0               37
  CLUS_3              3               61
  CLUS_4              4               36
  CLUS_5              1               79
  CLUS_6              1               31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        6      2      1
  ZNF814 WILD-TYPE    110     77     86
D3V8, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              6              110
  CLUS_2              2               77
  CLUS_3              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        2      3      2
  ZNF814 WILD-TYPE     68     71     72
D3V9, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              3               71
  CLUS_3              2               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        3      4      0
  ZNF814 WILD-TYPE     88     91     32
D3V10, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              3               88
  CLUS_2              4               91
  CLUS_3              0               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MET MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MET MUTATED        7      8      3      3
  MET WILD-TYPE     95     63     45     56
D4V1, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           7            95
  CLUS_2           8            63
  CLUS_3           3            45
  CLUS_4           3            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MET MUTATED        4      1     13      2      0      0
  MET WILD-TYPE     52     41     45     56     26     27
D4V2, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           4            52
  CLUS_2           1            41
  CLUS_3          13            45
  CLUS_4           2            56
  CLUS_5           0            26
  CLUS_6           0            27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        8      9      1
  MET WILD-TYPE     67     70     54
D4V3, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           8            67
  CLUS_2           9            70
  CLUS_3           1            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
  MET MUTATED        3      9      6      0
  MET WILD-TYPE     36     56     57     42
D4V4, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           3            36
  CLUS_2           9            56
  CLUS_3           6            57
  CLUS_4           0            42
[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
  MET MUTATED        5      8      1      5      2
  MET WILD-TYPE     27     80     68     26     59
D4V5, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           5            27
  CLUS_2           8            80
  CLUS_3           1            68
  CLUS_4           5            26
  CLUS_5           2            59
[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
  MET MUTATED        2     17      2
  MET WILD-TYPE    112    104     44
D4V6, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           2           112
  CLUS_2          17           104
  CLUS_3           2            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MET MUTATED        0      0      4      3      8      6
  MET WILD-TYPE     29     37     60     37     72     26
D4V7, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           0            29
  CLUS_2           0            37
  CLUS_3           4            60
  CLUS_4           3            37
  CLUS_5           8            72
  CLUS_6           6            26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        8      4      9
  MET WILD-TYPE    108     75     78
D4V8, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           8           108
  CLUS_2           4            75
  CLUS_3           9            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
  MET MUTATED        4      6      6
  MET WILD-TYPE     66     68     68
D4V9, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           4            66
  CLUS_2           6            68
  CLUS_3           6            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        7      3      6
  MET WILD-TYPE     84     92     26
D4V10, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           7            84
  CLUS_2           3            92
  CLUS_3           6            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = NEFH MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        0      1      4      1
  NEFH WILD-TYPE    102     70     44     58
D5V1, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0            102
  CLUS_2            1             70
  CLUS_3            4             44
  CLUS_4            1             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 CLUS_6
  NEFH MUTATED        2      0      0      4      0      0
  NEFH WILD-TYPE     54     42     58     54     26     27
D5V2, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             54
  CLUS_2            0             42
  CLUS_3            0             58
  CLUS_4            4             54
  CLUS_5            0             26
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        2      2      0
  NEFH WILD-TYPE     73     77     55
D5V3, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             73
  CLUS_2            2             77
  CLUS_3            0             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
  NEFH MUTATED        2      1      1      0
  NEFH WILD-TYPE     37     64     62     42
D5V4, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             37
  CLUS_2            1             64
  CLUS_3            1             62
  CLUS_4            0             42
[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
  NEFH MUTATED        2      2      2      0      0
  NEFH WILD-TYPE     30     86     67     31     61
D5V5, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             30
  CLUS_2            2             86
  CLUS_3            2             67
  CLUS_4            0             31
  CLUS_5            0             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        2      4      0
  NEFH WILD-TYPE    112    117     46
D5V6, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2            112
  CLUS_2            4            117
  CLUS_3            0             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NEFH MUTATED        0      0      3      1      1      1
  NEFH WILD-TYPE     29     37     61     39     79     31
D5V7, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0             29
  CLUS_2            0             37
  CLUS_3            3             61
  CLUS_4            1             39
  CLUS_5            1             79
  CLUS_6            1             31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      2      1
  NEFH WILD-TYPE    113     77     86
D5V8, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3            113
  CLUS_2            2             77
  CLUS_3            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        1      3      0
  NEFH WILD-TYPE     69     71     74
D5V9, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            1             69
  CLUS_2            3             71
  CLUS_3            0             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      1      0
  NEFH WILD-TYPE     88     94     32
D5V10, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             88
  CLUS_2            1             94
  CLUS_3            0             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        3      0      0      2
  KRAS WILD-TYPE     99     71     48     57
D6V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             99
  CLUS_2            0             71
  CLUS_3            0             48
  CLUS_4            2             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 CLUS_6
  KRAS MUTATED        0      0      2      0      0      3
  KRAS WILD-TYPE     56     42     56     58     26     24
D6V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             56
  CLUS_2            0             42
  CLUS_3            2             56
  CLUS_4            0             58
  CLUS_5            0             26
  CLUS_6            3             24
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        1      0      1
  KRAS WILD-TYPE     74     79     54
D6V3, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            207 
    TCGA-2K-A9WE     TCGA-2Z-A9J1     TCGA-2Z-A9J3     TCGA-2Z-A9J5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J6     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JI     TCGA-2Z-A9JJ     TCGA-2Z-A9JL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-2Z-A9JP     TCGA-2Z-A9JQ     TCGA-2Z-A9JT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-5P-A9JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-5P-A9JY     TCGA-5P-A9KE     TCGA-A4-7288     TCGA-A4-7583 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7734     TCGA-A4-7915 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7996     TCGA-A4-7997     TCGA-A4-8098     TCGA-A4-8311 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8630     TCGA-A4-A57E     TCGA-AL-3472 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-AL-A5DJ     TCGA-B1-5398 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-7332     TCGA-B1-A47M     TCGA-B1-A47N     TCGA-B1-A47O 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A654     TCGA-B1-A657     TCGA-B3-8121     TCGA-B3-A6W5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268     TCGA-B9-A44B 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-A5W7     TCGA-B9-A5W8     TCGA-B9-A5W9     TCGA-B9-A69E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-A8YH     TCGA-B9-A8YI     TCGA-BQ-5875     TCGA-BQ-5877 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7046 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-DZ-6131     TCGA-DZ-6132 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A4JJ     TCGA-F9-A7Q0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-F9-A7VF     TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-6846     TCGA-GL-7773     TCGA-GL-7966 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-8500     TCGA-GL-A4EM     TCGA-GL-A59R     TCGA-GL-A9DD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-A9DE     TCGA-HE-7128     TCGA-HE-7129     TCGA-HE-7130 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HE-A5NF     TCGA-HE-A5NH     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-HE-A5NL     TCGA-IA-A40U     TCGA-IA-A40X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-IA-A83V     TCGA-IA-A83W     TCGA-IZ-8195 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IZ-8196     TCGA-IZ-A6M8     TCGA-J7-6720     TCGA-J7-8537 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J7-A8I2     TCGA-KV-A6GD     TCGA-KV-A6GE     TCGA-KV-A74V 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MH-A55Z     TCGA-MH-A560     TCGA-MH-A562     TCGA-MH-A855 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E7     TCGA-P4-A5E8     TCGA-P4-A5EA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5EB     TCGA-P4-A5ED     TCGA-P4-AAVL     TCGA-P4-AAVM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-PJ-A5Z8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-Q2-A5QZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PJ     TCGA-UZ-A9PK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PL     TCGA-UZ-A9PM     TCGA-UZ-A9PN     TCGA-UZ-A9PO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PP     TCGA-UZ-A9PR     TCGA-UZ-A9PS     TCGA-UZ-A9PU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PV     TCGA-UZ-A9PX     TCGA-UZ-A9PZ     TCGA-UZ-A9Q0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9Q1     TCGA-V9-A7HT     TCGA-WN-A9G9     TCGA-Y8-A894 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A895     TCGA-Y8-A896     TCGA-Y8-A897     TCGA-Y8-A8RY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-Y8-A8S0     TCGA-Y8-A8S1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        1      0      0      1
  KRAS WILD-TYPE     38     65     63     41
D6V4, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            207 
    TCGA-2K-A9WE     TCGA-2Z-A9J1     TCGA-2Z-A9J3     TCGA-2Z-A9J5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J6     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JI     TCGA-2Z-A9JJ     TCGA-2Z-A9JL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-2Z-A9JP     TCGA-2Z-A9JQ     TCGA-2Z-A9JT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-5P-A9JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-5P-A9JY     TCGA-5P-A9KE     TCGA-A4-7288     TCGA-A4-7583 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7734     TCGA-A4-7915 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7996     TCGA-A4-7997     TCGA-A4-8098     TCGA-A4-8311 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8630     TCGA-A4-A57E     TCGA-AL-3472 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-AL-A5DJ     TCGA-B1-5398 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-7332     TCGA-B1-A47M     TCGA-B1-A47N     TCGA-B1-A47O 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A654     TCGA-B1-A657     TCGA-B3-8121     TCGA-B3-A6W5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268     TCGA-B9-A44B 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-A5W7     TCGA-B9-A5W8     TCGA-B9-A5W9     TCGA-B9-A69E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-A8YH     TCGA-B9-A8YI     TCGA-BQ-5875     TCGA-BQ-5877 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7046 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-DZ-6131     TCGA-DZ-6132 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A4JJ     TCGA-F9-A7Q0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-F9-A7VF     TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-6846     TCGA-GL-7773     TCGA-GL-7966 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-8500     TCGA-GL-A4EM     TCGA-GL-A59R     TCGA-GL-A9DD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-A9DE     TCGA-HE-7128     TCGA-HE-7129     TCGA-HE-7130 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HE-A5NF     TCGA-HE-A5NH     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-HE-A5NL     TCGA-IA-A40U     TCGA-IA-A40X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-IA-A83V     TCGA-IA-A83W     TCGA-IZ-8195 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IZ-8196     TCGA-IZ-A6M8     TCGA-J7-6720     TCGA-J7-8537 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J7-A8I2     TCGA-KV-A6GD     TCGA-KV-A6GE     TCGA-KV-A74V 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MH-A55Z     TCGA-MH-A560     TCGA-MH-A562     TCGA-MH-A855 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E7     TCGA-P4-A5E8     TCGA-P4-A5EA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5EB     TCGA-P4-A5ED     TCGA-P4-AAVL     TCGA-P4-AAVM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-PJ-A5Z8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-Q2-A5QZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PJ     TCGA-UZ-A9PK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PL     TCGA-UZ-A9PM     TCGA-UZ-A9PN     TCGA-UZ-A9PO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PP     TCGA-UZ-A9PR     TCGA-UZ-A9PS     TCGA-UZ-A9PU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PV     TCGA-UZ-A9PX     TCGA-UZ-A9PZ     TCGA-UZ-A9Q0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9Q1     TCGA-V9-A7HT     TCGA-WN-A9G9     TCGA-Y8-A894 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A895     TCGA-Y8-A896     TCGA-Y8-A897     TCGA-Y8-A8RY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-Y8-A8S0     TCGA-Y8-A8S1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        0      2      0      1      2
  KRAS WILD-TYPE     32     86     69     30     59
D6V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             32
  CLUS_2            2             86
  CLUS_3            0             69
  CLUS_4            1             30
  CLUS_5            2             59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        0      2      3
  KRAS WILD-TYPE    114    119     43
D6V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0            114
  CLUS_2            2            119
  CLUS_3            3             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        0      0      1      1      3      0
  KRAS WILD-TYPE     29     37     63     39     77     32
D6V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             29
  CLUS_2            0             37
  CLUS_3            1             63
  CLUS_4            1             39
  CLUS_5            3             77
  CLUS_6            0             32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        1      1      3
  KRAS WILD-TYPE    115     78     84
D6V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1            115
  CLUS_2            1             78
  CLUS_3            3             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
  KRAS MUTATED        0      2      3
  KRAS WILD-TYPE     70     72     71
D6V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             70
  CLUS_2            2             72
  CLUS_3            3             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        1      3      1
  KRAS WILD-TYPE     90     92     31
D6V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1             90
  CLUS_2            3             92
  CLUS_3            1             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = CUL3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CUL3 MUTATED        8      1      0      1
  CUL3 WILD-TYPE     94     70     48     58
D7V1, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            8             94
  CLUS_2            1             70
  CLUS_3            0             48
  CLUS_4            1             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 CLUS_6
  CUL3 MUTATED        2      2      1      1      4      0
  CUL3 WILD-TYPE     54     40     57     57     22     27
D7V2, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            2             54
  CLUS_2            2             40
  CLUS_3            1             57
  CLUS_4            1             57
  CLUS_5            4             22
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CUL3 MUTATED        2      5      1
  CUL3 WILD-TYPE     73     74     54
D7V3, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            2             73
  CLUS_2            5             74
  CLUS_3            1             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
  CUL3 MUTATED        0      4      3      1
  CUL3 WILD-TYPE     39     61     60     41
D7V4, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            0             39
  CLUS_2            4             61
  CLUS_3            3             60
  CLUS_4            1             41
[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
  CUL3 MUTATED        0      1      5      1      3
  CUL3 WILD-TYPE     32     87     64     30     58
D7V5, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            1             87
  CLUS_3            5             64
  CLUS_4            1             30
  CLUS_5            3             58
[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
  CUL3 MUTATED        7      2      1
  CUL3 WILD-TYPE    107    119     45
D7V6, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            7            107
  CLUS_2            2            119
  CLUS_3            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CUL3 MUTATED        0      3      1      3      1      2
  CUL3 WILD-TYPE     29     34     63     37     79     30
D7V7, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            0             29
  CLUS_2            3             34
  CLUS_3            1             63
  CLUS_4            3             37
  CLUS_5            1             79
  CLUS_6            2             30
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CUL3 MUTATED        7      1      2
  CUL3 WILD-TYPE    109     78     85
D7V8, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            7            109
  CLUS_2            1             78
  CLUS_3            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CUL3 MUTATED        5      1      2
  CUL3 WILD-TYPE     65     73     72
D7V9, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            5             65
  CLUS_2            1             73
  CLUS_3            2             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CUL3 MUTATED        5      2      1
  CUL3 WILD-TYPE     86     93     31
D7V10, multiclass
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  CLUS_1            5             86
  CLUS_2            2             93
  CLUS_3            1             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = PCF11 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCF11 MUTATED        5      4      0      1
  PCF11 WILD-TYPE     97     67     48     58
D8V1, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             5              97
  CLUS_2             4              67
  CLUS_3             0              48
  CLUS_4             1              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 CLUS_6
  PCF11 MUTATED        3      4      2      1      0      0
  PCF11 WILD-TYPE     53     38     56     57     26     27
D8V2, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             3              53
  CLUS_2             4              38
  CLUS_3             2              56
  CLUS_4             1              57
  CLUS_5             0              26
  CLUS_6             0              27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCF11 MUTATED        3      1      3
  PCF11 WILD-TYPE     72     78     52
D8V3, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             3              72
  CLUS_2             1              78
  CLUS_3             3              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCF11 MUTATED        3      0      1      3
  PCF11 WILD-TYPE     36     65     62     39
D8V4, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             3              36
  CLUS_2             0              65
  CLUS_3             1              62
  CLUS_4             3              39
[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
  PCF11 MUTATED        0      3      5      2      0
  PCF11 WILD-TYPE     32     85     64     29     61
D8V5, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             3              85
  CLUS_3             5              64
  CLUS_4             2              29
  CLUS_5             0              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCF11 MUTATED        6      4      0
  PCF11 WILD-TYPE    108    117     46
D8V6, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             6             108
  CLUS_2             4             117
  CLUS_3             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCF11 MUTATED        1      2      2      2      4      0
  PCF11 WILD-TYPE     28     35     62     38     76     32
D8V7, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             2              35
  CLUS_3             2              62
  CLUS_4             2              38
  CLUS_5             4              76
  CLUS_6             0              32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCF11 MUTATED        7      2      2
  PCF11 WILD-TYPE    109     77     85
D8V8, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             7             109
  CLUS_2             2              77
  CLUS_3             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCF11 MUTATED        3      2      4
  PCF11 WILD-TYPE     67     72     70
D8V9, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             2              72
  CLUS_3             4              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCF11 MUTATED        3      6      0
  PCF11 WILD-TYPE     88     89     32
D8V10, multiclass
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  CLUS_1             3              88
  CLUS_2             6              89
  CLUS_3             0              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = BCLAF1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BCLAF1 MUTATED        2      1      1      2
  BCLAF1 WILD-TYPE    100     70     47     57
D9V1, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              2              100
  CLUS_2              1               70
  CLUS_3              1               47
  CLUS_4              2               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 CLUS_6
  BCLAF1 MUTATED        2      0      0      2      1      1
  BCLAF1 WILD-TYPE     54     42     58     56     25     26
D9V2, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              0               42
  CLUS_3              0               58
  CLUS_4              2               56
  CLUS_5              1               25
  CLUS_6              1               26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BCLAF1 MUTATED        2      1      2
  BCLAF1 WILD-TYPE     73     78     53
D9V3, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              2               73
  CLUS_2              1               78
  CLUS_3              2               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
  BCLAF1 MUTATED        1      2      2      0
  BCLAF1 WILD-TYPE     38     63     61     42
D9V4, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              1               38
  CLUS_2              2               63
  CLUS_3              2               61
  CLUS_4              0               42
[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
  BCLAF1 MUTATED        0      2      1      1      2
  BCLAF1 WILD-TYPE     32     86     68     30     59
D9V5, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              2               86
  CLUS_3              1               68
  CLUS_4              1               30
  CLUS_5              2               59
[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
  BCLAF1 MUTATED        3      2      1
  BCLAF1 WILD-TYPE    111    119     45
D9V6, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              3              111
  CLUS_2              2              119
  CLUS_3              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BCLAF1 MUTATED        0      2      2      0      1      1
  BCLAF1 WILD-TYPE     29     35     62     40     79     31
D9V7, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              2               35
  CLUS_3              2               62
  CLUS_4              0               40
  CLUS_5              1               79
  CLUS_6              1               31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BCLAF1 MUTATED        2      2      2
  BCLAF1 WILD-TYPE    114     77     85
D9V8, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              2              114
  CLUS_2              2               77
  CLUS_3              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BCLAF1 MUTATED        1      1      2
  BCLAF1 WILD-TYPE     69     73     72
D9V9, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              1               73
  CLUS_3              2               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  BCLAF1 MUTATED        2      2      0
  BCLAF1 WILD-TYPE     89     93     32
D9V10, multiclass
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  CLUS_1              2               89
  CLUS_2              2               93
  CLUS_3              0               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = PAM MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PAM MUTATED        1      1      1      0
  PAM WILD-TYPE    101     70     47     59
D10V1, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           1           101
  CLUS_2           1            70
  CLUS_3           1            47
  CLUS_4           0            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 CLUS_6
  PAM MUTATED        0      0      0      3      0      0
  PAM WILD-TYPE     56     42     58     55     26     27
D10V2, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           0            56
  CLUS_2           0            42
  CLUS_3           0            58
  CLUS_4           3            55
  CLUS_5           0            26
  CLUS_6           0            27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  PAM MUTATED        3      0      0
  PAM WILD-TYPE     72     79     55
D10V3, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           3            72
  CLUS_2           0            79
  CLUS_3           0            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
  PAM MUTATED        0      1      2      0
  PAM WILD-TYPE     39     64     61     42
D10V4, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           0            39
  CLUS_2           1            64
  CLUS_3           2            61
  CLUS_4           0            42
[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
  PAM MUTATED        1      1      1      0      0
  PAM WILD-TYPE     31     87     68     31     61
D10V5, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           1            31
  CLUS_2           1            87
  CLUS_3           1            68
  CLUS_4           0            31
  CLUS_5           0            61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  PAM MUTATED        1      2      0
  PAM WILD-TYPE    113    119     46
D10V6, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           1           113
  CLUS_2           2           119
  CLUS_3           0            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PAM MUTATED        0      0      2      0      0      1
  PAM WILD-TYPE     29     37     62     40     80     31
D10V7, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           0            29
  CLUS_2           0            37
  CLUS_3           2            62
  CLUS_4           0            40
  CLUS_5           0            80
  CLUS_6           1            31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  PAM MUTATED        0      3      0
  PAM WILD-TYPE    116     76     87
D10V8, multiclass
        clus
vv       PAM MUTATED PAM WILD-TYPE
  CLUS_1           0           116
  CLUS_2           3            76
  CLUS_3           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  PAM MUTATED        2      0      0
  PAM WILD-TYPE     68     74     74
D10V9, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2           216 
   TCGA-2K-A9WE    TCGA-2Z-A9J1    TCGA-2Z-A9J2    TCGA-2Z-A9J3    TCGA-2Z-A9J5 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9J6    TCGA-2Z-A9JD    TCGA-2Z-A9JG    TCGA-2Z-A9JI    TCGA-2Z-A9JJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JK    TCGA-2Z-A9JL    TCGA-2Z-A9JM    TCGA-2Z-A9JN    TCGA-2Z-A9JO 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JP    TCGA-2Z-A9JQ    TCGA-2Z-A9JR    TCGA-2Z-A9JT    TCGA-4A-A93W 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-5P-A9JV    TCGA-5P-A9JW    TCGA-5P-A9JY 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9JZ    TCGA-5P-A9K0    TCGA-5P-A9K6    TCGA-5P-A9K8    TCGA-5P-A9KA 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9KC    TCGA-5P-A9KE    TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7734    TCGA-A4-7828    TCGA-A4-7915    TCGA-A4-7996 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7997    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8312    TCGA-A4-8515 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A57E    TCGA-A4-A5XZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-A4-A5Y1    TCGA-A4-A772    TCGA-AL-3466    TCGA-AL-3472 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3473    TCGA-AL-7173    TCGA-AT-A5NU    TCGA-B1-5398    TCGA-B1-A47N 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A47O    TCGA-B1-A654    TCGA-B1-A656    TCGA-B1-A657    TCGA-B3-3925 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B3-4104    TCGA-B3-8121    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-5155 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-5156    TCGA-B9-A44B    TCGA-B9-A5W9    TCGA-B9-A69E    TCGA-B9-A8YH 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A8YI    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7836    TCGA-DW-7837    TCGA-DW-7838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5903    TCGA-F9-A4JJ    TCGA-F9-A7Q0    TCGA-F9-A8NY    TCGA-F9-A97G 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6796    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-G7-A8LB 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A8LC    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-6846    TCGA-GL-7773 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7966    TCGA-GL-8500    TCGA-GL-A4EM    TCGA-GL-A59T    TCGA-GL-A9DC 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A9DD    TCGA-GL-A9DE    TCGA-HE-7128    TCGA-HE-7130    TCGA-HE-A5NJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-HE-A5NL    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-IA-A83S    TCGA-IA-A83T 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A83V    TCGA-IA-A83W    TCGA-IZ-8195    TCGA-IZ-8196    TCGA-IZ-A6M9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-6720    TCGA-J7-8537    TCGA-J7-A8I2    TCGA-KV-A6GD    TCGA-KV-A6GE 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KV-A74V    TCGA-MH-A854    TCGA-MH-A855    TCGA-MH-A856    TCGA-MH-A857 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-O9-A75Z    TCGA-P4-A5E7    TCGA-P4-A5E8    TCGA-P4-A5EA    TCGA-P4-AAVL 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-AAVM    TCGA-PJ-A5Z8    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ    TCGA-SX-A71R 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A71W    TCGA-SX-A7SL    TCGA-SX-A7SM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SN    TCGA-SX-A7SO    TCGA-SX-A7SP    TCGA-SX-A7SR    TCGA-SX-A7SS 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SU    TCGA-UZ-A9PJ    TCGA-UZ-A9PK    TCGA-UZ-A9PL    TCGA-UZ-A9PN 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PO    TCGA-UZ-A9PP    TCGA-UZ-A9PR    TCGA-UZ-A9PU    TCGA-UZ-A9PV 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PX    TCGA-UZ-A9PZ    TCGA-V9-A7HT    TCGA-WN-A9G9    TCGA-WN-AB4C 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A897    TCGA-Y8-A898    TCGA-Y8-A8RY    TCGA-Y8-A8RZ    TCGA-Y8-A8S0 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A8S1 
"PAM WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  PAM MUTATED        2      0      0
  PAM WILD-TYPE     89     95     32
D10V10, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2           216 
   TCGA-2K-A9WE    TCGA-2Z-A9J1    TCGA-2Z-A9J2    TCGA-2Z-A9J3    TCGA-2Z-A9J5 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9J6    TCGA-2Z-A9JD    TCGA-2Z-A9JG    TCGA-2Z-A9JI    TCGA-2Z-A9JJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JK    TCGA-2Z-A9JL    TCGA-2Z-A9JM    TCGA-2Z-A9JN    TCGA-2Z-A9JO 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JP    TCGA-2Z-A9JQ    TCGA-2Z-A9JR    TCGA-2Z-A9JT    TCGA-4A-A93W 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-5P-A9JV    TCGA-5P-A9JW    TCGA-5P-A9JY 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9JZ    TCGA-5P-A9K0    TCGA-5P-A9K6    TCGA-5P-A9K8    TCGA-5P-A9KA 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9KC    TCGA-5P-A9KE    TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7734    TCGA-A4-7828    TCGA-A4-7915    TCGA-A4-7996 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7997    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8312    TCGA-A4-8515 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A57E    TCGA-A4-A5XZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-A4-A5Y1    TCGA-A4-A772    TCGA-AL-3466    TCGA-AL-3472 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3473    TCGA-AL-7173    TCGA-AT-A5NU    TCGA-B1-5398    TCGA-B1-A47N 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A47O    TCGA-B1-A654    TCGA-B1-A656    TCGA-B1-A657    TCGA-B3-3925 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B3-4104    TCGA-B3-8121    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-5155 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-5156    TCGA-B9-A44B    TCGA-B9-A5W9    TCGA-B9-A69E    TCGA-B9-A8YH 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A8YI    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7836    TCGA-DW-7837    TCGA-DW-7838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5903    TCGA-F9-A4JJ    TCGA-F9-A7Q0    TCGA-F9-A8NY    TCGA-F9-A97G 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6796    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-G7-A8LB 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A8LC    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-6846    TCGA-GL-7773 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7966    TCGA-GL-8500    TCGA-GL-A4EM    TCGA-GL-A59T    TCGA-GL-A9DC 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A9DD    TCGA-GL-A9DE    TCGA-HE-7128    TCGA-HE-7130    TCGA-HE-A5NJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-HE-A5NL    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-IA-A83S    TCGA-IA-A83T 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A83V    TCGA-IA-A83W    TCGA-IZ-8195    TCGA-IZ-8196    TCGA-IZ-A6M9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-6720    TCGA-J7-8537    TCGA-J7-A8I2    TCGA-KV-A6GD    TCGA-KV-A6GE 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KV-A74V    TCGA-MH-A854    TCGA-MH-A855    TCGA-MH-A856    TCGA-MH-A857 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-O9-A75Z    TCGA-P4-A5E7    TCGA-P4-A5E8    TCGA-P4-A5EA    TCGA-P4-AAVL 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-AAVM    TCGA-PJ-A5Z8    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ    TCGA-SX-A71R 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A71W    TCGA-SX-A7SL    TCGA-SX-A7SM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SN    TCGA-SX-A7SO    TCGA-SX-A7SP    TCGA-SX-A7SR    TCGA-SX-A7SS 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SU    TCGA-UZ-A9PJ    TCGA-UZ-A9PK    TCGA-UZ-A9PL    TCGA-UZ-A9PN 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PO    TCGA-UZ-A9PP    TCGA-UZ-A9PR    TCGA-UZ-A9PU    TCGA-UZ-A9PV 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PX    TCGA-UZ-A9PZ    TCGA-V9-A7HT    TCGA-WN-A9G9    TCGA-WN-AB4C 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A897    TCGA-Y8-A898    TCGA-Y8-A8RY    TCGA-Y8-A8RZ    TCGA-Y8-A8S0 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A8S1 
"PAM WILD-TYPE" 

Clustering(11) Variable = SMARCB1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCB1 MUTATED        3      3      0      0
  SMARCB1 WILD-TYPE     99     68     48     59
D11V1, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               3                99
  CLUS_2               3                68
  CLUS_3               0                48
  CLUS_4               0                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 CLUS_6
  SMARCB1 MUTATED        0      4      0      1      1      0
  SMARCB1 WILD-TYPE     56     38     58     57     25     27
D11V2, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               0                56
  CLUS_2               4                38
  CLUS_3               0                58
  CLUS_4               1                57
  CLUS_5               1                25
  CLUS_6               0                27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCB1 MUTATED        1      2      1
  SMARCB1 WILD-TYPE     74     77     54
D11V3, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               1                74
  CLUS_2               2                77
  CLUS_3               1                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
  SMARCB1 MUTATED        1      2      0      1
  SMARCB1 WILD-TYPE     38     63     63     41
D11V4, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               1                38
  CLUS_2               2                63
  CLUS_3               0                63
  CLUS_4               1                41
[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
  SMARCB1 MUTATED        1      0      4      0      1
  SMARCB1 WILD-TYPE     31     88     65     31     60
D11V5, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               1                31
  CLUS_2               0                88
  CLUS_3               4                65
  CLUS_4               0                31
  CLUS_5               1                60
[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
  SMARCB1 MUTATED        5      1      0
  SMARCB1 WILD-TYPE    109    120     46
D11V6, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               5               109
  CLUS_2               1               120
  CLUS_3               0                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SMARCB1 MUTATED        0      1      0      0      4      1
  SMARCB1 WILD-TYPE     29     36     64     40     76     31
D11V7, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               0                29
  CLUS_2               1                36
  CLUS_3               0                64
  CLUS_4               0                40
  CLUS_5               4                76
  CLUS_6               1                31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCB1 MUTATED        3      0      3
  SMARCB1 WILD-TYPE    113     79     84
D11V8, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               3               113
  CLUS_2               0                79
  CLUS_3               3                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
  SMARCB1 MUTATED        0      0      4
  SMARCB1 WILD-TYPE     70     74     70
D11V9, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               0                70
  CLUS_2               0                74
  CLUS_3               4                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCB1 MUTATED        0      4      0
  SMARCB1 WILD-TYPE     91     91     32
D11V10, multiclass
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  CLUS_1               0                91
  CLUS_2               4                91
  CLUS_3               0                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = KDM6A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM6A MUTATED        4      1      1      4
  KDM6A WILD-TYPE     98     70     47     55
D12V1, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              98
  CLUS_2             1              70
  CLUS_3             1              47
  CLUS_4             4              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 CLUS_6
  KDM6A MUTATED        1      4      0      3      0      2
  KDM6A WILD-TYPE     55     38     58     55     26     25
D12V2, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              55
  CLUS_2             4              38
  CLUS_3             0              58
  CLUS_4             3              55
  CLUS_5             0              26
  CLUS_6             2              25
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        2      3      2
  KDM6A WILD-TYPE     73     76     53
D12V3, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             2              73
  CLUS_2             3              76
  CLUS_3             2              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
  KDM6A MUTATED        1      1      3      2
  KDM6A WILD-TYPE     38     64     60     40
D12V4, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              38
  CLUS_2             1              64
  CLUS_3             3              60
  CLUS_4             2              40
[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
  KDM6A MUTATED        1      2      5      0      2
  KDM6A WILD-TYPE     31     86     64     31     59
D12V5, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              31
  CLUS_2             2              86
  CLUS_3             5              64
  CLUS_4             0              31
  CLUS_5             2              59
[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
  KDM6A MUTATED        6      2      2
  KDM6A WILD-TYPE    108    119     44
D12V6, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             6             108
  CLUS_2             2             119
  CLUS_3             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KDM6A MUTATED        3      3      2      0      1      1
  KDM6A WILD-TYPE     26     34     62     40     79     31
D12V7, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             3              26
  CLUS_2             3              34
  CLUS_3             2              62
  CLUS_4             0              40
  CLUS_5             1              79
  CLUS_6             1              31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        6      2      2
  KDM6A WILD-TYPE    110     77     85
D12V8, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             6             110
  CLUS_2             2              77
  CLUS_3             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        4      1      2
  KDM6A WILD-TYPE     66     73     72
D12V9, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              66
  CLUS_2             1              73
  CLUS_3             2              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        4      3      0
  KDM6A WILD-TYPE     87     92     32
D12V10, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              87
  CLUS_2             3              92
  CLUS_3             0              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AR MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AR MUTATED        6      4      0      3
  AR WILD-TYPE     96     67     48     56
D13V1, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          6           96
  CLUS_2          4           67
  CLUS_3          0           48
  CLUS_4          3           56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AR MUTATED        1      4      4      2      2      0
  AR WILD-TYPE     55     38     54     56     24     27
D13V2, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           55
  CLUS_2          4           38
  CLUS_3          4           54
  CLUS_4          2           56
  CLUS_5          2           24
  CLUS_6          0           27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        3      3      2
  AR WILD-TYPE     72     76     53
D13V3, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          3           72
  CLUS_2          3           76
  CLUS_3          2           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
  AR MUTATED        2      2      2      2
  AR WILD-TYPE     37     63     61     40
D13V4, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          2           37
  CLUS_2          2           63
  CLUS_3          2           61
  CLUS_4          2           40
[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
  AR MUTATED        1      6      3      0      3
  AR WILD-TYPE     31     82     66     31     58
D13V5, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           31
  CLUS_2          6           82
  CLUS_3          3           66
  CLUS_4          0           31
  CLUS_5          3           58
[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
  AR MUTATED        7      6      0
  AR WILD-TYPE    107    115     46
D13V6, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          7          107
  CLUS_2          6          115
  CLUS_3          0           46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AR MUTATED        1      2      3      4      2      1
  AR WILD-TYPE     28     35     61     36     78     31
D13V7, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          1           28
  CLUS_2          2           35
  CLUS_3          3           61
  CLUS_4          4           36
  CLUS_5          2           78
  CLUS_6          1           31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        7      3      3
  AR WILD-TYPE    109     76     84
D13V8, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          7          109
  CLUS_2          3           76
  CLUS_3          3           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
  AR MUTATED        3      6      3
  AR WILD-TYPE     67     68     71
D13V9, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          3           67
  CLUS_2          6           68
  CLUS_3          3           71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  AR MUTATED        7      4      1
  AR WILD-TYPE     84     91     31
D13V10, multiclass
        clus
vv       AR MUTATED AR WILD-TYPE
  CLUS_1          7           84
  CLUS_2          4           91
  CLUS_3          1           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        3      0      1      3
  TP53 WILD-TYPE     99     71     47     56
D14V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             99
  CLUS_2            0             71
  CLUS_3            1             47
  CLUS_4            3             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        1      3      0      0      1      1
  TP53 WILD-TYPE     55     39     58     58     25     26
D14V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             55
  CLUS_2            3             39
  CLUS_3            0             58
  CLUS_4            0             58
  CLUS_5            1             25
  CLUS_6            1             26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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        0      1      2
  TP53 WILD-TYPE     75     78     53
D14V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             75
  CLUS_2            1             78
  CLUS_3            2             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
  TP53 MUTATED        0      1      1      1
  TP53 WILD-TYPE     39     64     62     41
D14V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             39
  CLUS_2            1             64
  CLUS_3            1             62
  CLUS_4            1             41
[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        0      0      3      1      3
  TP53 WILD-TYPE     32     88     66     30     58
D14V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            0             88
  CLUS_3            3             66
  CLUS_4            1             30
  CLUS_5            3             58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        4      0      3
  TP53 WILD-TYPE    110    121     43
D14V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4            110
  CLUS_2            0            121
  CLUS_3            3             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        1      2      1      2      1      0
  TP53 WILD-TYPE     28     35     63     38     79     32
D14V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             28
  CLUS_2            2             35
  CLUS_3            1             63
  CLUS_4            2             38
  CLUS_5            1             79
  CLUS_6            0             32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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        4      1      2
  TP53 WILD-TYPE    112     78     85
D14V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4            112
  CLUS_2            1             78
  CLUS_3            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      0      2
  TP53 WILD-TYPE     68     74     72
D14V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            0             74
  CLUS_3            2             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        0      4      0
  TP53 WILD-TYPE     91     91     32
D14V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             91
  CLUS_2            4             91
  CLUS_3            0             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = KRTAP4-5 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP4-5 MUTATED        2      2      1      0
  KRTAP4-5 WILD-TYPE    100     69     47     59
D15V1, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                100
  CLUS_2                2                 69
  CLUS_3                1                 47
  CLUS_4                0                 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 CLUS_6
  KRTAP4-5 MUTATED        1      1      2      0      0      1
  KRTAP4-5 WILD-TYPE     55     41     56     58     26     26
D15V2, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                1                 41
  CLUS_3                2                 56
  CLUS_4                0                 58
  CLUS_5                0                 26
  CLUS_6                1                 26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        2      1      1
  KRTAP4-5 WILD-TYPE     73     78     54
D15V3, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 73
  CLUS_2                1                 78
  CLUS_3                1                 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
  KRTAP4-5 MUTATED        2      0      1      1
  KRTAP4-5 WILD-TYPE     37     65     62     41
D15V4, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                0                 65
  CLUS_3                1                 62
  CLUS_4                1                 41
[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
  KRTAP4-5 MUTATED        1      2      1      0      1
  KRTAP4-5 WILD-TYPE     31     86     68     31     60
D15V5, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                2                 86
  CLUS_3                1                 68
  CLUS_4                0                 31
  CLUS_5                1                 60
[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
  KRTAP4-5 MUTATED        2      2      1
  KRTAP4-5 WILD-TYPE    112    119     45
D15V6, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                112
  CLUS_2                2                119
  CLUS_3                1                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRTAP4-5 MUTATED        1      2      1      0      0      1
  KRTAP4-5 WILD-TYPE     28     35     63     40     80     31
D15V7, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                2                 35
  CLUS_3                1                 63
  CLUS_4                0                 40
  CLUS_5                0                 80
  CLUS_6                1                 31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        3      1      1
  KRTAP4-5 WILD-TYPE    113     78     86
D15V8, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                3                113
  CLUS_2                1                 78
  CLUS_3                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        2      1      1
  KRTAP4-5 WILD-TYPE     68     73     73
D15V9, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 73
  CLUS_3                1                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP4-5 MUTATED        3      1      0
  KRTAP4-5 WILD-TYPE     88     94     32
D15V10, multiclass
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                1                 94
  CLUS_3                0                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        3      0      0      1
  BRAF WILD-TYPE     99     71     48     58
D16V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             99
  CLUS_2            0             71
  CLUS_3            0             48
  CLUS_4            1             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 CLUS_6
  BRAF MUTATED        2      0      1      0      0      0
  BRAF WILD-TYPE     54     42     57     58     26     27
D16V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             54
  CLUS_2            0             42
  CLUS_3            1             57
  CLUS_4            0             58
  CLUS_5            0             26
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      1      1
  BRAF WILD-TYPE     74     78     54
D16V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             74
  CLUS_2            1             78
  CLUS_3            1             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
  BRAF MUTATED        1      1      0      1
  BRAF WILD-TYPE     38     64     63     41
D16V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             38
  CLUS_2            1             64
  CLUS_3            0             63
  CLUS_4            1             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        0      1      2      0      1
  BRAF WILD-TYPE     32     87     67     31     60
D16V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             32
  CLUS_2            1             87
  CLUS_3            2             67
  CLUS_4            0             31
  CLUS_5            1             60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        2      2      0
  BRAF WILD-TYPE    112    119     46
D16V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2            112
  CLUS_2            2            119
  CLUS_3            0             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BRAF MUTATED        1      0      0      1      1      1
  BRAF WILD-TYPE     28     37     64     39     79     31
D16V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             28
  CLUS_2            0             37
  CLUS_3            0             64
  CLUS_4            1             39
  CLUS_5            1             79
  CLUS_6            1             31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      0      1
  BRAF WILD-TYPE    113     79     86
D16V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3            113
  CLUS_2            0             79
  CLUS_3            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        2      1      0
  BRAF WILD-TYPE     68     73     74
D16V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             68
  CLUS_2            1             73
  CLUS_3            0             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        3      0      0
  BRAF WILD-TYPE     88     95     32
D16V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             88
  CLUS_2            0             95
  CLUS_3            0             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = KIAA0922 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA0922 MUTATED        2      1      0      2
  KIAA0922 WILD-TYPE    100     70     48     57
D17V1, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                2                100
  CLUS_2                1                 70
  CLUS_3                0                 48
  CLUS_4                2                 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 CLUS_6
  KIAA0922 MUTATED        2      1      1      1      0      0
  KIAA0922 WILD-TYPE     54     41     57     57     26     27
D17V2, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                2                 54
  CLUS_2                1                 41
  CLUS_3                1                 57
  CLUS_4                1                 57
  CLUS_5                0                 26
  CLUS_6                0                 27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0922 MUTATED        1      1      0
  KIAA0922 WILD-TYPE     74     78     55
D17V3, multiclass
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 2                207 
        TCGA-2K-A9WE         TCGA-2Z-A9J1         TCGA-2Z-A9J3 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J6         TCGA-2Z-A9J7 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JI 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JJ         TCGA-2Z-A9JL         TCGA-2Z-A9JO 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JP         TCGA-2Z-A9JQ         TCGA-2Z-A9JT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-5P-A9JU         TCGA-5P-A9JY         TCGA-5P-A9KE 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7583         TCGA-A4-7584 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7915 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         TCGA-A4-8098 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8517         TCGA-A4-8630 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3472         TCGA-AL-3473 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-7173         TCGA-AL-A5DJ         TCGA-B1-5398 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-7332         TCGA-B1-A47M         TCGA-B1-A47N 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-A47O         TCGA-B1-A654         TCGA-B1-A657 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B3-8121         TCGA-B3-A6W5         TCGA-B9-5155 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-B9-A44B 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-A5W7         TCGA-B9-A5W8         TCGA-B9-A5W9 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-A69E         TCGA-B9-A8YH         TCGA-B9-A8YI 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5877         TCGA-BQ-5878 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5885 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-6846         TCGA-GL-7773 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-8500         TCGA-GL-A4EM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-GL-A9DD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-A9DE         TCGA-HE-7128         TCGA-HE-7129 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-7130         TCGA-HE-A5NF         TCGA-HE-A5NH 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-A5NL         TCGA-IA-A40U         TCGA-IA-A40X 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83V         TCGA-IA-A83W 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M8 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-MH-A55Z         TCGA-MH-A560         TCGA-MH-A562 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-MH-A855         TCGA-P4-A5E6         TCGA-P4-A5E7 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-P4-A5EB 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5ED         TCGA-P4-AAVL         TCGA-P4-AAVM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9         TCGA-PJ-A8JU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71U 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PJ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PK         TCGA-UZ-A9PL         TCGA-UZ-A9PM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PN         TCGA-UZ-A9PO         TCGA-UZ-A9PP 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PV         TCGA-UZ-A9PX         TCGA-UZ-A9PZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9Q0         TCGA-UZ-A9Q1         TCGA-V9-A7HT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A895 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A897         TCGA-Y8-A8RY 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA0922 MUTATED        1      1      0      0
  KIAA0922 WILD-TYPE     38     64     63     42
D17V4, multiclass
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 2                207 
        TCGA-2K-A9WE         TCGA-2Z-A9J1         TCGA-2Z-A9J3 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J6         TCGA-2Z-A9J7 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JI 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JJ         TCGA-2Z-A9JL         TCGA-2Z-A9JO 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JP         TCGA-2Z-A9JQ         TCGA-2Z-A9JT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-5P-A9JU         TCGA-5P-A9JY         TCGA-5P-A9KE 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7583         TCGA-A4-7584 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7915 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         TCGA-A4-8098 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8517         TCGA-A4-8630 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3472         TCGA-AL-3473 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-7173         TCGA-AL-A5DJ         TCGA-B1-5398 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-7332         TCGA-B1-A47M         TCGA-B1-A47N 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-A47O         TCGA-B1-A654         TCGA-B1-A657 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B3-8121         TCGA-B3-A6W5         TCGA-B9-5155 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-B9-A44B 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-A5W7         TCGA-B9-A5W8         TCGA-B9-A5W9 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-A69E         TCGA-B9-A8YH         TCGA-B9-A8YI 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5877         TCGA-BQ-5878 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5885 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-6846         TCGA-GL-7773 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-8500         TCGA-GL-A4EM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-GL-A9DD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-A9DE         TCGA-HE-7128         TCGA-HE-7129 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-7130         TCGA-HE-A5NF         TCGA-HE-A5NH 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-HE-A5NL         TCGA-IA-A40U         TCGA-IA-A40X 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83V         TCGA-IA-A83W 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M8 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-MH-A55Z         TCGA-MH-A560         TCGA-MH-A562 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-MH-A855         TCGA-P4-A5E6         TCGA-P4-A5E7 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-P4-A5EB 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5ED         TCGA-P4-AAVL         TCGA-P4-AAVM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9         TCGA-PJ-A8JU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71U 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PJ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PK         TCGA-UZ-A9PL         TCGA-UZ-A9PM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PN         TCGA-UZ-A9PO         TCGA-UZ-A9PP 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PV         TCGA-UZ-A9PX         TCGA-UZ-A9PZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9Q0         TCGA-UZ-A9Q1         TCGA-V9-A7HT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A895 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A897         TCGA-Y8-A8RY 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIAA0922 MUTATED        2      2      1      0      0
  KIAA0922 WILD-TYPE     30     86     68     31     61
D17V5, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                2                 30
  CLUS_2                2                 86
  CLUS_3                1                 68
  CLUS_4                0                 31
  CLUS_5                0                 61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0922 MUTATED        1      3      1
  KIAA0922 WILD-TYPE    113    118     45
D17V6, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                1                113
  CLUS_2                3                118
  CLUS_3                1                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KIAA0922 MUTATED        1      0      2      0      2      0
  KIAA0922 WILD-TYPE     28     37     62     40     78     32
D17V7, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                0                 37
  CLUS_3                2                 62
  CLUS_4                0                 40
  CLUS_5                2                 78
  CLUS_6                0                 32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0922 MUTATED        1      2      2
  KIAA0922 WILD-TYPE    115     77     85
D17V8, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                1                115
  CLUS_2                2                 77
  CLUS_3                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0922 MUTATED        0      0      3
  KIAA0922 WILD-TYPE     70     74     71
D17V9, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                0                 70
  CLUS_2                0                 74
  CLUS_3                3                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0922 MUTATED        0      3      0
  KIAA0922 WILD-TYPE     91     92     32
D17V10, multiclass
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  CLUS_1                0                 91
  CLUS_2                3                 92
  CLUS_3                0                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = KRT2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRT2 MUTATED        1      4      0      0
  KRT2 WILD-TYPE    101     67     48     59
D18V1, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            1            101
  CLUS_2            4             67
  CLUS_3            0             48
  CLUS_4            0             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 CLUS_6
  KRT2 MUTATED        1      1      2      1      0      0
  KRT2 WILD-TYPE     55     41     56     57     26     27
D18V2, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            1             55
  CLUS_2            1             41
  CLUS_3            2             56
  CLUS_4            1             57
  CLUS_5            0             26
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT2 MUTATED        2      2      1
  KRT2 WILD-TYPE     73     77     54
D18V3, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            2             73
  CLUS_2            2             77
  CLUS_3            1             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
  KRT2 MUTATED        1      2      1      1
  KRT2 WILD-TYPE     38     63     62     41
D18V4, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            1             38
  CLUS_2            2             63
  CLUS_3            1             62
  CLUS_4            1             41
[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
  KRT2 MUTATED        0      2      2      1      0
  KRT2 WILD-TYPE     32     86     67     30     61
D18V5, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            2             86
  CLUS_3            2             67
  CLUS_4            1             30
  CLUS_5            0             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT2 MUTATED        2      2      1
  KRT2 WILD-TYPE    112    119     45
D18V6, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            2            112
  CLUS_2            2            119
  CLUS_3            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRT2 MUTATED        0      1      2      0      1      1
  KRT2 WILD-TYPE     29     36     62     40     79     31
D18V7, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            0             29
  CLUS_2            1             36
  CLUS_3            2             62
  CLUS_4            0             40
  CLUS_5            1             79
  CLUS_6            1             31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT2 MUTATED        3      1      1
  KRT2 WILD-TYPE    113     78     86
D18V8, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            3            113
  CLUS_2            1             78
  CLUS_3            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT2 MUTATED        2      0      1
  KRT2 WILD-TYPE     68     74     73
D18V9, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            0             74
  CLUS_3            1             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRT2 MUTATED        1      1      1
  KRT2 WILD-TYPE     90     94     31
D18V10, multiclass
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  CLUS_1            1             90
  CLUS_2            1             94
  CLUS_3            1             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = ALMS1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ALMS1 MUTATED        5      1      0      2
  ALMS1 WILD-TYPE     97     70     48     57
D19V1, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             5              97
  CLUS_2             1              70
  CLUS_3             0              48
  CLUS_4             2              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 CLUS_6
  ALMS1 MUTATED        2      2      2      1      0      1
  ALMS1 WILD-TYPE     54     40     56     57     26     26
D19V2, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             2              54
  CLUS_2             2              40
  CLUS_3             2              56
  CLUS_4             1              57
  CLUS_5             0              26
  CLUS_6             1              26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ALMS1 MUTATED        3      2      2
  ALMS1 WILD-TYPE     72     77     53
D19V3, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             3              72
  CLUS_2             2              77
  CLUS_3             2              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
  ALMS1 MUTATED        0      1      4      2
  ALMS1 WILD-TYPE     39     64     59     40
D19V4, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             1              64
  CLUS_3             4              59
  CLUS_4             2              40
[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
  ALMS1 MUTATED        0      3      2      1      2
  ALMS1 WILD-TYPE     32     85     67     30     59
D19V5, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             3              85
  CLUS_3             2              67
  CLUS_4             1              30
  CLUS_5             2              59
[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
  ALMS1 MUTATED        3      3      2
  ALMS1 WILD-TYPE    111    118     44
D19V6, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             3             111
  CLUS_2             3             118
  CLUS_3             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ALMS1 MUTATED        0      1      1      2      3      1
  ALMS1 WILD-TYPE     29     36     63     38     77     31
D19V7, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             1              36
  CLUS_3             1              63
  CLUS_4             2              38
  CLUS_5             3              77
  CLUS_6             1              31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ALMS1 MUTATED        3      2      3
  ALMS1 WILD-TYPE    113     77     84
D19V8, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             3             113
  CLUS_2             2              77
  CLUS_3             3              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
  ALMS1 MUTATED        2      3      2
  ALMS1 WILD-TYPE     68     71     72
D19V9, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             2              68
  CLUS_2             3              71
  CLUS_3             2              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ALMS1 MUTATED        4      2      1
  ALMS1 WILD-TYPE     87     93     31
D19V10, multiclass
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  CLUS_1             4              87
  CLUS_2             2              93
  CLUS_3             1              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = GXYLT1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GXYLT1 MUTATED        0      2      1      1
  GXYLT1 WILD-TYPE    102     69     47     58
D20V1, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0              102
  CLUS_2              2               69
  CLUS_3              1               47
  CLUS_4              1               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 CLUS_6
  GXYLT1 MUTATED        0      1      1      1      1      0
  GXYLT1 WILD-TYPE     56     41     57     57     25     27
D20V2, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0               56
  CLUS_2              1               41
  CLUS_3              1               57
  CLUS_4              1               57
  CLUS_5              1               25
  CLUS_6              0               27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GXYLT1 MUTATED        0      2      1
  GXYLT1 WILD-TYPE     75     77     54
D20V3, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0               75
  CLUS_2              2               77
  CLUS_3              1               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
  GXYLT1 MUTATED        0      2      0      1
  GXYLT1 WILD-TYPE     39     63     63     41
D20V4, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0               39
  CLUS_2              2               63
  CLUS_3              0               63
  CLUS_4              1               41
[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
  GXYLT1 MUTATED        0      2      1      0      1
  GXYLT1 WILD-TYPE     32     86     68     31     60
D20V5, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              2               86
  CLUS_3              1               68
  CLUS_4              0               31
  CLUS_5              1               60
[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
  GXYLT1 MUTATED        2      2      0
  GXYLT1 WILD-TYPE    112    119     46
D20V6, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              2              112
  CLUS_2              2              119
  CLUS_3              0               46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GXYLT1 MUTATED        0      1      3      0      0      0
  GXYLT1 WILD-TYPE     29     36     61     40     80     32
D20V7, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              1               36
  CLUS_3              3               61
  CLUS_4              0               40
  CLUS_5              0               80
  CLUS_6              0               32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GXYLT1 MUTATED        1      2      1
  GXYLT1 WILD-TYPE    115     77     86
D20V8, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              1              115
  CLUS_2              2               77
  CLUS_3              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GXYLT1 MUTATED        1      2      0
  GXYLT1 WILD-TYPE     69     72     74
D20V9, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              2               72
  CLUS_3              0               74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GXYLT1 MUTATED        1      0      2
  GXYLT1 WILD-TYPE     90     95     30
D20V10, multiclass
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  CLUS_1              1               90
  CLUS_2              0               95
  CLUS_3              2               30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = ATP1B1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATP1B1 MUTATED        3      0      3      1
  ATP1B1 WILD-TYPE     99     71     45     58
D21V1, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              3               99
  CLUS_2              0               71
  CLUS_3              3               45
  CLUS_4              1               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 CLUS_6
  ATP1B1 MUTATED        2      1      0      1      1      1
  ATP1B1 WILD-TYPE     54     41     58     57     25     26
D21V2, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              1               41
  CLUS_3              0               58
  CLUS_4              1               57
  CLUS_5              1               25
  CLUS_6              1               26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ATP1B1 MUTATED        1      2      2
  ATP1B1 WILD-TYPE     74     77     53
D21V3, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              2               77
  CLUS_3              2               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
  ATP1B1 MUTATED        0      1      2      2
  ATP1B1 WILD-TYPE     39     64     61     40
D21V4, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              0               39
  CLUS_2              1               64
  CLUS_3              2               61
  CLUS_4              2               40
[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
  ATP1B1 MUTATED        0      0      4      0      3
  ATP1B1 WILD-TYPE     32     88     65     31     58
D21V5, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              0               88
  CLUS_3              4               65
  CLUS_4              0               31
  CLUS_5              3               58
[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
  ATP1B1 MUTATED        5      1      1
  ATP1B1 WILD-TYPE    109    120     45
D21V6, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              5              109
  CLUS_2              1              120
  CLUS_3              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ATP1B1 MUTATED        1      1      0      3      2      0
  ATP1B1 WILD-TYPE     28     36     64     37     78     32
D21V7, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              1               28
  CLUS_2              1               36
  CLUS_3              0               64
  CLUS_4              3               37
  CLUS_5              2               78
  CLUS_6              0               32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ATP1B1 MUTATED        4      1      2
  ATP1B1 WILD-TYPE    112     78     85
D21V8, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              4              112
  CLUS_2              1               78
  CLUS_3              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ATP1B1 MUTATED        4      0      1
  ATP1B1 WILD-TYPE     66     74     73
D21V9, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              4               66
  CLUS_2              0               74
  CLUS_3              1               73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ATP1B1 MUTATED        2      3      0
  ATP1B1 WILD-TYPE     89     92     32
D21V10, multiclass
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  CLUS_1              2               89
  CLUS_2              3               92
  CLUS_3              0               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = PBRM1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PBRM1 MUTATED        5      2      1      3
  PBRM1 WILD-TYPE     97     69     47     56
D22V1, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             5              97
  CLUS_2             2              69
  CLUS_3             1              47
  CLUS_4             3              56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PBRM1 MUTATED        0      3      2      1      5      0
  PBRM1 WILD-TYPE     56     39     56     57     21     27
D22V2, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             3              39
  CLUS_3             2              56
  CLUS_4             1              57
  CLUS_5             5              21
  CLUS_6             0              27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED        3      2      5
  PBRM1 WILD-TYPE     72     77     50
D22V3, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             3              72
  CLUS_2             2              77
  CLUS_3             5              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
  PBRM1 MUTATED        1      2      2      5
  PBRM1 WILD-TYPE     38     63     61     37
D22V4, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1              38
  CLUS_2             2              63
  CLUS_3             2              61
  CLUS_4             5              37
[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
  PBRM1 MUTATED        1      2      7      0      1
  PBRM1 WILD-TYPE     31     86     62     31     60
D22V5, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1              31
  CLUS_2             2              86
  CLUS_3             7              62
  CLUS_4             0              31
  CLUS_5             1              60
[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
  PBRM1 MUTATED        8      3      0
  PBRM1 WILD-TYPE    106    118     46
D22V6, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             8             106
  CLUS_2             3             118
  CLUS_3             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PBRM1 MUTATED        1      3      2      4      0      1
  PBRM1 WILD-TYPE     28     34     62     36     80     31
D22V7, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             3              34
  CLUS_3             2              62
  CLUS_4             4              36
  CLUS_5             0              80
  CLUS_6             1              31
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       10      1      0
  PBRM1 WILD-TYPE    106     78     87
D22V8, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            10             106
  CLUS_2             1              78
  CLUS_3             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED        4      1      3
  PBRM1 WILD-TYPE     66     73     71
D22V9, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             1              73
  CLUS_3             3              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED        5      3      0
  PBRM1 WILD-TYPE     86     92     32
D22V10, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             5              86
  CLUS_2             3              92
  CLUS_3             0              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        2      1      1      2
  PTEN WILD-TYPE    100     70     47     57
D23V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2            100
  CLUS_2            1             70
  CLUS_3            1             47
  CLUS_4            2             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 CLUS_6
  PTEN MUTATED        0      2      1      4      0      0
  PTEN WILD-TYPE     56     40     57     54     26     27
D23V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             56
  CLUS_2            2             40
  CLUS_3            1             57
  CLUS_4            4             54
  CLUS_5            0             26
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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        2      3      2
  PTEN WILD-TYPE     73     76     53
D23V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             73
  CLUS_2            3             76
  CLUS_3            2             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
  PTEN MUTATED        2      2      1      2
  PTEN WILD-TYPE     37     63     62     40
D23V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             37
  CLUS_2            2             63
  CLUS_3            1             62
  CLUS_4            2             40
[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      1      3      1      0
  PTEN WILD-TYPE     31     87     66     30     61
D23V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             31
  CLUS_2            1             87
  CLUS_3            3             66
  CLUS_4            1             30
  CLUS_5            0             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      4      1
  PTEN WILD-TYPE    113    117     45
D23V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1            113
  CLUS_2            4            117
  CLUS_3            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        1      3      1      0      2      0
  PTEN WILD-TYPE     28     34     63     40     78     32
D23V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             28
  CLUS_2            3             34
  CLUS_3            1             63
  CLUS_4            0             40
  CLUS_5            2             78
  CLUS_6            0             32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      3      1
  PTEN WILD-TYPE    113     76     86
D23V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3            113
  CLUS_2            3             76
  CLUS_3            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        2      2      1
  PTEN WILD-TYPE     68     72     73
D23V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             68
  CLUS_2            2             72
  CLUS_3            1             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      0      1
  PTEN WILD-TYPE     87     95     31
D23V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             87
  CLUS_2            0             95
  CLUS_3            1             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = SAV1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SAV1 MUTATED        1      0      1      4
  SAV1 WILD-TYPE    101     71     47     55
D24V1, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            1            101
  CLUS_2            0             71
  CLUS_3            1             47
  CLUS_4            4             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 CLUS_6
  SAV1 MUTATED        1      0      0      0      1      3
  SAV1 WILD-TYPE     55     42     58     58     25     24
D24V2, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            1             55
  CLUS_2            0             42
  CLUS_3            0             58
  CLUS_4            0             58
  CLUS_5            1             25
  CLUS_6            3             24
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SAV1 MUTATED        3      1      0
  SAV1 WILD-TYPE     72     78     55
D24V3, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            3             72
  CLUS_2            1             78
  CLUS_3            0             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
  SAV1 MUTATED        0      1      3      0
  SAV1 WILD-TYPE     39     64     60     42
D24V4, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            0             39
  CLUS_2            1             64
  CLUS_3            3             60
  CLUS_4            0             42
[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
  SAV1 MUTATED        0      0      0      0      6
  SAV1 WILD-TYPE     32     88     69     31     55
D24V5, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            0             88
  CLUS_3            0             69
  CLUS_4            0             31
  CLUS_5            6             55
[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
  SAV1 MUTATED        1      0      5
  SAV1 WILD-TYPE    113    121     41
D24V6, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            1            113
  CLUS_2            0            121
  CLUS_3            5             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SAV1 MUTATED        0      1      1      3      1      0
  SAV1 WILD-TYPE     29     36     63     37     79     32
D24V7, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            0             29
  CLUS_2            1             36
  CLUS_3            1             63
  CLUS_4            3             37
  CLUS_5            1             79
  CLUS_6            0             32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SAV1 MUTATED        1      4      1
  SAV1 WILD-TYPE    115     75     86
D24V8, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            1            115
  CLUS_2            4             75
  CLUS_3            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SAV1 MUTATED        0      3      1
  SAV1 WILD-TYPE     70     71     73
D24V9, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            0             70
  CLUS_2            3             71
  CLUS_3            1             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SAV1 MUTATED        3      1      0
  SAV1 WILD-TYPE     88     94     32
D24V10, multiclass
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  CLUS_1            3             88
  CLUS_2            1             94
  CLUS_3            0             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = CALCR MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CALCR MUTATED        1      1      0      1
  CALCR WILD-TYPE    101     70     48     58
D25V1, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             1             101
  CLUS_2             1              70
  CLUS_3             0              48
  CLUS_4             1              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 CLUS_6
  CALCR MUTATED        1      0      2      0      0      0
  CALCR WILD-TYPE     55     42     56     58     26     27
D25V2, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             1              55
  CLUS_2             0              42
  CLUS_3             2              56
  CLUS_4             0              58
  CLUS_5             0              26
  CLUS_6             0              27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CALCR MUTATED        2      1      0
  CALCR WILD-TYPE     73     78     55
D25V3, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             2              73
  CLUS_2             1              78
  CLUS_3             0              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
  CALCR MUTATED        1      1      1      0
  CALCR WILD-TYPE     38     64     62     42
D25V4, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             1              38
  CLUS_2             1              64
  CLUS_3             1              62
  CLUS_4             0              42
[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
  CALCR MUTATED        0      2      0      1      0
  CALCR WILD-TYPE     32     86     69     30     61
D25V5, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             0              32
  CLUS_2             2              86
  CLUS_3             0              69
  CLUS_4             1              30
  CLUS_5             0              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CALCR MUTATED        0      1      2
  CALCR WILD-TYPE    114    120     44
D25V6, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             0             114
  CLUS_2             1             120
  CLUS_3             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CALCR MUTATED        0      0      0      1      2      0
  CALCR WILD-TYPE     29     37     64     39     78     32
D25V7, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             0              29
  CLUS_2             0              37
  CLUS_3             0              64
  CLUS_4             1              39
  CLUS_5             2              78
  CLUS_6             0              32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CALCR MUTATED        1      0      2
  CALCR WILD-TYPE    115     79     85
D25V8, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             1             115
  CLUS_2             0              79
  CLUS_3             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CALCR MUTATED        0      1      2
  CALCR WILD-TYPE     70     73     72
D25V9, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             0              70
  CLUS_2             1              73
  CLUS_3             2              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CALCR MUTATED        1      2      0
  CALCR WILD-TYPE     90     93     32
D25V10, multiclass
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  CLUS_1             1              90
  CLUS_2             2              93
  CLUS_3             0              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = IGSF3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IGSF3 MUTATED        3      1      0      0
  IGSF3 WILD-TYPE     99     70     48     59
D26V1, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3              99
  CLUS_2             1              70
  CLUS_3             0              48
  CLUS_4             0              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 CLUS_6
  IGSF3 MUTATED        1      2      1      0      0      0
  IGSF3 WILD-TYPE     55     40     57     58     26     27
D26V2, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             1              55
  CLUS_2             2              40
  CLUS_3             1              57
  CLUS_4             0              58
  CLUS_5             0              26
  CLUS_6             0              27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        0      1      3
  IGSF3 WILD-TYPE     75     78     52
D26V3, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             1              78
  CLUS_3             3              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IGSF3 MUTATED        0      1      0      3
  IGSF3 WILD-TYPE     39     64     63     39
D26V4, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             1              64
  CLUS_3             0              63
  CLUS_4             3              39
[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
  IGSF3 MUTATED        0      1      3      0      0
  IGSF3 WILD-TYPE     32     87     66     31     61
D26V5, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             1              87
  CLUS_3             3              66
  CLUS_4             0              31
  CLUS_5             0              61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        3      1      0
  IGSF3 WILD-TYPE    111    120     46
D26V6, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3             111
  CLUS_2             1             120
  CLUS_3             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IGSF3 MUTATED        0      1      1      1      1      0
  IGSF3 WILD-TYPE     29     36     63     39     79     32
D26V7, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             1              36
  CLUS_3             1              63
  CLUS_4             1              39
  CLUS_5             1              79
  CLUS_6             0              32
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        4      0      0
  IGSF3 WILD-TYPE    112     79     87
D26V8, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             4             112
  CLUS_2             0              79
  CLUS_3             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        3      0      0
  IGSF3 WILD-TYPE     67     74     74
D26V9, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             0              74
  CLUS_3             0              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGSF3 MUTATED        1      2      0
  IGSF3 WILD-TYPE     90     93     32
D26V10, multiclass
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  CLUS_1             1              90
  CLUS_2             2              93
  CLUS_3             0              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
