[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTCESC-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/CESC-TP/11589698/CESC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/11562021/transformed.cor.cli.txt"

nPatients in clinical file=307, in cluster file=194, common to both=194
[1]  38 194
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
[1] "FAT2 MUTATION ANALYSIS"
[1] 3
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              184 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              184 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
[1] "RAB35 MUTATION ANALYSIS"
[1] 3
  RAB35 MUTATED RAB35 WILD-TYPE 
              4             190 
  RAB35 MUTATED RAB35 WILD-TYPE 
              4             190 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             11             183 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             11             183 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             187 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             187 
[1] "TCTE1 MUTATION ANALYSIS"
[1] 3
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              5             189 
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              5             189 
[1] "NHS MUTATION ANALYSIS"
[1] 3
  NHS MUTATED NHS WILD-TYPE 
           12           182 
  NHS MUTATED NHS WILD-TYPE 
           12           182 
[1] "LIN9 MUTATION ANALYSIS"
[1] 3
  LIN9 MUTATED LIN9 WILD-TYPE 
             7            187 
  LIN9 MUTATED LIN9 WILD-TYPE 
             7            187 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
[1] "MED1 MUTATION ANALYSIS"
[1] 3
  MED1 MUTATED MED1 WILD-TYPE 
            11            183 
  MED1 MUTATED MED1 WILD-TYPE 
            11            183 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
[1] "IDS MUTATION ANALYSIS"
[1] 3
  IDS MUTATED IDS WILD-TYPE 
            7           187 
  IDS MUTATED IDS WILD-TYPE 
            7           187 
[1] "TRIM9 MUTATION ANALYSIS"
[1] 3
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              8             186 
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              8             186 
[1] "SEMA4B MUTATION ANALYSIS"
[1] 3
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               7              187 
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               7              187 
[1] "ARHGAP4 MUTATION ANALYSIS"
[1] 3
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                6               188 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                6               188 
[1] "POU2F1 MUTATION ANALYSIS"
[1] 3
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               3              191 
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               3              191 
[1] "IFNGR1 MUTATION ANALYSIS"
[1] 3
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
[1] "IGFN1 MUTATION ANALYSIS"
[1] 3
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             11             183 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             11             183 
[1] "RPGR MUTATION ANALYSIS"
[1] 3
  RPGR MUTATED RPGR WILD-TYPE 
             9            185 
  RPGR MUTATED RPGR WILD-TYPE 
             9            185 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
             4            190 
  GAS6 MUTATED GAS6 WILD-TYPE 
             4            190 
[1] "ABCD1 MUTATION ANALYSIS"
[1] 3
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              7             187 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              7             187 
[1] "RPAP1 MUTATION ANALYSIS"
[1] 3
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              4             190 
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              4             190 
[1] "HIST1H4E MUTATION ANALYSIS"
[1] 3
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 4                190 
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 4                190 
[1] "NLRC5 MUTATION ANALYSIS"
[1] 3
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             187 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             187 
[1] "DDX41 MUTATION ANALYSIS"
[1] 3
  DDX41 MUTATED DDX41 WILD-TYPE 
              5             189 
  DDX41 MUTATED DDX41 WILD-TYPE 
              5             189 
[1] "MCM7 MUTATION ANALYSIS"
[1] 3
  MCM7 MUTATED MCM7 WILD-TYPE 
             3            191 
  MCM7 MUTATED MCM7 WILD-TYPE 
             3            191 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 194 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 194 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        7      1      3
  KRAS WILD-TYPE     83     39     58
D1V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7             83
  CLUS_2            1             39
  CLUS_3            3             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED       10      0      0      0      0      1
  KRAS WILD-TYPE     38     34     37     35     28     11
D1V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             38
  CLUS_2            0             34
  CLUS_3            0             37
  CLUS_4            0             35
  CLUS_5            0             28
  CLUS_6            1             11
[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       10      0      1
  KRAS WILD-TYPE     56     80     44
D1V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             56
  CLUS_2            0             80
  CLUS_3            1             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
  KRAS MUTATED        8      2      1
  KRAS WILD-TYPE     40    118     22
D1V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8             40
  CLUS_2            2            118
  CLUS_3            1             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        7      4      0
  KRAS WILD-TYPE     52     52     79
D1V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7             52
  CLUS_2            4             52
  CLUS_3            0             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        8      0      2      1      0
  KRAS WILD-TYPE     33     50     56     14     30
D1V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8             33
  CLUS_2            0             50
  CLUS_3            2             56
  CLUS_4            1             14
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        6      5      0
  KRAS WILD-TYPE     63     52     58
D1V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             63
  CLUS_2            5             52
  CLUS_3            0             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        9      1      0      1
  KRAS WILD-TYPE     33     31     28     81
D1V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             33
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            1             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = HLA-A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        9      4      2
  HLA-A WILD-TYPE     81     36     59
D2V1, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             9              81
  CLUS_2             4              36
  CLUS_3             2              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HLA-A MUTATED        1      3      5      6      1      0
  HLA-A WILD-TYPE     47     31     32     29     27     12
D2V2, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              47
  CLUS_2             3              31
  CLUS_3             5              32
  CLUS_4             6              29
  CLUS_5             1              27
  CLUS_6             0              12
[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
  HLA-A MUTATED        1      6      8
  HLA-A WILD-TYPE     65     74     37
D2V3, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              65
  CLUS_2             6              74
  CLUS_3             8              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        1     11      3
  HLA-A WILD-TYPE     47    109     20
D2V4, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              47
  CLUS_2            11             109
  CLUS_3             3              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        3      4      9
  HLA-A WILD-TYPE     56     52     70
D2V5, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             3              56
  CLUS_2             4              52
  CLUS_3             9              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 CLUS_4 CLUS_5
  HLA-A MUTATED        0      4      3      3      6
  HLA-A WILD-TYPE     41     46     55     12     24
D2V6, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             0              41
  CLUS_2             4              46
  CLUS_3             3              55
  CLUS_4             3              12
  CLUS_5             6              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-A MUTATED        4      4      6
  HLA-A WILD-TYPE     65     53     52
D2V7, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             4              65
  CLUS_2             4              53
  CLUS_3             6              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
  HLA-A MUTATED        1      2      2      9
  HLA-A WILD-TYPE     41     30     26     73
D2V8, multiclass
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  CLUS_1             1              41
  CLUS_2             2              30
  CLUS_3             2              26
  CLUS_4             9              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED       11      3      4
  FBXW7 WILD-TYPE     79     37     57
D3V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            11              79
  CLUS_2             3              37
  CLUS_3             4              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FBXW7 MUTATED        6      4      4      5      0      0
  FBXW7 WILD-TYPE     42     30     33     30     28     12
D3V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              42
  CLUS_2             4              30
  CLUS_3             4              33
  CLUS_4             5              30
  CLUS_5             0              28
  CLUS_6             0              12
[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
  FBXW7 MUTATED        6      8      4
  FBXW7 WILD-TYPE     60     72     41
D3V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              60
  CLUS_2             8              72
  CLUS_3             4              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
  FBXW7 MUTATED        6     11      1
  FBXW7 WILD-TYPE     42    109     22
D3V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              42
  CLUS_2            11             109
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        6      3     10
  FBXW7 WILD-TYPE     53     53     69
D3V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              53
  CLUS_2             3              53
  CLUS_3            10              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 CLUS_4 CLUS_5
  FBXW7 MUTATED        4      8      3      1      3
  FBXW7 WILD-TYPE     37     42     55     14     27
D3V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              37
  CLUS_2             8              42
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             3              27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED       10      3      6
  FBXW7 WILD-TYPE     59     54     52
D3V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            10              59
  CLUS_2             3              54
  CLUS_3             6              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
  FBXW7 MUTATED        5      1      3     10
  FBXW7 WILD-TYPE     37     31     25     72
D3V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5              37
  CLUS_2             1              31
  CLUS_3             3              25
  CLUS_4            10              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = HLA-B MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        7      2      2
  HLA-B WILD-TYPE     83     38     59
D4V1, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             7              83
  CLUS_2             2              38
  CLUS_3             2              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HLA-B MUTATED        0      4      3      2      1      1
  HLA-B WILD-TYPE     48     30     34     33     27     11
D4V2, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4              30
  CLUS_3             3              34
  CLUS_4             2              33
  CLUS_5             1              27
  CLUS_6             1              11
[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
  HLA-B MUTATED        1      4      6
  HLA-B WILD-TYPE     65     76     39
D4V3, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              65
  CLUS_2             4              76
  CLUS_3             6              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        0     10      1
  HLA-B WILD-TYPE     48    110     22
D4V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              48
  CLUS_2            10             110
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        1      1      9
  HLA-B WILD-TYPE     58     55     70
D4V5, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              58
  CLUS_2             1              55
  CLUS_3             9              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 CLUS_4 CLUS_5
  HLA-B MUTATED        0      5      2      1      3
  HLA-B WILD-TYPE     41     45     56     14     27
D4V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              41
  CLUS_2             5              45
  CLUS_3             2              56
  CLUS_4             1              14
  CLUS_5             3              27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        3      0      7
  HLA-B WILD-TYPE     66     57     51
D4V7, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              66
  CLUS_2             0              57
  CLUS_3             7              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-B MUTATED        0      0      2      8
  HLA-B WILD-TYPE     42     32     26     74
D4V8, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              32
  CLUS_3             2              26
  CLUS_4             8              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        9      3      3
  PTEN WILD-TYPE     81     37     58
D5V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            9             81
  CLUS_2            3             37
  CLUS_3            3             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        5      2      3      1      4      0
  PTEN WILD-TYPE     43     32     34     34     24     12
D5V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             43
  CLUS_2            2             32
  CLUS_3            3             34
  CLUS_4            1             34
  CLUS_5            4             24
  CLUS_6            0             12
[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        6      9      0
  PTEN WILD-TYPE     60     71     45
D5V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             60
  CLUS_2            9             71
  CLUS_3            0             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
  PTEN MUTATED        6      9      0
  PTEN WILD-TYPE     42    111     23
D5V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             42
  CLUS_2            9            111
  CLUS_3            0             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      3      5
  PTEN WILD-TYPE     52     53     74
D5V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             52
  CLUS_2            3             53
  CLUS_3            5             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        4      6      3      2      0
  PTEN WILD-TYPE     37     44     55     13     30
D5V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             37
  CLUS_2            6             44
  CLUS_3            3             55
  CLUS_4            2             13
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        6      4      5
  PTEN WILD-TYPE     63     53     53
D5V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             63
  CLUS_2            4             53
  CLUS_3            5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        4      4      3      4
  PTEN WILD-TYPE     38     28     25     78
D5V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             38
  CLUS_2            4             28
  CLUS_3            3             25
  CLUS_4            4             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       11      3      0
  ARID1A WILD-TYPE     79     37     61
D6V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             11               79
  CLUS_2              3               37
  CLUS_3              0               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED       10      2      2      0      0      0
  ARID1A WILD-TYPE     38     32     35     35     28     12
D6V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               38
  CLUS_2              2               32
  CLUS_3              2               35
  CLUS_4              0               35
  CLUS_5              0               28
  CLUS_6              0               12
[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
  ARID1A MUTATED       10      2      2
  ARID1A WILD-TYPE     56     78     43
D6V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               56
  CLUS_2              2               78
  CLUS_3              2               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
  ARID1A MUTATED       10      4      0
  ARID1A WILD-TYPE     38    116     23
D6V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               38
  CLUS_2              4              116
  CLUS_3              0               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        8      2      4
  ARID1A WILD-TYPE     51     54     75
D6V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              8               51
  CLUS_2              2               54
  CLUS_3              4               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        7      1      1      3      2
  ARID1A WILD-TYPE     34     49     57     12     28
D6V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               34
  CLUS_2              1               49
  CLUS_3              1               57
  CLUS_4              3               12
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        6      3      3
  ARID1A WILD-TYPE     63     54     55
D6V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               63
  CLUS_2              3               54
  CLUS_3              3               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        7      0      3      2
  ARID1A WILD-TYPE     35     32     25     80
D6V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               35
  CLUS_2              0               32
  CLUS_3              3               25
  CLUS_4              2               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MAPK1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        6      1      2
  MAPK1 WILD-TYPE     84     39     59
D7V1, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             6              84
  CLUS_2             1              39
  CLUS_3             2              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MAPK1 MUTATED        0      2      3      1      2      1
  MAPK1 WILD-TYPE     48     32     34     34     26     11
D7V2, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             2              32
  CLUS_3             3              34
  CLUS_4             1              34
  CLUS_5             2              26
  CLUS_6             1              11
[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
  MAPK1 MUTATED        0      7      2
  MAPK1 WILD-TYPE     66     73     43
D7V3, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              66
  CLUS_2             7              73
  CLUS_3             2              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
  MAPK1 MUTATED        0      9      0
  MAPK1 WILD-TYPE     48    111     23
D7V4, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             9             111
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        1      5      3
  MAPK1 WILD-TYPE     58     51     76
D7V5, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             1              58
  CLUS_2             5              51
  CLUS_3             3              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MAPK1 MUTATED        0      2      6      1      0
  MAPK1 WILD-TYPE     41     48     52     14     30
D7V6, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              48
  CLUS_3             6              52
  CLUS_4             1              14
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MAPK1 MUTATED        0      5      4
  MAPK1 WILD-TYPE     69     52     54
D7V7, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              69
  CLUS_2             5              52
  CLUS_3             4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAPK1 MUTATED        0      5      1      3
  MAPK1 WILD-TYPE     42     27     27     79
D7V8, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             5              27
  CLUS_3             1              27
  CLUS_4             3              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = EP300 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED       10      4      6
  EP300 WILD-TYPE     80     36     55
D8V1, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1            10              80
  CLUS_2             4              36
  CLUS_3             6              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EP300 MUTATED        3      7      5      1      3      2
  EP300 WILD-TYPE     45     27     32     34     25     10
D8V2, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             7              27
  CLUS_3             5              32
  CLUS_4             1              34
  CLUS_5             3              25
  CLUS_6             2              10
[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
  EP300 MUTATED        4     14      3
  EP300 WILD-TYPE     62     66     42
D8V3, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             4              62
  CLUS_2            14              66
  CLUS_3             3              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
  EP300 MUTATED        2     18      1
  EP300 WILD-TYPE     46    102     22
D8V4, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              46
  CLUS_2            18             102
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        6      5     10
  EP300 WILD-TYPE     53     51     69
D8V5, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             6              53
  CLUS_2             5              51
  CLUS_3            10              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 CLUS_4 CLUS_5
  EP300 MUTATED        1      9     10      1      0
  EP300 WILD-TYPE     40     41     48     14     30
D8V6, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             9              41
  CLUS_3            10              48
  CLUS_4             1              14
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        7      5      6
  EP300 WILD-TYPE     62     52     52
D8V7, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             7              62
  CLUS_2             5              52
  CLUS_3             6              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
  EP300 MUTATED        2      3      1     12
  EP300 WILD-TYPE     40     29     27     70
D8V8, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             3              29
  CLUS_3             1              27
  CLUS_4            12              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       33      7     13
  PIK3CA WILD-TYPE     57     33     48
D9V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             33               57
  CLUS_2              7               33
  CLUS_3             13               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 CLUS_5 CLUS_6
  PIK3CA MUTATED       17     10     11      5      9      1
  PIK3CA WILD-TYPE     31     24     26     30     19     11
D9V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             17               31
  CLUS_2             10               24
  CLUS_3             11               26
  CLUS_4              5               30
  CLUS_5              9               19
  CLUS_6              1               11
[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
  PIK3CA MUTATED       22     22      8
  PIK3CA WILD-TYPE     44     58     37
D9V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             22               44
  CLUS_2             22               58
  CLUS_3              8               37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       18     32      2
  PIK3CA WILD-TYPE     30     88     21
D9V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             18               30
  CLUS_2             32               88
  CLUS_3              2               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       20     12     21
  PIK3CA WILD-TYPE     39     44     58
D9V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             20               39
  CLUS_2             12               44
  CLUS_3             21               58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED       14     17     13      4      5
  PIK3CA WILD-TYPE     27     33     45     11     25
D9V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             14               27
  CLUS_2             17               33
  CLUS_3             13               45
  CLUS_4              4               11
  CLUS_5              5               25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       22     13     14
  PIK3CA WILD-TYPE     47     44     44
D9V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             22               47
  CLUS_2             13               44
  CLUS_3             14               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
  PIK3CA MUTATED       16      9      7     17
  PIK3CA WILD-TYPE     26     23     21     65
D9V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             16               26
  CLUS_2              9               23
  CLUS_3              7               21
  CLUS_4             17               65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = NFE2L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        5      3      4
  NFE2L2 WILD-TYPE     85     37     57
D10V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              5               85
  CLUS_2              3               37
  CLUS_3              4               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NFE2L2 MUTATED        0      5      2      2      3      0
  NFE2L2 WILD-TYPE     48     29     35     33     25     12
D10V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              5               29
  CLUS_3              2               35
  CLUS_4              2               33
  CLUS_5              3               25
  CLUS_6              0               12
[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
  NFE2L2 MUTATED        1      7      4
  NFE2L2 WILD-TYPE     65     73     41
D10V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              7               73
  CLUS_3              4               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
  NFE2L2 MUTATED        0     11      1
  NFE2L2 WILD-TYPE     48    109     22
D10V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               48
  CLUS_2             11              109
  CLUS_3              1               22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0      5      7
  NFE2L2 WILD-TYPE     59     51     72
D10V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               59
  CLUS_2              5               51
  CLUS_3              7               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED        0      1      6      3      2
  NFE2L2 WILD-TYPE     41     49     52     12     28
D10V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              1               49
  CLUS_3              6               52
  CLUS_4              3               12
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        2      4      5
  NFE2L2 WILD-TYPE     67     53     53
D10V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               67
  CLUS_2              4               53
  CLUS_3              5               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED        0      2      4      5
  NFE2L2 WILD-TYPE     42     30     24     77
D10V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              2               30
  CLUS_3              4               24
  CLUS_4              5               77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = FAT2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        6      3      2
  FAT2 WILD-TYPE     84     37     59
D11V1, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            6             84
  CLUS_2            3             37
  CLUS_3            2             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAT2 MUTATED        1      5      2      2      1      0
  FAT2 WILD-TYPE     47     29     35     33     27     12
D11V2, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            5             29
  CLUS_3            2             35
  CLUS_4            2             33
  CLUS_5            1             27
  CLUS_6            0             12
[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
  FAT2 MUTATED        1      5      5
  FAT2 WILD-TYPE     65     75     40
D11V3, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             65
  CLUS_2            5             75
  CLUS_3            5             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        1      9      1
  FAT2 WILD-TYPE     47    111     22
D11V4, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            9            111
  CLUS_3            1             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        2      3      6
  FAT2 WILD-TYPE     57     53     73
D11V5, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            2             57
  CLUS_2            3             53
  CLUS_3            6             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 CLUS_4 CLUS_5
  FAT2 MUTATED        1      4      4      0      2
  FAT2 WILD-TYPE     40     46     54     15     28
D11V6, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            4             46
  CLUS_3            4             54
  CLUS_4            0             15
  CLUS_5            2             28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FAT2 MUTATED        3      1      7
  FAT2 WILD-TYPE     66     56     51
D11V7, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            3             66
  CLUS_2            1             56
  CLUS_3            7             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAT2 MUTATED        1      0      1      9
  FAT2 WILD-TYPE     41     32     27     73
D11V8, multiclass
        clus
vv       FAT2 MUTATED FAT2 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            0             32
  CLUS_3            1             27
  CLUS_4            9             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = ZNF750 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        8      0      2
  ZNF750 WILD-TYPE     82     40     59
D12V1, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              8               82
  CLUS_2              0               40
  CLUS_3              2               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZNF750 MUTATED        1      3      4      1      0      1
  ZNF750 WILD-TYPE     47     31     33     34     28     11
D12V2, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              1               47
  CLUS_2              3               31
  CLUS_3              4               33
  CLUS_4              1               34
  CLUS_5              0               28
  CLUS_6              1               11
[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
  ZNF750 MUTATED        2      5      3
  ZNF750 WILD-TYPE     64     75     42
D12V3, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               64
  CLUS_2              5               75
  CLUS_3              3               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
  ZNF750 MUTATED        0      9      1
  ZNF750 WILD-TYPE     48    111     22
D12V4, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              9              111
  CLUS_3              1               22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        2      1      7
  ZNF750 WILD-TYPE     57     55     72
D12V5, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              2               57
  CLUS_2              1               55
  CLUS_3              7               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZNF750 MUTATED        0      5      2      1      2
  ZNF750 WILD-TYPE     41     45     56     14     28
D12V6, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              5               45
  CLUS_3              2               56
  CLUS_4              1               14
  CLUS_5              2               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF750 MUTATED        4      1      4
  ZNF750 WILD-TYPE     65     56     54
D12V7, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              4               65
  CLUS_2              1               56
  CLUS_3              4               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF750 MUTATED        0      0      2      7
  ZNF750 WILD-TYPE     42     32     26     75
D12V8, multiclass
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               32
  CLUS_3              2               26
  CLUS_4              7               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        4      0      0
  BAP1 WILD-TYPE     86     40     61
D13V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4             86
  CLUS_2            0             40
  CLUS_3            0             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BAP1 MUTATED        0      3      1      0      0      0
  BAP1 WILD-TYPE     48     31     36     35     28     12
D13V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            3             31
  CLUS_3            1             36
  CLUS_4            0             35
  CLUS_5            0             28
  CLUS_6            0             12
[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
  BAP1 MUTATED        0      4      0
  BAP1 WILD-TYPE     66     76     45
D13V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             66
  CLUS_2            4             76
  CLUS_3            0             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
  BAP1 MUTATED        0      4      0
  BAP1 WILD-TYPE     48    116     23
D13V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            4            116
  CLUS_3            0             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        1      2      1
  BAP1 WILD-TYPE     58     54     78
D13V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             58
  CLUS_2            2             54
  CLUS_3            1             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 CLUS_4 CLUS_5
  BAP1 MUTATED        0      2      1      1      0
  BAP1 WILD-TYPE     41     48     57     14     30
D13V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            2             48
  CLUS_3            1             57
  CLUS_4            1             14
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        0      2      2
  BAP1 WILD-TYPE     69     55     56
D13V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             69
  CLUS_2            2             55
  CLUS_3            2             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED        0      2      1      1
  BAP1 WILD-TYPE     42     30     27     81
D13V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            2             30
  CLUS_3            1             27
  CLUS_4            1             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = RAB35 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RAB35 MUTATED        1      0      3
  RAB35 WILD-TYPE     89     40     58
D14V1, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             0              40
  CLUS_3             3              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RAB35 MUTATED        0      0      2      1      0      1
  RAB35 WILD-TYPE     48     34     35     34     28     11
D14V2, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             0              34
  CLUS_3             2              35
  CLUS_4             1              34
  CLUS_5             0              28
  CLUS_6             1              11
[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
  RAB35 MUTATED        1      2      1
  RAB35 WILD-TYPE     65     78     44
D14V3, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             2              78
  CLUS_3             1              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
  RAB35 MUTATED        0      4      0
  RAB35 WILD-TYPE     48    116     23
D14V4, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4             116
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RAB35 MUTATED        0      2      2
  RAB35 WILD-TYPE     59     54     77
D14V5, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              59
  CLUS_2             2              54
  CLUS_3             2              77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RAB35 MUTATED        0      0      3      1      0
  RAB35 WILD-TYPE     41     50     55     14     30
D14V6, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             0              50
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RAB35 MUTATED        0      1      2
  RAB35 WILD-TYPE     69     56     56
D14V7, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              69
  CLUS_2             1              56
  CLUS_3             2              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RAB35 MUTATED        0      1      2      0
  RAB35 WILD-TYPE     42     31     26     82
D14V8, multiclass
        clus
vv       RAB35 MUTATED RAB35 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              31
  CLUS_3             2              26
  CLUS_4             0              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = ERBB3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB3 MUTATED        5      5      1
  ERBB3 WILD-TYPE     85     35     60
D15V1, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             5              85
  CLUS_2             5              35
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ERBB3 MUTATED        5      3      1      1      1      0
  ERBB3 WILD-TYPE     43     31     36     34     27     12
D15V2, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             5              43
  CLUS_2             3              31
  CLUS_3             1              36
  CLUS_4             1              34
  CLUS_5             1              27
  CLUS_6             0              12
[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
  ERBB3 MUTATED        8      1      2
  ERBB3 WILD-TYPE     58     79     43
D15V3, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             8              58
  CLUS_2             1              79
  CLUS_3             2              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
  ERBB3 MUTATED        7      3      1
  ERBB3 WILD-TYPE     41    117     22
D15V4, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             7              41
  CLUS_2             3             117
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB3 MUTATED        5      5      1
  ERBB3 WILD-TYPE     54     51     78
D15V5, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             5              54
  CLUS_2             5              51
  CLUS_3             1              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 CLUS_4 CLUS_5
  ERBB3 MUTATED        7      2      1      0      1
  ERBB3 WILD-TYPE     34     48     57     15     29
D15V6, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             7              34
  CLUS_2             2              48
  CLUS_3             1              57
  CLUS_4             0              15
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB3 MUTATED        4      4      3
  ERBB3 WILD-TYPE     65     53     55
D15V7, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             4              53
  CLUS_3             3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB3 MUTATED        5      2      1      3
  ERBB3 WILD-TYPE     37     30     27     79
D15V8, multiclass
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  CLUS_1             5              37
  CLUS_2             2              30
  CLUS_3             1              27
  CLUS_4             3              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = SMAD4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD4 MUTATED        4      0      2
  SMAD4 WILD-TYPE     86     40     59
D16V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             4              86
  CLUS_2             0              40
  CLUS_3             2              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SMAD4 MUTATED        2      0      3      0      1      1
  SMAD4 WILD-TYPE     46     34     34     35     27     11
D16V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             0              34
  CLUS_3             3              34
  CLUS_4             0              35
  CLUS_5             1              27
  CLUS_6             1              11
[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
  SMAD4 MUTATED        2      2      3
  SMAD4 WILD-TYPE     64     78     42
D16V3, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             2              78
  CLUS_3             3              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
  SMAD4 MUTATED        2      4      1
  SMAD4 WILD-TYPE     46    116     22
D16V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             4             116
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD4 MUTATED        2      1      4
  SMAD4 WILD-TYPE     57     55     75
D16V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              57
  CLUS_2             1              55
  CLUS_3             4              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD4 MUTATED        1      3      1      0      2
  SMAD4 WILD-TYPE     40     47     57     15     28
D16V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             3              47
  CLUS_3             1              57
  CLUS_4             0              15
  CLUS_5             2              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD4 MUTATED        3      2      2
  SMAD4 WILD-TYPE     66     55     56
D16V7, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             3              66
  CLUS_2             2              55
  CLUS_3             2              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD4 MUTATED        1      1      1      4
  SMAD4 WILD-TYPE     41     31     27     78
D16V8, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             1              31
  CLUS_3             1              27
  CLUS_4             4              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = TCTE1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCTE1 MUTATED        3      2      0
  TCTE1 WILD-TYPE     87     38     61
D17V1, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             2              38
  CLUS_3             0              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TCTE1 MUTATED        0      2      1      2      0      0
  TCTE1 WILD-TYPE     48     32     36     33     28     12
D17V2, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             2              32
  CLUS_3             1              36
  CLUS_4             2              33
  CLUS_5             0              28
  CLUS_6             0              12
[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
  TCTE1 MUTATED        0      1      4
  TCTE1 WILD-TYPE     66     79     41
D17V3, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              66
  CLUS_2             1              79
  CLUS_3             4              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
  TCTE1 MUTATED        0      4      1
  TCTE1 WILD-TYPE     48    116     22
D17V4, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4             116
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCTE1 MUTATED        0      0      5
  TCTE1 WILD-TYPE     59     56     74
D17V5, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              59
  CLUS_2             0              56
  CLUS_3             5              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCTE1 MUTATED        0      1      1      2      1
  TCTE1 WILD-TYPE     41     49     57     13     29
D17V6, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             1              49
  CLUS_3             1              57
  CLUS_4             2              13
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCTE1 MUTATED        1      0      3
  TCTE1 WILD-TYPE     68     57     55
D17V7, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             0              57
  CLUS_3             3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCTE1 MUTATED        0      0      0      4
  TCTE1 WILD-TYPE     42     32     28     78
D17V8, multiclass
        clus
vv       TCTE1 MUTATED TCTE1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              32
  CLUS_3             0              28
  CLUS_4             4              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = NHS MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NHS MUTATED        6      3      3
  NHS WILD-TYPE     84     37     58
D18V1, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           6            84
  CLUS_2           3            37
  CLUS_3           3            58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NHS MUTATED        4      3      1      2      2      0
  NHS WILD-TYPE     44     31     36     33     26     12
D18V2, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           4            44
  CLUS_2           3            31
  CLUS_3           1            36
  CLUS_4           2            33
  CLUS_5           2            26
  CLUS_6           0            12
[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
  NHS MUTATED        3      5      4
  NHS WILD-TYPE     63     75     41
D18V3, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           3            63
  CLUS_2           5            75
  CLUS_3           4            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
  NHS MUTATED        3      6      3
  NHS WILD-TYPE     45    114     20
D18V4, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           3            45
  CLUS_2           6           114
  CLUS_3           3            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NHS MUTATED        3      4      5
  NHS WILD-TYPE     56     52     74
D18V5, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           3            56
  CLUS_2           4            52
  CLUS_3           5            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NHS MUTATED        3      3      3      0      3
  NHS WILD-TYPE     38     47     55     15     27
D18V6, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           3            38
  CLUS_2           3            47
  CLUS_3           3            55
  CLUS_4           0            15
  CLUS_5           3            27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NHS MUTATED        6      3      2
  NHS WILD-TYPE     63     54     56
D18V7, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           6            63
  CLUS_2           3            54
  CLUS_3           2            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NHS MUTATED        3      1      0      7
  NHS WILD-TYPE     39     31     28     75
D18V8, multiclass
        clus
vv       NHS MUTATED NHS WILD-TYPE
  CLUS_1           3            39
  CLUS_2           1            31
  CLUS_3           0            28
  CLUS_4           7            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = LIN9 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIN9 MUTATED        1      1      4
  LIN9 WILD-TYPE     89     39     57
D19V1, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            1             89
  CLUS_2            1             39
  CLUS_3            4             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LIN9 MUTATED        1      1      2      0      1      2
  LIN9 WILD-TYPE     47     33     35     35     27     10
D19V2, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            1             33
  CLUS_3            2             35
  CLUS_4            0             35
  CLUS_5            1             27
  CLUS_6            2             10
[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
  LIN9 MUTATED        3      3      1
  LIN9 WILD-TYPE     63     77     44
D19V3, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            3             63
  CLUS_2            3             77
  CLUS_3            1             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
  LIN9 MUTATED        2      5      0
  LIN9 WILD-TYPE     46    115     23
D19V4, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            2             46
  CLUS_2            5            115
  CLUS_3            0             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIN9 MUTATED        3      2      2
  LIN9 WILD-TYPE     56     54     77
D19V5, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            3             56
  CLUS_2            2             54
  CLUS_3            2             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LIN9 MUTATED        0      2      4      1      0
  LIN9 WILD-TYPE     41     48     54     14     30
D19V6, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            2             48
  CLUS_3            4             54
  CLUS_4            1             14
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  LIN9 MUTATED        1      2      4
  LIN9 WILD-TYPE     68     55     54
D19V7, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            2             55
  CLUS_3            4             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LIN9 MUTATED        1      2      1      3
  LIN9 WILD-TYPE     41     30     27     79
D19V8, multiclass
        clus
vv       LIN9 MUTATED LIN9 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            2             30
  CLUS_3            1             27
  CLUS_4            3             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = C12ORF43 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        2      2      0
  C12ORF43 WILD-TYPE     88     38     61
D20V1, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                2                 88
  CLUS_2                2                 38
  CLUS_3                0                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  C12ORF43 MUTATED        0      1      1      1      1      0
  C12ORF43 WILD-TYPE     48     33     36     34     27     12
D20V2, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 48
  CLUS_2                1                 33
  CLUS_3                1                 36
  CLUS_4                1                 34
  CLUS_5                1                 27
  CLUS_6                0                 12
[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
  C12ORF43 MUTATED        1      2      1
  C12ORF43 WILD-TYPE     65     78     44
D20V3, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                1                 65
  CLUS_2                2                 78
  CLUS_3                1                 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
  C12ORF43 MUTATED        0      4      0
  C12ORF43 WILD-TYPE     48    116     23
D20V4, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 48
  CLUS_2                4                116
  CLUS_3                0                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        0      2      2
  C12ORF43 WILD-TYPE     59     54     77
D20V5, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 59
  CLUS_2                2                 54
  CLUS_3                2                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  C12ORF43 MUTATED        0      0      2      1      1
  C12ORF43 WILD-TYPE     41     50     56     14     29
D20V6, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 41
  CLUS_2                0                 50
  CLUS_3                2                 56
  CLUS_4                1                 14
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  C12ORF43 MUTATED        0      1      2
  C12ORF43 WILD-TYPE     69     56     56
D20V7, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 69
  CLUS_2                1                 56
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  C12ORF43 MUTATED        0      0      2      1
  C12ORF43 WILD-TYPE     42     32     26     81
D20V8, multiclass
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CLUS_1                0                 42
  CLUS_2                0                 32
  CLUS_3                2                 26
  CLUS_4                1                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = MED1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MED1 MUTATED        6      2      3
  MED1 WILD-TYPE     84     38     58
D21V1, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            6             84
  CLUS_2            2             38
  CLUS_3            3             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MED1 MUTATED        0      1      3      3      1      3
  MED1 WILD-TYPE     48     33     34     32     27      9
D21V2, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            1             33
  CLUS_3            3             34
  CLUS_4            3             32
  CLUS_5            1             27
  CLUS_6            3              9
[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
  MED1 MUTATED        1      4      6
  MED1 WILD-TYPE     65     76     39
D21V3, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            1             65
  CLUS_2            4             76
  CLUS_3            6             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MED1 MUTATED        0      9      2
  MED1 WILD-TYPE     48    111     21
D21V4, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            9            111
  CLUS_3            2             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MED1 MUTATED        1      3      7
  MED1 WILD-TYPE     58     53     72
D21V5, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            1             58
  CLUS_2            3             53
  CLUS_3            7             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MED1 MUTATED        0      4      4      0      3
  MED1 WILD-TYPE     41     46     54     15     27
D21V6, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            4             46
  CLUS_3            4             54
  CLUS_4            0             15
  CLUS_5            3             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MED1 MUTATED        3      2      5
  MED1 WILD-TYPE     66     55     53
D21V7, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            3             66
  CLUS_2            2             55
  CLUS_3            5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MED1 MUTATED        0      1      3      6
  MED1 WILD-TYPE     42     31     25     76
D21V8, multiclass
        clus
vv       MED1 MUTATED MED1 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            1             31
  CLUS_3            3             25
  CLUS_4            6             76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = USP28 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        2      2      0
  USP28 WILD-TYPE     88     38     61
D22V1, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             2              88
  CLUS_2             2              38
  CLUS_3             0              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  USP28 MUTATED        1      2      1      0      0      0
  USP28 WILD-TYPE     47     32     36     35     28     12
D22V2, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             2              32
  CLUS_3             1              36
  CLUS_4             0              35
  CLUS_5             0              28
  CLUS_6             0              12
[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
  USP28 MUTATED        1      1      2
  USP28 WILD-TYPE     65     79     43
D22V3, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             1              79
  CLUS_3             2              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
  USP28 MUTATED        1      3      0
  USP28 WILD-TYPE     47    117     23
D22V4, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             3             117
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        1      0      3
  USP28 WILD-TYPE     58     56     76
D22V5, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              58
  CLUS_2             0              56
  CLUS_3             3              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  USP28 MUTATED        1      1      2      0      0
  USP28 WILD-TYPE     40     49     56     15     30
D22V6, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             1              49
  CLUS_3             2              56
  CLUS_4             0              15
  CLUS_5             0              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  USP28 MUTATED        1      0      3
  USP28 WILD-TYPE     68     57     55
D22V7, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             0              57
  CLUS_3             3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  USP28 MUTATED        1      0      0      3
  USP28 WILD-TYPE     41     32     28     79
D22V8, multiclass
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              32
  CLUS_3             0              28
  CLUS_4             3              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = IDS MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  IDS MUTATED        4      2      0
  IDS WILD-TYPE     86     38     61
D23V1, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           4            86
  CLUS_2           2            38
  CLUS_3           0            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IDS MUTATED        2      3      1      0      1      0
  IDS WILD-TYPE     46     31     36     35     27     12
D23V2, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           2            46
  CLUS_2           3            31
  CLUS_3           1            36
  CLUS_4           0            35
  CLUS_5           1            27
  CLUS_6           0            12
[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
  IDS MUTATED        2      4      1
  IDS WILD-TYPE     64     76     44
D23V3, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           2            64
  CLUS_2           4            76
  CLUS_3           1            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
  IDS MUTATED        2      5      0
  IDS WILD-TYPE     46    115     23
D23V4, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           2            46
  CLUS_2           5           115
  CLUS_3           0            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  IDS MUTATED        1      3      3
  IDS WILD-TYPE     58     53     76
D23V5, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           1            58
  CLUS_2           3            53
  CLUS_3           3            76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDS MUTATED        1      1      3      2      0
  IDS WILD-TYPE     40     49     55     13     30
D23V6, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           1            40
  CLUS_2           1            49
  CLUS_3           3            55
  CLUS_4           2            13
  CLUS_5           0            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  IDS MUTATED        1      3      3
  IDS WILD-TYPE     68     54     55
D23V7, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           1            68
  CLUS_2           3            54
  CLUS_3           3            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDS MUTATED        2      2      0      3
  IDS WILD-TYPE     40     30     28     79
D23V8, multiclass
        clus
vv       IDS MUTATED IDS WILD-TYPE
  CLUS_1           2            40
  CLUS_2           2            30
  CLUS_3           0            28
  CLUS_4           3            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = TRIM9 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TRIM9 MUTATED        6      1      1
  TRIM9 WILD-TYPE     84     39     60
D24V1, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             6              84
  CLUS_2             1              39
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TRIM9 MUTATED        3      2      1      2      0      0
  TRIM9 WILD-TYPE     45     32     36     33     28     12
D24V2, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             2              32
  CLUS_3             1              36
  CLUS_4             2              33
  CLUS_5             0              28
  CLUS_6             0              12
[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
  TRIM9 MUTATED        3      1      4
  TRIM9 WILD-TYPE     63     79     41
D24V3, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             1              79
  CLUS_3             4              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
  TRIM9 MUTATED        3      4      1
  TRIM9 WILD-TYPE     45    116     22
D24V4, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             4             116
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TRIM9 MUTATED        2      1      5
  TRIM9 WILD-TYPE     57     55     74
D24V5, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             2              57
  CLUS_2             1              55
  CLUS_3             5              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TRIM9 MUTATED        3      1      0      2      2
  TRIM9 WILD-TYPE     38     49     58     13     28
D24V6, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             3              38
  CLUS_2             1              49
  CLUS_3             0              58
  CLUS_4             2              13
  CLUS_5             2              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TRIM9 MUTATED        4      1      2
  TRIM9 WILD-TYPE     65     56     56
D24V7, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             1              56
  CLUS_3             2              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIM9 MUTATED        3      0      0      4
  TRIM9 WILD-TYPE     39     32     28     78
D24V8, multiclass
        clus
vv       TRIM9 MUTATED TRIM9 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             0              32
  CLUS_3             0              28
  CLUS_4             4              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = SEMA4B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA4B MUTATED        4      1      2
  SEMA4B WILD-TYPE     86     39     59
D25V1, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              4               86
  CLUS_2              1               39
  CLUS_3              2               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SEMA4B MUTATED        1      2      1      2      1      0
  SEMA4B WILD-TYPE     47     32     36     33     27     12
D25V2, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              1               47
  CLUS_2              2               32
  CLUS_3              1               36
  CLUS_4              2               33
  CLUS_5              1               27
  CLUS_6              0               12
[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
  SEMA4B MUTATED        1      3      3
  SEMA4B WILD-TYPE     65     77     42
D25V3, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              1               65
  CLUS_2              3               77
  CLUS_3              3               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
  SEMA4B MUTATED        0      5      2
  SEMA4B WILD-TYPE     48    115     21
D25V4, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              0               48
  CLUS_2              5              115
  CLUS_3              2               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA4B MUTATED        1      0      6
  SEMA4B WILD-TYPE     58     56     73
D25V5, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              1               58
  CLUS_2              0               56
  CLUS_3              6               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 CLUS_4 CLUS_5
  SEMA4B MUTATED        0      2      2      0      3
  SEMA4B WILD-TYPE     41     48     56     15     27
D25V6, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              0               41
  CLUS_2              2               48
  CLUS_3              2               56
  CLUS_4              0               15
  CLUS_5              3               27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA4B MUTATED        2      1      4
  SEMA4B WILD-TYPE     67     56     54
D25V7, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              2               67
  CLUS_2              1               56
  CLUS_3              4               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA4B MUTATED        0      0      1      6
  SEMA4B WILD-TYPE     42     32     27     76
D25V8, multiclass
        clus
vv       SEMA4B MUTATED SEMA4B WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               32
  CLUS_3              1               27
  CLUS_4              6               76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = ARHGAP4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ARHGAP4 MUTATED        3      1      2
  ARHGAP4 WILD-TYPE     87     39     59
D26V1, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               3                87
  CLUS_2               1                39
  CLUS_3               2                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARHGAP4 MUTATED        2      2      0      2      0      0
  ARHGAP4 WILD-TYPE     46     32     37     33     28     12
D26V2, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               2                46
  CLUS_2               2                32
  CLUS_3               0                37
  CLUS_4               2                33
  CLUS_5               0                28
  CLUS_6               0                12
[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
  ARHGAP4 MUTATED        1      2      3
  ARHGAP4 WILD-TYPE     65     78     42
D26V3, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                65
  CLUS_2               2                78
  CLUS_3               3                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
  ARHGAP4 MUTATED        1      4      1
  ARHGAP4 WILD-TYPE     47    116     22
D26V4, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                47
  CLUS_2               4               116
  CLUS_3               1                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ARHGAP4 MUTATED        1      1      4
  ARHGAP4 WILD-TYPE     58     55     75
D26V5, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                58
  CLUS_2               1                55
  CLUS_3               4                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARHGAP4 MUTATED        1      1      2      2      0
  ARHGAP4 WILD-TYPE     40     49     56     13     30
D26V6, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                40
  CLUS_2               1                49
  CLUS_3               2                56
  CLUS_4               2                13
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  ARHGAP4 MUTATED        1      2      1
  ARHGAP4 WILD-TYPE     68     55     57
D26V7, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                68
  CLUS_2               2                55
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARHGAP4 MUTATED        1      1      0      2
  ARHGAP4 WILD-TYPE     41     31     28     80
D26V8, multiclass
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               1                31
  CLUS_3               0                28
  CLUS_4               2                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = POU2F1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POU2F1 MUTATED        2      1      0
  POU2F1 WILD-TYPE     88     39     61
D27V1, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              2               88
  CLUS_2              1               39
  CLUS_3              0               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  POU2F1 MUTATED        0      1      2      0      0      0
  POU2F1 WILD-TYPE     48     33     35     35     28     12
D27V2, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              1               33
  CLUS_3              2               35
  CLUS_4              0               35
  CLUS_5              0               28
  CLUS_6              0               12
[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
  POU2F1 MUTATED        0      2      1
  POU2F1 WILD-TYPE     66     78     44
D27V3, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               66
  CLUS_2              2               78
  CLUS_3              1               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
  POU2F1 MUTATED        0      3      0
  POU2F1 WILD-TYPE     48    117     23
D27V4, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               48
  CLUS_2              3              117
  CLUS_3              0               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POU2F1 MUTATED        0      1      2
  POU2F1 WILD-TYPE     59     55     77
D27V5, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               59
  CLUS_2              1               55
  CLUS_3              2               77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  POU2F1 MUTATED        0      0      2      0      1
  POU2F1 WILD-TYPE     41     50     56     15     29
D27V6, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              0               50
  CLUS_3              2               56
  CLUS_4              0               15
  CLUS_5              1               29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POU2F1 MUTATED        0      1      2
  POU2F1 WILD-TYPE     69     56     56
D27V7, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               69
  CLUS_2              1               56
  CLUS_3              2               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POU2F1 MUTATED        0      0      2      1
  POU2F1 WILD-TYPE     42     32     26     81
D27V8, multiclass
        clus
vv       POU2F1 MUTATED POU2F1 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               32
  CLUS_3              2               26
  CLUS_4              1               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = IFNGR1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        3      1      2
  IFNGR1 WILD-TYPE     87     39     59
D28V1, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              3               87
  CLUS_2              1               39
  CLUS_3              2               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IFNGR1 MUTATED        2      2      0      1      0      1
  IFNGR1 WILD-TYPE     46     32     37     34     28     11
D28V2, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               46
  CLUS_2              2               32
  CLUS_3              0               37
  CLUS_4              1               34
  CLUS_5              0               28
  CLUS_6              1               11
[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
  IFNGR1 MUTATED        3      2      1
  IFNGR1 WILD-TYPE     63     78     44
D28V3, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              3               63
  CLUS_2              2               78
  CLUS_3              1               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
  IFNGR1 MUTATED        2      4      0
  IFNGR1 WILD-TYPE     46    116     23
D28V4, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               46
  CLUS_2              4              116
  CLUS_3              0               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        3      0      3
  IFNGR1 WILD-TYPE     56     56     76
D28V5, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              3               56
  CLUS_2              0               56
  CLUS_3              3               76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IFNGR1 MUTATED        1      3      0      2      0
  IFNGR1 WILD-TYPE     40     47     58     13     30
D28V6, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              1               40
  CLUS_2              3               47
  CLUS_3              0               58
  CLUS_4              2               13
  CLUS_5              0               30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFNGR1 MUTATED        5      0      1
  IFNGR1 WILD-TYPE     64     57     57
D28V7, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              5               64
  CLUS_2              0               57
  CLUS_3              1               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFNGR1 MUTATED        2      0      1      3
  IFNGR1 WILD-TYPE     40     32     27     79
D28V8, multiclass
        clus
vv       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CLUS_1              2               40
  CLUS_2              0               32
  CLUS_3              1               27
  CLUS_4              3               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = IGFN1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGFN1 MUTATED        7      0      4
  IGFN1 WILD-TYPE     83     40     57
D29V1, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             7              83
  CLUS_2             0              40
  CLUS_3             4              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IGFN1 MUTATED        2      3      3      1      2      0
  IGFN1 WILD-TYPE     46     31     34     34     26     12
D29V2, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             2              46
  CLUS_2             3              31
  CLUS_3             3              34
  CLUS_4             1              34
  CLUS_5             2              26
  CLUS_6             0              12
[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
  IGFN1 MUTATED        3      6      2
  IGFN1 WILD-TYPE     63     74     43
D29V3, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             6              74
  CLUS_3             2              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
  IGFN1 MUTATED        3      8      0
  IGFN1 WILD-TYPE     45    112     23
D29V4, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             8             112
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGFN1 MUTATED        4      1      6
  IGFN1 WILD-TYPE     55     55     73
D29V5, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             4              55
  CLUS_2             1              55
  CLUS_3             6              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 CLUS_4 CLUS_5
  IGFN1 MUTATED        3      3      3      1      1
  IGFN1 WILD-TYPE     38     47     55     14     29
D29V6, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             3              38
  CLUS_2             3              47
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  IGFN1 MUTATED        5      1      4
  IGFN1 WILD-TYPE     64     56     54
D29V7, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             5              64
  CLUS_2             1              56
  CLUS_3             4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IGFN1 MUTATED        2      1      1      6
  IGFN1 WILD-TYPE     40     31     27     76
D29V8, multiclass
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             1              31
  CLUS_3             1              27
  CLUS_4             6              76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = RPGR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPGR MUTATED        4      2      3
  RPGR WILD-TYPE     86     38     58
D30V1, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            4             86
  CLUS_2            2             38
  CLUS_3            3             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RPGR MUTATED        3      2      1      1      1      1
  RPGR WILD-TYPE     45     32     36     34     27     11
D30V2, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            3             45
  CLUS_2            2             32
  CLUS_3            1             36
  CLUS_4            1             34
  CLUS_5            1             27
  CLUS_6            1             11
[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
  RPGR MUTATED        4      3      2
  RPGR WILD-TYPE     62     77     43
D30V3, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            4             62
  CLUS_2            3             77
  CLUS_3            2             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
  RPGR MUTATED        3      5      1
  RPGR WILD-TYPE     45    115     22
D30V4, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            3             45
  CLUS_2            5            115
  CLUS_3            1             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPGR MUTATED        3      3      3
  RPGR WILD-TYPE     56     53     76
D30V5, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            3             56
  CLUS_2            3             53
  CLUS_3            3             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPGR MUTATED        2      2      4      0      1
  RPGR WILD-TYPE     39     48     54     15     29
D30V6, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            2             39
  CLUS_2            2             48
  CLUS_3            4             54
  CLUS_4            0             15
  CLUS_5            1             29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPGR MUTATED        3      2      4
  RPGR WILD-TYPE     66     55     54
D30V7, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            3             66
  CLUS_2            2             55
  CLUS_3            4             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPGR MUTATED        3      2      1      3
  RPGR WILD-TYPE     39     30     27     79
D30V8, multiclass
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  CLUS_1            3             39
  CLUS_2            2             30
  CLUS_3            1             27
  CLUS_4            3             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = CASP8 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        3      2      4
  CASP8 WILD-TYPE     87     38     57
D31V1, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             2              38
  CLUS_3             4              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CASP8 MUTATED        1      1      3      2      1      1
  CASP8 WILD-TYPE     47     33     34     33     27     11
D31V2, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             1              33
  CLUS_3             3              34
  CLUS_4             2              33
  CLUS_5             1              27
  CLUS_6             1              11
[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
  CASP8 MUTATED        1      5      3
  CASP8 WILD-TYPE     65     75     42
D31V3, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             5              75
  CLUS_3             3              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
  CASP8 MUTATED        1      6      2
  CASP8 WILD-TYPE     47    114     21
D31V4, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             6             114
  CLUS_3             2              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        3      1      5
  CASP8 WILD-TYPE     56     55     74
D31V5, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              56
  CLUS_2             1              55
  CLUS_3             5              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CASP8 MUTATED        0      3      3      1      2
  CASP8 WILD-TYPE     41     47     55     14     28
D31V6, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             3              47
  CLUS_3             3              55
  CLUS_4             1              14
  CLUS_5             2              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        4      0      4
  CASP8 WILD-TYPE     65     57     54
D31V7, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             0              57
  CLUS_3             4              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CASP8 MUTATED        1      0      1      6
  CASP8 WILD-TYPE     41     32     27     76
D31V8, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              32
  CLUS_3             1              27
  CLUS_4             6              76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = GAS6 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GAS6 MUTATED        2      0      2
  GAS6 WILD-TYPE     88     40     59
D32V1, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            2             88
  CLUS_2            0             40
  CLUS_3            2             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GAS6 MUTATED        0      0      3      1      0      0
  GAS6 WILD-TYPE     48     34     34     34     28     12
D32V2, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            0             34
  CLUS_3            3             34
  CLUS_4            1             34
  CLUS_5            0             28
  CLUS_6            0             12
[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
  GAS6 MUTATED        0      3      1
  GAS6 WILD-TYPE     66     77     44
D32V3, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             66
  CLUS_2            3             77
  CLUS_3            1             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
  GAS6 MUTATED        0      4      0
  GAS6 WILD-TYPE     48    116     23
D32V4, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            4            116
  CLUS_3            0             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GAS6 MUTATED        1      1      2
  GAS6 WILD-TYPE     58     55     77
D32V5, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            1             58
  CLUS_2            1             55
  CLUS_3            2             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GAS6 MUTATED        0      3      1      0      0
  GAS6 WILD-TYPE     41     47     57     15     30
D32V6, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            3             47
  CLUS_3            1             57
  CLUS_4            0             15
  CLUS_5            0             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GAS6 MUTATED        0      1      2
  GAS6 WILD-TYPE     69     56     56
D32V7, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             69
  CLUS_2            1             56
  CLUS_3            2             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GAS6 MUTATED        0      1      0      2
  GAS6 WILD-TYPE     42     31     28     80
D32V8, multiclass
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            2             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = ABCD1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ABCD1 MUTATED        2      2      1
  ABCD1 WILD-TYPE     88     38     60
D33V1, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             2              88
  CLUS_2             2              38
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ABCD1 MUTATED        1      1      1      2      2      0
  ABCD1 WILD-TYPE     47     33     36     33     26     12
D33V2, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             1              33
  CLUS_3             1              36
  CLUS_4             2              33
  CLUS_5             2              26
  CLUS_6             0              12
[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
  ABCD1 MUTATED        1      2      3
  ABCD1 WILD-TYPE     65     78     42
D33V3, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             2              78
  CLUS_3             3              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
  ABCD1 MUTATED        0      4      2
  ABCD1 WILD-TYPE     48    116     21
D33V4, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4             116
  CLUS_3             2              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ABCD1 MUTATED        1      3      3
  ABCD1 WILD-TYPE     58     53     76
D33V5, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             1              58
  CLUS_2             3              53
  CLUS_3             3              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ABCD1 MUTATED        0      2      3      0      2
  ABCD1 WILD-TYPE     41     48     55     15     28
D33V6, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              48
  CLUS_3             3              55
  CLUS_4             0              15
  CLUS_5             2              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ABCD1 MUTATED        0      4      3
  ABCD1 WILD-TYPE     69     53     55
D33V7, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             0              69
  CLUS_2             4              53
  CLUS_3             3              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ABCD1 MUTATED        0      1      2      4
  ABCD1 WILD-TYPE     42     31     26     78
D33V8, multiclass
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              31
  CLUS_3             2              26
  CLUS_4             4              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = RPAP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RPAP1 MUTATED        3      0      1
  RPAP1 WILD-TYPE     87     40     60
D34V1, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             0              40
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RPAP1 MUTATED        1      1      2      0      0      0
  RPAP1 WILD-TYPE     47     33     35     35     28     12
D34V2, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             1              33
  CLUS_3             2              35
  CLUS_4             0              35
  CLUS_5             0              28
  CLUS_6             0              12
[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
  RPAP1 MUTATED        1      1      2
  RPAP1 WILD-TYPE     65     79     43
D34V3, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             1              79
  CLUS_3             2              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
  RPAP1 MUTATED        1      3      0
  RPAP1 WILD-TYPE     47    117     23
D34V4, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             3             117
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RPAP1 MUTATED        1      1      2
  RPAP1 WILD-TYPE     58     55     77
D34V5, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             1              58
  CLUS_2             1              55
  CLUS_3             2              77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RPAP1 MUTATED        0      2      1      0      1
  RPAP1 WILD-TYPE     41     48     57     15     29
D34V6, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              48
  CLUS_3             1              57
  CLUS_4             0              15
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RPAP1 MUTATED        2      1      1
  RPAP1 WILD-TYPE     67     56     57
D34V7, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             2              67
  CLUS_2             1              56
  CLUS_3             1              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPAP1 MUTATED        1      0      1      2
  RPAP1 WILD-TYPE     41     32     27     80
D34V8, multiclass
        clus
vv       RPAP1 MUTATED RPAP1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              32
  CLUS_3             1              27
  CLUS_4             2              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = HIST1H4E MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  HIST1H4E MUTATED        2      2      0
  HIST1H4E WILD-TYPE     88     38     61
D35V1, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                2                 88
  CLUS_2                2                 38
  CLUS_3                0                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HIST1H4E MUTATED        0      1      1      1      1      0
  HIST1H4E WILD-TYPE     48     33     36     34     27     12
D35V2, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 48
  CLUS_2                1                 33
  CLUS_3                1                 36
  CLUS_4                1                 34
  CLUS_5                1                 27
  CLUS_6                0                 12
[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
  HIST1H4E MUTATED        0      3      1
  HIST1H4E WILD-TYPE     66     77     44
D35V3, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 66
  CLUS_2                3                 77
  CLUS_3                1                 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
  HIST1H4E MUTATED        0      3      1
  HIST1H4E WILD-TYPE     48    117     22
D35V4, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 48
  CLUS_2                3                117
  CLUS_3                1                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  HIST1H4E MUTATED        0      2      2
  HIST1H4E WILD-TYPE     59     54     77
D35V5, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 59
  CLUS_2                2                 54
  CLUS_3                2                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HIST1H4E MUTATED        0      1      2      0      1
  HIST1H4E WILD-TYPE     41     49     56     15     29
D35V6, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 41
  CLUS_2                1                 49
  CLUS_3                2                 56
  CLUS_4                0                 15
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  HIST1H4E MUTATED        1      2      0
  HIST1H4E WILD-TYPE     68     55     58
D35V7, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                2                 55
  CLUS_3                0                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HIST1H4E MUTATED        0      1      1      1
  HIST1H4E WILD-TYPE     42     31     27     81
D35V8, multiclass
        clus
vv       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CLUS_1                0                 42
  CLUS_2                1                 31
  CLUS_3                1                 27
  CLUS_4                1                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = NLRC5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRC5 MUTATED        4      2      1
  NLRC5 WILD-TYPE     86     38     60
D36V1, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              86
  CLUS_2             2              38
  CLUS_3             1              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NLRC5 MUTATED        4      2      0      0      0      1
  NLRC5 WILD-TYPE     44     32     37     35     28     11
D36V2, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              44
  CLUS_2             2              32
  CLUS_3             0              37
  CLUS_4             0              35
  CLUS_5             0              28
  CLUS_6             1              11
[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
  NLRC5 MUTATED        4      1      2
  NLRC5 WILD-TYPE     62     79     43
D36V3, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              62
  CLUS_2             1              79
  CLUS_3             2              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
  NLRC5 MUTATED        4      3      0
  NLRC5 WILD-TYPE     44    117     23
D36V4, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              44
  CLUS_2             3             117
  CLUS_3             0              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRC5 MUTATED        4      0      3
  NLRC5 WILD-TYPE     55     56     76
D36V5, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              55
  CLUS_2             0              56
  CLUS_3             3              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NLRC5 MUTATED        3      0      2      1      1
  NLRC5 WILD-TYPE     38     50     56     14     29
D36V6, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             3              38
  CLUS_2             0              50
  CLUS_3             2              56
  CLUS_4             1              14
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NLRC5 MUTATED        4      1      2
  NLRC5 WILD-TYPE     65     56     56
D36V7, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             1              56
  CLUS_3             2              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NLRC5 MUTATED        4      0      1      2
  NLRC5 WILD-TYPE     38     32     27     80
D36V8, multiclass
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  CLUS_1             4              38
  CLUS_2             0              32
  CLUS_3             1              27
  CLUS_4             2              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DDX41 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DDX41 MUTATED        0      1      4
  DDX41 WILD-TYPE     90     39     57
D37V1, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             1              39
  CLUS_3             4              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DDX41 MUTATED        0      3      0      1      1      0
  DDX41 WILD-TYPE     48     31     37     34     27     12
D37V2, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             3              31
  CLUS_3             0              37
  CLUS_4             1              34
  CLUS_5             1              27
  CLUS_6             0              12
[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
  DDX41 MUTATED        0      4      1
  DDX41 WILD-TYPE     66     76     44
D37V3, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              66
  CLUS_2             4              76
  CLUS_3             1              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
  DDX41 MUTATED        0      4      1
  DDX41 WILD-TYPE     48    116     22
D37V4, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             4             116
  CLUS_3             1              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DDX41 MUTATED        0      2      3
  DDX41 WILD-TYPE     59     54     76
D37V5, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              59
  CLUS_2             2              54
  CLUS_3             3              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DDX41 MUTATED        0      2      2      0      1
  DDX41 WILD-TYPE     41     48     56     15     29
D37V6, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              48
  CLUS_3             2              56
  CLUS_4             0              15
  CLUS_5             1              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DDX41 MUTATED        2      1      1
  DDX41 WILD-TYPE     67     56     57
D37V7, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             2              67
  CLUS_2             1              56
  CLUS_3             1              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX41 MUTATED        0      1      0      3
  DDX41 WILD-TYPE     42     31     28     79
D37V8, multiclass
        clus
vv       DDX41 MUTATED DDX41 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              31
  CLUS_3             0              28
  CLUS_4             3              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = MCM7 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM7 MUTATED        0      0      2
  MCM7 WILD-TYPE     90     40     59
D38V1, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2            189 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A2LS 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2     TCGA-C5-A3HD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UC     TCGA-C5-A7UH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A3LQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439     TCGA-EA-A43B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD     TCGA-EA-A5ZE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R     TCGA-EK-A2GZ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2IP     TCGA-EK-A2PG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PI     TCGA-EK-A2PK     TCGA-EK-A2PL     TCGA-EK-A2PM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9     TCGA-EK-A2RA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RB     TCGA-EK-A2RC     TCGA-EK-A2RD     TCGA-EK-A2RE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A3GM     TCGA-EK-A3GN     TCGA-EX-A1H5     TCGA-EX-A1H6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AW 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-WL-A834 
"MCM7 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MCM7 MUTATED        0      0      0      1      1      1
  MCM7 WILD-TYPE     48     34     37     34     27     11
D38V2, multiclass
        clus
vv       MCM7 MUTATED MCM7 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            0             34
  CLUS_3            0             37
  CLUS_4            1             34
  CLUS_5            1             27
  CLUS_6            1             11
[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
  MCM7 MUTATED        0      2      0
  MCM7 WILD-TYPE     66     78     45
D38V3, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2            189 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A2LS 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2     TCGA-C5-A3HD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UC     TCGA-C5-A7UH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A3LQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2GZ     TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2IP 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PG     TCGA-EK-A2PI     TCGA-EK-A2PK     TCGA-EK-A2PL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RB     TCGA-EK-A2RC     TCGA-EK-A2RE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A3GM     TCGA-EK-A3GN     TCGA-EX-A1H5     TCGA-EX-A1H6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AW 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-WL-A834 
"MCM7 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM7 MUTATED        0      2      0
  MCM7 WILD-TYPE     48    118     23
D38V4, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2            189 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A2LS 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2     TCGA-C5-A3HD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UC     TCGA-C5-A7UH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A3LQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2GZ     TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2IP 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PG     TCGA-EK-A2PI     TCGA-EK-A2PK     TCGA-EK-A2PL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RB     TCGA-EK-A2RC     TCGA-EK-A2RE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A3GM     TCGA-EK-A3GN     TCGA-EX-A1H5     TCGA-EX-A1H6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AW 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-WL-A834 
"MCM7 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM7 MUTATED        1      1      1
  MCM7 WILD-TYPE     58     55     78
D38V5, multiclass
        clus
vv       MCM7 MUTATED MCM7 WILD-TYPE
  CLUS_1            1             58
  CLUS_2            1             55
  CLUS_3            1             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 CLUS_4 CLUS_5
  MCM7 MUTATED        0      0      2      0      1
  MCM7 WILD-TYPE     41     50     56     15     29
D38V6, multiclass
        clus
vv       MCM7 MUTATED MCM7 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            0             50
  CLUS_3            2             56
  CLUS_4            0             15
  CLUS_5            1             29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM7 MUTATED        0      0      3
  MCM7 WILD-TYPE     69     57     55
D38V7, multiclass
        clus
vv       MCM7 MUTATED MCM7 WILD-TYPE
  CLUS_1            0             69
  CLUS_2            0             57
  CLUS_3            3             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MCM7 MUTATED        0      0      2      1
  MCM7 WILD-TYPE     42     32     26     81
D38V8, multiclass
        clus
vv       MCM7 MUTATED MCM7 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             32
  CLUS_3            2             26
  CLUS_4            1             81
[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"
