[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"        "-oTPCPG-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/PCPG-TP/11589218/PCPG-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/10685824/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=178, common to both=178
[1]   9 178
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           172 
  RET MUTATED RET WILD-TYPE 
            6           172 
[1] "CSDE1 MUTATION ANALYSIS"
[1] 3
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             174 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             174 
[1] "GPR128 MUTATION ANALYSIS"
[1] 3
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
[1] "FAM83D MUTATION ANALYSIS"
[1] 3
  FAM83D MUTATED FAM83D WILD-TYPE 
               3              175 
  FAM83D MUTATED FAM83D WILD-TYPE 
               3              175 
[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 178 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	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 178 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED       14      0      1
  HRAS WILD-TYPE     46     63     37
D1V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           14             46
  CLUS_2            0             63
  CLUS_3            1             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
  HRAS MUTATED        0     17      1
  HRAS WILD-TYPE     44     68     48
D1V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             44
  CLUS_2           17             68
  CLUS_3            1             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
  HRAS MUTATED        0     18      0      0
  HRAS WILD-TYPE     39     51     49     21
D1V3, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             39
  CLUS_2           18             51
  CLUS_3            0             49
  CLUS_4            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        0     18      0      0
  HRAS WILD-TYPE     38     53     48     21
D1V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             38
  CLUS_2           18             53
  CLUS_3            0             48
  CLUS_4            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        1     15      2
  HRAS WILD-TYPE     73     50     37
D1V5, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             73
  CLUS_2           15             50
  CLUS_3            2             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 CLUS_4
  HRAS MUTATED        1     14      1      2
  HRAS WILD-TYPE     75     45     17     23
D1V6, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             75
  CLUS_2           14             45
  CLUS_3            1             17
  CLUS_4            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HRAS MUTATED        1     15      2      0      0
  HRAS WILD-TYPE     35     49     10     41     24
D1V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             35
  CLUS_2           15             49
  CLUS_3            2             10
  CLUS_4            0             41
  CLUS_5            0             24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED       16      0      1      1
  HRAS WILD-TYPE     64     60     17     18
D1V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           16             64
  CLUS_2            0             60
  CLUS_3            1             17
  CLUS_4            1             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = EPAS1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EPAS1 MUTATED        0      7      1
  EPAS1 WILD-TYPE     60     56     37
D2V1, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             0              60
  CLUS_2             7              56
  CLUS_3             1              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
  EPAS1 MUTATED        4      0      4
  EPAS1 WILD-TYPE     40     85     45
D2V2, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             4              40
  CLUS_2             0              85
  CLUS_3             4              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EPAS1 MUTATED        1      0      7      0
  EPAS1 WILD-TYPE     38     69     42     21
D2V3, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             1              38
  CLUS_2             0              69
  CLUS_3             7              42
  CLUS_4             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EPAS1 MUTATED        1      0      7      0
  EPAS1 WILD-TYPE     37     71     41     21
D2V4, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             1              37
  CLUS_2             0              71
  CLUS_3             7              41
  CLUS_4             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EPAS1 MUTATED        8      0      0
  EPAS1 WILD-TYPE     66     65     39
D2V5, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             8              66
  CLUS_2             0              65
  CLUS_3             0              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 CLUS_4
  EPAS1 MUTATED        8      0      0      0
  EPAS1 WILD-TYPE     68     59     18     25
D2V6, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             8              68
  CLUS_2             0              59
  CLUS_3             0              18
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EPAS1 MUTATED        0      0      1      7      0
  EPAS1 WILD-TYPE     36     64     11     34     24
D2V7, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             0              36
  CLUS_2             0              64
  CLUS_3             1              11
  CLUS_4             7              34
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EPAS1 MUTATED        0      8      0      0
  EPAS1 WILD-TYPE     80     52     18     19
D2V8, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             0              80
  CLUS_2             8              52
  CLUS_3             0              18
  CLUS_4             0              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        3      1     10
  NF1 WILD-TYPE     57     62     28
D3V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            57
  CLUS_2           1            62
  CLUS_3          10            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        0     14      1
  NF1 WILD-TYPE     44     71     48
D3V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            44
  CLUS_2          14            71
  CLUS_3           1            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
  NF1 MUTATED        3     11      0      1
  NF1 WILD-TYPE     36     58     49     20
D3V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            36
  CLUS_2          11            58
  CLUS_3           0            49
  CLUS_4           1            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        0     14      0      1
  NF1 WILD-TYPE     38     57     48     20
D3V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            38
  CLUS_2          14            57
  CLUS_3           0            48
  CLUS_4           1            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        1     13      1
  NF1 WILD-TYPE     73     52     38
D3V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            73
  CLUS_2          13            52
  CLUS_3           1            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        2     11      0      2
  NF1 WILD-TYPE     74     48     18     23
D3V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            74
  CLUS_2          11            48
  CLUS_3           0            18
  CLUS_4           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        3     10      2      0      0
  NF1 WILD-TYPE     33     54     10     41     24
D3V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            33
  CLUS_2          10            54
  CLUS_3           2            10
  CLUS_4           0            41
  CLUS_5           0            24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED       13      0      0      2
  NF1 WILD-TYPE     67     60     18     17
D3V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          13            67
  CLUS_2           0            60
  CLUS_3           0            18
  CLUS_4           2            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RET MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RET MUTATED        6      0      0
  RET WILD-TYPE     54     63     38
D4V1, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           6            54
  CLUS_2           0            63
  CLUS_3           0            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RET MUTATED        0      4      2
  RET WILD-TYPE     44     81     47
D4V2, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            44
  CLUS_2           4            81
  CLUS_3           2            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RET MUTATED        0      5      0      1
  RET WILD-TYPE     39     64     49     20
D4V3, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            39
  CLUS_2           5            64
  CLUS_3           0            49
  CLUS_4           1            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RET MUTATED        0      5      0      1
  RET WILD-TYPE     38     66     48     20
D4V4, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            38
  CLUS_2           5            66
  CLUS_3           0            48
  CLUS_4           1            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RET MUTATED        1      3      2
  RET WILD-TYPE     73     62     37
D4V5, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           1            73
  CLUS_2           3            62
  CLUS_3           2            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 CLUS_4
  RET MUTATED        0      4      1      1
  RET WILD-TYPE     76     55     17     24
D4V6, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            76
  CLUS_2           4            55
  CLUS_3           1            17
  CLUS_4           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RET MUTATED        1      4      1      0      0
  RET WILD-TYPE     35     60     11     41     24
D4V7, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           1            35
  CLUS_2           4            60
  CLUS_3           1            11
  CLUS_4           0            41
  CLUS_5           0            24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RET MUTATED        4      0      1      1
  RET WILD-TYPE     76     60     17     18
D4V8, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           4            76
  CLUS_2           0            60
  CLUS_3           1            17
  CLUS_4           1            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CSDE1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CSDE1 MUTATED        0      3      1
  CSDE1 WILD-TYPE     60     60     37
D5V1, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             0              60
  CLUS_2             3              60
  CLUS_3             1              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
  CSDE1 MUTATED        1      3      0
  CSDE1 WILD-TYPE     43     82     49
D5V2, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              43
  CLUS_2             3              82
  CLUS_3             0              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSDE1 MUTATED        1      3      0      0
  CSDE1 WILD-TYPE     38     66     49     21
D5V3, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              38
  CLUS_2             3              66
  CLUS_3             0              49
  CLUS_4             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSDE1 MUTATED        4      0      0      0
  CSDE1 WILD-TYPE     34     71     48     21
D5V4, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             4              34
  CLUS_2             0              71
  CLUS_3             0              48
  CLUS_4             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CSDE1 MUTATED        1      3      0
  CSDE1 WILD-TYPE     73     62     39
D5V5, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              73
  CLUS_2             3              62
  CLUS_3             0              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 CLUS_4
  CSDE1 MUTATED        1      0      3      0
  CSDE1 WILD-TYPE     75     59     15     25
D5V6, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              75
  CLUS_2             0              59
  CLUS_3             3              15
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CSDE1 MUTATED        4      0      0      0      0
  CSDE1 WILD-TYPE     32     64     12     41     24
D5V7, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             4              32
  CLUS_2             0              64
  CLUS_3             0              12
  CLUS_4             0              41
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CSDE1 MUTATED        1      0      3      0
  CSDE1 WILD-TYPE     79     60     15     19
D5V8, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              79
  CLUS_2             0              60
  CLUS_3             3              15
  CLUS_4             0              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = GPR128 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPR128 MUTATED        1      1      1
  GPR128 WILD-TYPE     59     62     37
D6V1, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              1               59
  CLUS_2              1               62
  CLUS_3              1               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
  GPR128 MUTATED        3      1      0
  GPR128 WILD-TYPE     41     84     49
D6V2, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              3               41
  CLUS_2              1               84
  CLUS_3              0               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR128 MUTATED        1      1      2      0
  GPR128 WILD-TYPE     38     68     47     21
D6V3, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              1               38
  CLUS_2              1               68
  CLUS_3              2               47
  CLUS_4              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR128 MUTATED        1      1      2      0
  GPR128 WILD-TYPE     37     70     46     21
D6V4, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              1               37
  CLUS_2              1               70
  CLUS_3              2               46
  CLUS_4              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPR128 MUTATED        3      1      0
  GPR128 WILD-TYPE     71     64     39
D6V5, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              3               71
  CLUS_2              1               64
  CLUS_3              0               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 CLUS_4
  GPR128 MUTATED        3      1      0      0
  GPR128 WILD-TYPE     73     58     18     25
D6V6, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              3               73
  CLUS_2              1               58
  CLUS_3              0               18
  CLUS_4              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GPR128 MUTATED        0      1      0      2      1
  GPR128 WILD-TYPE     36     63     12     39     23
D6V7, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              0               36
  CLUS_2              1               63
  CLUS_3              0               12
  CLUS_4              2               39
  CLUS_5              1               23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR128 MUTATED        1      3      0      0
  GPR128 WILD-TYPE     79     57     18     19
D6V8, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              1               79
  CLUS_2              3               57
  CLUS_3              0               18
  CLUS_4              0               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMMECR1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMMECR1 MUTATED        1      2      0
  AMMECR1 WILD-TYPE     59     61     38
D7V1, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               1                59
  CLUS_2               2                61
  CLUS_3               0                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMMECR1 MUTATED        1      1      1
  AMMECR1 WILD-TYPE     43     84     48
D7V2, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               1                43
  CLUS_2               1                84
  CLUS_3               1                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
  AMMECR1 MUTATED        1      0      2      0
  AMMECR1 WILD-TYPE     38     69     47     21
D7V3, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               1                38
  CLUS_2               0                69
  CLUS_3               2                47
  CLUS_4               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMMECR1 MUTATED        0      1      2      0
  AMMECR1 WILD-TYPE     38     70     46     21
D7V4, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               0                38
  CLUS_2               1                70
  CLUS_3               2                46
  CLUS_4               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMMECR1 MUTATED        2      1      0
  AMMECR1 WILD-TYPE     72     64     39
D7V5, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               2                72
  CLUS_2               1                64
  CLUS_3               0                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 CLUS_4
  AMMECR1 MUTATED        2      1      0      0
  AMMECR1 WILD-TYPE     74     58     18     25
D7V6, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               2                74
  CLUS_2               1                58
  CLUS_3               0                18
  CLUS_4               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMMECR1 MUTATED        0      1      0      2      0
  AMMECR1 WILD-TYPE     36     63     12     39     24
D7V7, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               0                36
  CLUS_2               1                63
  CLUS_3               0                12
  CLUS_4               2                39
  CLUS_5               0                24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMMECR1 MUTATED        1      2      0      0
  AMMECR1 WILD-TYPE     79     58     18     19
D7V8, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               1                79
  CLUS_2               2                58
  CLUS_3               0                18
  CLUS_4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = SHROOM4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        1      1      0
  SHROOM4 WILD-TYPE     59     62     38
D8V1, multiclass
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2               159 
       TCGA-P7-A5NY        TCGA-P8-A5KC        TCGA-P8-A5KD        TCGA-P8-A6RX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-P8-A6RY        TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6GO        TCGA-QR-A6GR        TCGA-QR-A6GS        TCGA-QR-A6GT 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6GU        TCGA-QR-A6GX        TCGA-QR-A6GY        TCGA-QR-A6GZ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H0        TCGA-QR-A6H1        TCGA-QR-A6H2        TCGA-QR-A6H3 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H5        TCGA-QR-A6H6        TCGA-QR-A702        TCGA-QR-A706 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70C        TCGA-QR-A70D        TCGA-QR-A70E        TCGA-QR-A70G 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70H        TCGA-QR-A70I        TCGA-QR-A70J        TCGA-QR-A70K 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70N        TCGA-QR-A70P        TCGA-QR-A70R        TCGA-QR-A70W 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70X        TCGA-QR-A7IN        TCGA-QR-A7IP        TCGA-QT-A5XJ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QT-A5XK        TCGA-QT-A5XL        TCGA-QT-A5XM        TCGA-QT-A5XN 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QT-A5XO        TCGA-QT-A5XP        TCGA-QT-A69Q        TCGA-QT-A7U0 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RM-A68T        TCGA-RM-A68W        TCGA-RT-A6Y9        TCGA-RT-A6YA 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RW-A67V        TCGA-RW-A67W        TCGA-RW-A67X 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A67Y        TCGA-RW-A680        TCGA-RW-A681        TCGA-RW-A684 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A685        TCGA-RW-A686        TCGA-RW-A688        TCGA-RW-A689 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68A        TCGA-RW-A68B        TCGA-RW-A68C        TCGA-RW-A68D 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68F        TCGA-RW-A68G        TCGA-RW-A7CZ        TCGA-RW-A7D0 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WQ        TCGA-S7-A7WR 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WU        TCGA-S7-A7WV        TCGA-S7-A7WW 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WX        TCGA-S7-A7X0        TCGA-S7-A7X1        TCGA-S7-A7X2 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SA-A6C2        TCGA-SP-A6QC        TCGA-SP-A6QD        TCGA-SP-A6QF 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ        TCGA-SP-A6QK 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SQ-A6I4        TCGA-SQ-A6I6        TCGA-SR-A6MP        TCGA-SR-A6MQ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MS        TCGA-SR-A6MT        TCGA-SR-A6MU        TCGA-SR-A6MV 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MX        TCGA-SR-A6MY        TCGA-SR-A6MZ        TCGA-SR-A6N0 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-TT-A6YJ        TCGA-TT-A6YK        TCGA-TT-A6YN        TCGA-TT-A6YO 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-TT-A6YP        TCGA-W2-A7H5        TCGA-W2-A7H7        TCGA-W2-A7HA 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7HB        TCGA-W2-A7HC        TCGA-W2-A7HD        TCGA-W2-A7HE 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7HF        TCGA-W2-A7HH        TCGA-W2-A7UY        TCGA-WB-A80K 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A80L        TCGA-WB-A80M        TCGA-WB-A80N        TCGA-WB-A80O 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A80P        TCGA-WB-A80Q        TCGA-WB-A80V        TCGA-WB-A80Y 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A814        TCGA-WB-A815        TCGA-WB-A817        TCGA-WB-A818 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A819        TCGA-WB-A81A        TCGA-WB-A81D        TCGA-WB-A81E 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81F        TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81J        TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81P        TCGA-WB-A81Q        TCGA-WB-A81R        TCGA-WB-A81S 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A81V        TCGA-WB-A81W        TCGA-WB-A820 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A821        TCGA-WB-A822        TCGA-XG-A823 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        1      1      1
  SHROOM4 WILD-TYPE     43     84     48
D8V2, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                43
  CLUS_2               1                84
  CLUS_3               1                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
  SHROOM4 MUTATED        1      1      0      1
  SHROOM4 WILD-TYPE     38     68     49     20
D8V3, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                38
  CLUS_2               1                68
  CLUS_3               0                49
  CLUS_4               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        0      1      1      1
  SHROOM4 WILD-TYPE     38     70     47     20
D8V4, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                38
  CLUS_2               1                70
  CLUS_3               1                47
  CLUS_4               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        1      1      1
  SHROOM4 WILD-TYPE     73     64     38
D8V5, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                73
  CLUS_2               1                64
  CLUS_3               1                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        1      1      0      1
  SHROOM4 WILD-TYPE     75     58     18     24
D8V6, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                75
  CLUS_2               1                58
  CLUS_3               0                18
  CLUS_4               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHROOM4 MUTATED        0      1      0      1      1
  SHROOM4 WILD-TYPE     36     63     12     40     23
D8V7, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                36
  CLUS_2               1                63
  CLUS_3               0                12
  CLUS_4               1                40
  CLUS_5               1                23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        1      1      0      1
  SHROOM4 WILD-TYPE     79     59     18     18
D8V8, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                79
  CLUS_2               1                59
  CLUS_3               0                18
  CLUS_4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = FAM83D MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM83D MUTATED        2      0      1
  FAM83D WILD-TYPE     58     63     37
D9V1, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              2               58
  CLUS_2              0               63
  CLUS_3              1               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
  FAM83D MUTATED        0      3      0
  FAM83D WILD-TYPE     44     82     49
D9V2, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               44
  CLUS_2              3               82
  CLUS_3              0               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM83D MUTATED        0      3      0      0
  FAM83D WILD-TYPE     39     66     49     21
D9V3, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               39
  CLUS_2              3               66
  CLUS_3              0               49
  CLUS_4              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM83D MUTATED        0      3      0      0
  FAM83D WILD-TYPE     38     68     48     21
D9V4, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               38
  CLUS_2              3               68
  CLUS_3              0               48
  CLUS_4              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM83D MUTATED        0      3      0
  FAM83D WILD-TYPE     74     62     39
D9V5, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               74
  CLUS_2              3               62
  CLUS_3              0               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 CLUS_4
  FAM83D MUTATED        1      2      0      0
  FAM83D WILD-TYPE     75     57     18     25
D9V6, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              1               75
  CLUS_2              2               57
  CLUS_3              0               18
  CLUS_4              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM83D MUTATED        0      2      1      0      0
  FAM83D WILD-TYPE     36     62     11     41     24
D9V7, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               36
  CLUS_2              2               62
  CLUS_3              1               11
  CLUS_4              0               41
  CLUS_5              0               24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM83D MUTATED        3      0      0      0
  FAM83D WILD-TYPE     77     60     18     19
D9V8, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              3               77
  CLUS_2              0               60
  CLUS_3              0               18
  CLUS_4              0               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
