[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/10667976/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=5,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	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=5, 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=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HRAS MUTATED        0      0     15      0      0
  HRAS WILD-TYPE     15     24     40     42     23
D1V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             15
  CLUS_2            0             24
  CLUS_3           15             40
  CLUS_4            0             42
  CLUS_5            0             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
  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
  HRAS MUTATED        0     17      1
  HRAS WILD-TYPE     44     58     58
D1V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             44
  CLUS_2           17             58
  CLUS_3            1             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
  HRAS MUTATED        0     16      2
  HRAS WILD-TYPE     78     45     37
D1V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             78
  CLUS_2           16             45
  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"

Clustering(2) Variable = EPAS1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EPAS1 MUTATED        1      1      0      5      1
  EPAS1 WILD-TYPE     14     23     55     37     22
D2V1, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1              23
  CLUS_3             0              55
  CLUS_4             5              37
  CLUS_5             1              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  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
  EPAS1 MUTATED        7      0      1
  EPAS1 WILD-TYPE     37     75     58
D2V7, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             7              37
  CLUS_2             0              75
  CLUS_3             1              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
  EPAS1 MUTATED        8      0      0
  EPAS1 WILD-TYPE     70     61     39
D2V8, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             8              70
  CLUS_2             0              61
  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"

Clustering(3) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        1      0      7      5      1
  NF1 WILD-TYPE     14     24     48     37     22
D3V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            14
  CLUS_2           0            24
  CLUS_3           7            48
  CLUS_4           5            37
  CLUS_5           1            22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  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
  NF1 MUTATED        0     15      0
  NF1 WILD-TYPE     44     60     59
D3V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            44
  CLUS_2          15            60
  CLUS_3           0            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
  NF1 MUTATED        1     12      2
  NF1 WILD-TYPE     77     49     37
D3V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            77
  CLUS_2          12            49
  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"

Clustering(4) Variable = RET MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RET MUTATED        0      0      5      0      1
  RET WILD-TYPE     15     24     50     42     22
D4V1, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            15
  CLUS_2           0            24
  CLUS_3           5            50
  CLUS_4           0            42
  CLUS_5           1            22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  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
  RET MUTATED        0      3      3
  RET WILD-TYPE     44     72     56
D4V7, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            44
  CLUS_2           3            72
  CLUS_3           3            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
  RET MUTATED        0      4      2
  RET WILD-TYPE     78     57     37
D4V8, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            78
  CLUS_2           4            57
  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"

Clustering(5) Variable = CSDE1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CSDE1 MUTATED        0      0      0      2      2
  CSDE1 WILD-TYPE     15     24     55     40     21
D5V1, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             0              24
  CLUS_3             0              55
  CLUS_4             2              40
  CLUS_5             2              21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  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
  CSDE1 MUTATED        1      3      0
  CSDE1 WILD-TYPE     43     72     59
D5V7, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              43
  CLUS_2             3              72
  CLUS_3             0              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
  CSDE1 MUTATED        1      0      3
  CSDE1 WILD-TYPE     77     61     36
D5V8, multiclass
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  CLUS_1             1              77
  CLUS_2             0              61
  CLUS_3             3              36
[1] 3 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 CLUS_4 CLUS_5
  GPR128 MUTATED        1      0      0      2      0
  GPR128 WILD-TYPE     14     24     55     40     23
D6V1, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0               24
  CLUS_3              0               55
  CLUS_4              2               40
  CLUS_5              0               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
  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
  GPR128 MUTATED        2      1      1
  GPR128 WILD-TYPE     42     74     58
D6V7, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              2               42
  CLUS_2              1               74
  CLUS_3              1               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
  GPR128 MUTATED        3      1      0
  GPR128 WILD-TYPE     75     60     39
D6V8, multiclass
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  CLUS_1              3               75
  CLUS_2              1               60
  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"

Clustering(7) Variable = AMMECR1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMMECR1 MUTATED        0      0      1      2      0
  AMMECR1 WILD-TYPE     15     24     54     40     23
D7V1, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               0                15
  CLUS_2               0                24
  CLUS_3               1                54
  CLUS_4               2                40
  CLUS_5               0                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
  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
  AMMECR1 MUTATED        2      1      0
  AMMECR1 WILD-TYPE     42     74     59
D7V7, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               2                42
  CLUS_2               1                74
  CLUS_3               0                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
  AMMECR1 MUTATED        2      1      0
  AMMECR1 WILD-TYPE     76     60     39
D7V8, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               2                76
  CLUS_2               1                60
  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"

Clustering(8) Variable = SHROOM4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SHROOM4 MUTATED        0      0      1      0      1
  SHROOM4 WILD-TYPE     15     24     54     42     22
D8V1, multiclass
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2               157 
       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-A5PG        TCGA-PR-A5PH        TCGA-QR-A6GO 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6GR        TCGA-QR-A6GS        TCGA-QR-A6GT        TCGA-QR-A6GU 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6GX        TCGA-QR-A6GY        TCGA-QR-A6GZ        TCGA-QR-A6H0 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H1        TCGA-QR-A6H2        TCGA-QR-A6H3        TCGA-QR-A6H5 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H6        TCGA-QR-A702        TCGA-QR-A706        TCGA-QR-A70C 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70D        TCGA-QR-A70E        TCGA-QR-A70G        TCGA-QR-A70H 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70I        TCGA-QR-A70J        TCGA-QR-A70K        TCGA-QR-A70N 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A70P        TCGA-QR-A70R        TCGA-QR-A70W        TCGA-QR-A70X 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A7IN        TCGA-QR-A7IP        TCGA-QT-A5XJ        TCGA-QT-A5XK 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QT-A5XL        TCGA-QT-A5XM        TCGA-QT-A5XN        TCGA-QT-A5XO 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QT-A5XP        TCGA-QT-A69Q        TCGA-QT-A7U0        TCGA-RM-A68T 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RM-A68W        TCGA-RT-A6Y9        TCGA-RT-A6YA        TCGA-RT-A6YC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A67V        TCGA-RW-A67W        TCGA-RW-A67X        TCGA-RW-A67Y 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A680        TCGA-RW-A681        TCGA-RW-A685        TCGA-RW-A686 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A688        TCGA-RW-A689        TCGA-RW-A68A        TCGA-RW-A68B 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68C        TCGA-RW-A68D        TCGA-RW-A68F        TCGA-RW-A68G 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A7CZ        TCGA-RW-A7D0        TCGA-RW-A8AZ        TCGA-RX-A8JQ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WL        TCGA-S7-A7WM        TCGA-S7-A7WO        TCGA-S7-A7WP 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WQ        TCGA-S7-A7WR        TCGA-S7-A7WT        TCGA-S7-A7WU 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX        TCGA-S7-A7X0 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7X1        TCGA-S7-A7X2        TCGA-SA-A6C2        TCGA-SP-A6QC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QD        TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QJ        TCGA-SP-A6QK        TCGA-SQ-A6I4        TCGA-SQ-A6I6 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MP        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MT 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MU        TCGA-SR-A6MV        TCGA-SR-A6MX        TCGA-SR-A6MY 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YJ        TCGA-TT-A6YK 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-TT-A6YN        TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-W2-A7H5 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7H7        TCGA-W2-A7HA        TCGA-W2-A7HB        TCGA-W2-A7HC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7HD        TCGA-W2-A7HE        TCGA-W2-A7HF        TCGA-W2-A7HH 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7UY        TCGA-WB-A80K        TCGA-WB-A80L        TCGA-WB-A80M 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A80N        TCGA-WB-A80O        TCGA-WB-A80P        TCGA-WB-A80Q 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A80V        TCGA-WB-A80Y        TCGA-WB-A814        TCGA-WB-A815 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A818        TCGA-WB-A819        TCGA-WB-A81A 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81D        TCGA-WB-A81E        TCGA-WB-A81F        TCGA-WB-A81G 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81P        TCGA-WB-A81Q 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81R        TCGA-WB-A81S        TCGA-WB-A81T        TCGA-WB-A81V 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81W        TCGA-WB-A820        TCGA-WB-A821        TCGA-WB-A822 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-XG-A823 
"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
  SHROOM4 MUTATED        1      1      1
  SHROOM4 WILD-TYPE     43     74     58
D8V7, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                43
  CLUS_2               1                74
  CLUS_3               1                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
  SHROOM4 MUTATED        1      1      1
  SHROOM4 WILD-TYPE     77     60     38
D8V8, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                77
  CLUS_2               1                60
  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"

Clustering(9) Variable = FAM83D MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM83D MUTATED        1      0      1      0      1
  FAM83D WILD-TYPE     14     24     54     42     22
D9V1, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0               24
  CLUS_3              1               54
  CLUS_4              0               42
  CLUS_5              1               22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  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
  FAM83D MUTATED        0      3      0
  FAM83D WILD-TYPE     44     72     59
D9V7, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               44
  CLUS_2              3               72
  CLUS_3              0               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
  FAM83D MUTATED        0      3      0
  FAM83D WILD-TYPE     78     58     39
D9V8, multiclass
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  CLUS_1              0               78
  CLUS_2              3               58
  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"
