[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/20140092/PCPG-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/19897197/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=178, common to both=178
[1] "Reduce the number of clustering variables from 9 to 8."
[1]   8 178
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              173 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              173 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           172 
  RET MUTATED RET WILD-TYPE 
            6           172 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
[1] "GPR128 MUTATION ANALYSIS"
[1] 3
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 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:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 178 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, 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        3      2      5      0
  HRAS WILD-TYPE     14     19     18     18
D1V3, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            3             14
  CLUS_2            2             19
  CLUS_3            5             18
  CLUS_4            0             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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        1      7      2
  HRAS WILD-TYPE     32     11     26
D1V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             32
  CLUS_2            7             11
  CLUS_3            2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        0     18      0      0
  HRAS WILD-TYPE     39     51     49     21
D1V5, 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
D1V6, 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
D1V7, 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
D1V8, 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
D1V9, 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
D1V10, 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 = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        3      1     10
  NF1 WILD-TYPE     57     62     28
D2V1, 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
D2V2, 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      0      6      0
  NF1 WILD-TYPE     14     21     17     18
D2V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            14
  CLUS_2           0            21
  CLUS_3           6            17
  CLUS_4           0            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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        1      4      4
  NF1 WILD-TYPE     32     14     24
D2V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            32
  CLUS_2           4            14
  CLUS_3           4            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
D2V5, 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
D2V6, 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
D2V7, 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
D2V8, 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
D2V9, 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
D2V10, 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(3) Variable = EPAS1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EPAS1 MUTATED        0      7      1
  EPAS1 WILD-TYPE     60     56     37
D3V1, 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
D3V2, 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      3      1      0
  EPAS1 WILD-TYPE     16     18     22     18
D3V3, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             3              18
  CLUS_3             1              22
  CLUS_4             0              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EPAS1 MUTATED        2      0      3
  EPAS1 WILD-TYPE     31     18     25
D3V4, multiclass
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  CLUS_1             2              31
  CLUS_2             0              18
  CLUS_3             3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
D3V5, 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
D3V6, 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
D3V7, 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
D3V8, 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
D3V9, 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
D3V10, 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(4) Variable = NUDT11 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NUDT11 MUTATED        1      2      2
  NUDT11 WILD-TYPE     59     61     36
D4V1, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              1               59
  CLUS_2              2               61
  CLUS_3              2               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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NUDT11 MUTATED        2      2      1
  NUDT11 WILD-TYPE     42     83     48
D4V2, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              2               42
  CLUS_2              2               83
  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
  NUDT11 MUTATED        1      0      1      1
  NUDT11 WILD-TYPE     16     21     22     17
D4V3, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              1               16
  CLUS_2              0               21
  CLUS_3              1               22
  CLUS_4              1               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NUDT11 MUTATED        1      1      1
  NUDT11 WILD-TYPE     32     17     27
D4V4, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              1               32
  CLUS_2              1               17
  CLUS_3              1               27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUDT11 MUTATED        2      3      0      0
  NUDT11 WILD-TYPE     37     66     49     21
D4V5, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              2               37
  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
  NUDT11 MUTATED        0      3      2      0
  NUDT11 WILD-TYPE     38     68     46     21
D4V6, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              0               38
  CLUS_2              3               68
  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
  NUDT11 MUTATED        2      3      0
  NUDT11 WILD-TYPE     72     62     39
D4V7, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              2               72
  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
  NUDT11 MUTATED        1      4      0      0
  NUDT11 WILD-TYPE     75     55     18     25
D4V8, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              1               75
  CLUS_2              4               55
  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
  NUDT11 MUTATED        1      3      0      1      0
  NUDT11 WILD-TYPE     35     61     12     40     24
D4V9, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              1               35
  CLUS_2              3               61
  CLUS_3              0               12
  CLUS_4              1               40
  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
  NUDT11 MUTATED        4      1      0      0
  NUDT11 WILD-TYPE     76     59     18     19
D4V10, multiclass
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  CLUS_1              4               76
  CLUS_2              1               59
  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(5) Variable = RET MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RET MUTATED        6      0      0
  RET WILD-TYPE     54     63     38
D5V1, 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
D5V2, 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        1      0      2      0
  RET WILD-TYPE     16     21     21     18
D5V3, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           1            16
  CLUS_2           0            21
  CLUS_3           2            21
  CLUS_4           0            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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RET MUTATED        0      1      2
  RET WILD-TYPE     33     17     26
D5V4, multiclass
        clus
vv       RET MUTATED RET WILD-TYPE
  CLUS_1           0            33
  CLUS_2           1            17
  CLUS_3           2            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RET MUTATED        0      5      0      1
  RET WILD-TYPE     39     64     49     20
D5V5, 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
D5V6, 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
D5V7, 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
D5V8, 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
D5V9, 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
D5V10, 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(6) Variable = SHROOM4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        1      1      0
  SHROOM4 WILD-TYPE     59     62     38
D6V1, 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
D6V2, 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        0      0      1      0
  SHROOM4 WILD-TYPE     17     21     22     18
D6V3, multiclass
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                1                78 
       TCGA-P7-A5NX        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-A6GT        TCGA-QR-A6GU        TCGA-QR-A6GZ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H2        TCGA-QR-A70W        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-A67X        TCGA-RW-A680        TCGA-RW-A681 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A685        TCGA-RW-A688        TCGA-RW-A689        TCGA-RW-A68A 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68B        TCGA-RW-A68C        TCGA-RW-A68D        TCGA-RW-A68F 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68G        TCGA-RW-A8AZ        TCGA-RX-A8JQ        TCGA-S7-A7WL 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WM        TCGA-S7-A7WP        TCGA-S7-A7WQ        TCGA-S7-A7WR 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WU        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X1        TCGA-S7-A7X2        TCGA-SA-A6C2 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QH        TCGA-SP-A6QJ        TCGA-SR-A6MQ        TCGA-SR-A6MX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MY        TCGA-SR-A6MZ        TCGA-TT-A6YN        TCGA-W2-A7HC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7HF        TCGA-WB-A80Q        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-A81G 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81P        TCGA-WB-A81S        TCGA-WB-A81T 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81V        TCGA-WB-A81W 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        0      0      1
  SHROOM4 WILD-TYPE     33     18     27
D6V4, multiclass
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                1                78 
       TCGA-P7-A5NX        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-A6GT        TCGA-QR-A6GU        TCGA-QR-A6GZ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-QR-A6H2        TCGA-QR-A70W        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-A67X        TCGA-RW-A680        TCGA-RW-A681 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A685        TCGA-RW-A688        TCGA-RW-A689        TCGA-RW-A68A 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68B        TCGA-RW-A68C        TCGA-RW-A68D        TCGA-RW-A68F 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-RW-A68G        TCGA-RW-A8AZ        TCGA-RX-A8JQ        TCGA-S7-A7WL 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WM        TCGA-S7-A7WP        TCGA-S7-A7WQ        TCGA-S7-A7WR 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WU        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X1        TCGA-S7-A7X2        TCGA-SA-A6C2 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QH        TCGA-SP-A6QJ        TCGA-SR-A6MQ        TCGA-SR-A6MX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MY        TCGA-SR-A6MZ        TCGA-TT-A6YN        TCGA-W2-A7HC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-W2-A7HF        TCGA-WB-A80Q        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-A81G 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81P        TCGA-WB-A81S        TCGA-WB-A81T 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81V        TCGA-WB-A81W 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        1      1      0      1
  SHROOM4 WILD-TYPE     38     68     49     20
D6V5, 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
D6V6, 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
D6V7, 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
D6V8, 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
D6V9, 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
D6V10, 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(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        0      2      1      0
  AMMECR1 WILD-TYPE     17     19     22     18
D7V3, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                19
  CLUS_3               1                22
  CLUS_4               0                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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMMECR1 MUTATED        1      1      1
  AMMECR1 WILD-TYPE     32     17     27
D7V4, multiclass
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  CLUS_1               1                32
  CLUS_2               1                17
  CLUS_3               1                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
D7V5, 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
D7V6, 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
D7V7, 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
D7V8, 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
D7V9, 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
D7V10, 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 = GPR128 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPR128 MUTATED        1      1      1
  GPR128 WILD-TYPE     59     62     37
D8V1, 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
D8V2, 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        0      0      0      0
  GPR128 WILD-TYPE     17     21     23     18
D8V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GPR128 MUTATED        0      0      0
  GPR128 WILD-TYPE     33     18     28
D8V4, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR128 MUTATED        1      1      2      0
  GPR128 WILD-TYPE     38     68     47     21
D8V5, 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
D8V6, 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
D8V7, 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
D8V8, 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
D8V9, 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
D8V10, 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"
