[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"       "-oTUCS-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/UCS-TP/10668103/UCS-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/10685777/transformed.cor.cli.txt"

nPatients in clinical file=57, in cluster file=57, common to both=57
[1] "Reduce the number of clustering variables from 15 to 13."
[1] 13 57
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
[1] "ZBTB7B MUTATION ANALYSIS"
[1] 3
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
            10             47 
  CHD4 MUTATED CHD4 WILD-TYPE 
            10             47 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
[1] "MAMLD1 MUTATION ANALYSIS"
[1] 3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
[1] "LYPLA2 MUTATION ANALYSIS"
[1] 3
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               3               54 
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               3               54 
[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 57 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	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 57 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       21     21      8
  TP53 WILD-TYPE      1      3      2
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           21              1
  CLUS_2           21              3
  CLUS_3            8              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       12      8      8     12     11
  TP53 WILD-TYPE      0      1      2      1      2
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12              0
  CLUS_2            8              1
  CLUS_3            8              2
  CLUS_4           12              1
  CLUS_5           11              2
[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
  TP53 MUTATED       14     18     10      9
  TP53 WILD-TYPE      1      2      2      1
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           14              1
  CLUS_2           18              2
  CLUS_3           10              2
  CLUS_4            9              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED       11      3      8      5      7      5     12
  TP53 WILD-TYPE      0      1      0      1      1      1      2
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11              0
  CLUS_2            3              1
  CLUS_3            8              0
  CLUS_4            5              1
  CLUS_5            7              1
  CLUS_6            5              1
  CLUS_7           12              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       10     20      4     17
  TP53 WILD-TYPE      1      2      0      2
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              1
  CLUS_2           20              2
  CLUS_3            4              0
  CLUS_4           17              2
[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
  TP53 MUTATED       21      8     16      6
  TP53 WILD-TYPE      3      0      2      0
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           21              3
  CLUS_2            8              0
  CLUS_3           16              2
  CLUS_4            6              0
[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
  TP53 MUTATED       10     21      5     15
  TP53 WILD-TYPE      1      2      0      2
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              1
  CLUS_2           21              2
  CLUS_3            5              0
  CLUS_4           15              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        9      7     13      9      8      5
  TP53 WILD-TYPE      1      0      2      1      1      0
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9              1
  CLUS_2            7              0
  CLUS_3           13              2
  CLUS_4            9              1
  CLUS_5            8              1
  CLUS_6            5              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED       12      9      1
  FBXW7 WILD-TYPE     10     15      9
D2V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            12              10
  CLUS_2             9              15
  CLUS_3             1               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        6      4      4      3      5
  FBXW7 WILD-TYPE      6      5      6     10      8
D2V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6               6
  CLUS_2             4               5
  CLUS_3             4               6
  CLUS_4             3              10
  CLUS_5             5               8
[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
  FBXW7 MUTATED        7      8      5      2
  FBXW7 WILD-TYPE      8     12      7      8
D2V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             7               8
  CLUS_2             8              12
  CLUS_3             5               7
  CLUS_4             2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FBXW7 MUTATED        4      4      5      2      2      2      3
  FBXW7 WILD-TYPE      7      0      3      4      6      4     11
D2V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4               7
  CLUS_2             4               0
  CLUS_3             5               3
  CLUS_4             2               4
  CLUS_5             2               6
  CLUS_6             2               4
  CLUS_7             3              11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        5      8      3      6
  FBXW7 WILD-TYPE      6     14      1     13
D2V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5               6
  CLUS_2             8              14
  CLUS_3             3               1
  CLUS_4             6              13
[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
  FBXW7 MUTATED        9      4      7      2
  FBXW7 WILD-TYPE     15      4     11      4
D2V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             9              15
  CLUS_2             4               4
  CLUS_3             7              11
  CLUS_4             2               4
[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
  FBXW7 MUTATED        5      9      2      6
  FBXW7 WILD-TYPE      6     14      3     11
D2V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5               6
  CLUS_2             9              14
  CLUS_3             2               3
  CLUS_4             6              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FBXW7 MUTATED        2      4      7      4      3      2
  FBXW7 WILD-TYPE      8      3      8      6      6      3
D2V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             4               3
  CLUS_3             7               8
  CLUS_4             4               6
  CLUS_5             3               6
  CLUS_6             2               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = PPP2R1A MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PPP2R1A MUTATED        6      7      3
  PPP2R1A WILD-TYPE     16     17      7
D3V1, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               6                16
  CLUS_2               7                17
  CLUS_3               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  PPP2R1A MUTATED        4      3      4      3      2
  PPP2R1A WILD-TYPE      8      6      6     10     11
D3V2, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               3                 6
  CLUS_3               4                 6
  CLUS_4               3                10
  CLUS_5               2                11
[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
  PPP2R1A MUTATED        6      5      2      3
  PPP2R1A WILD-TYPE      9     15     10      7
D3V3, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               6                 9
  CLUS_2               5                15
  CLUS_3               2                10
  CLUS_4               3                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PPP2R1A MUTATED        4      1      4      1      2      2      2
  PPP2R1A WILD-TYPE      7      3      4      5      6      4     12
D3V4, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               4                 7
  CLUS_2               1                 3
  CLUS_3               4                 4
  CLUS_4               1                 5
  CLUS_5               2                 6
  CLUS_6               2                 4
  CLUS_7               2                12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PPP2R1A MUTATED        5      5      1      5
  PPP2R1A WILD-TYPE      6     17      3     14
D3V5, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               5                 6
  CLUS_2               5                17
  CLUS_3               1                 3
  CLUS_4               5                14
[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
  PPP2R1A MUTATED        8      4      3      1
  PPP2R1A WILD-TYPE     16      4     15      5
D3V6, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               8                16
  CLUS_2               4                 4
  CLUS_3               3                15
  CLUS_4               1                 5
[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
  PPP2R1A MUTATED        6      5      1      4
  PPP2R1A WILD-TYPE      5     18      4     13
D3V7, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               6                 5
  CLUS_2               5                18
  CLUS_3               1                 4
  CLUS_4               4                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PPP2R1A MUTATED        3      4      5      2      1      1
  PPP2R1A WILD-TYPE      7      3     10      8      8      4
D3V8, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               3                 7
  CLUS_2               4                 3
  CLUS_3               5                10
  CLUS_4               2                 8
  CLUS_5               1                 8
  CLUS_6               1                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      9      1
  PTEN WILD-TYPE     21     15      9
D4V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             21
  CLUS_2            9             15
  CLUS_3            1              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        0      0      6      5      0
  PTEN WILD-TYPE     12      9      4      8     13
D4V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             12
  CLUS_2            0              9
  CLUS_3            6              4
  CLUS_4            5              8
  CLUS_5            0             13
[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
  PTEN MUTATED        0      8      0      3
  PTEN WILD-TYPE     15     12     12      7
D4V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             15
  CLUS_2            8             12
  CLUS_3            0             12
  CLUS_4            3              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        0      0      3      0      3      0      5
  PTEN WILD-TYPE     11      4      5      6      5      6      9
D4V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             11
  CLUS_2            0              4
  CLUS_3            3              5
  CLUS_4            0              6
  CLUS_5            3              5
  CLUS_6            0              6
  CLUS_7            5              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        2      1      1      6
  PTEN WILD-TYPE      9     21      3     13
D4V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             21
  CLUS_3            1              3
  CLUS_4            6             13
[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
  PTEN MUTATED        8      0      1      1
  PTEN WILD-TYPE     16      8     17      5
D4V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             16
  CLUS_2            0              8
  CLUS_3            1             17
  CLUS_4            1              5
[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
  PTEN MUTATED        1      1      2      6
  PTEN WILD-TYPE     10     22      3     11
D4V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             10
  CLUS_2            1             22
  CLUS_3            2              3
  CLUS_4            6             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        2      0      6      1      0      1
  PTEN WILD-TYPE      8      7      9      9      9      4
D4V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0              7
  CLUS_3            6              9
  CLUS_4            1              9
  CLUS_5            0              9
  CLUS_6            1              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        2      5      0
  KRAS WILD-TYPE     20     19     10
D5V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2             20
  CLUS_2            5             19
  CLUS_3            0             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        0      1      1      0      5
  KRAS WILD-TYPE     12      8      9     13      8
D5V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             12
  CLUS_2            1              8
  CLUS_3            1              9
  CLUS_4            0             13
  CLUS_5            5              8
[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
  KRAS MUTATED        0      3      4      0
  KRAS WILD-TYPE     15     17      8     10
D5V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             15
  CLUS_2            3             17
  CLUS_3            4              8
  CLUS_4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KRAS MUTATED        0      0      1      0      0      4      2
  KRAS WILD-TYPE     11      4      7      6      8      2     12
D5V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             11
  CLUS_2            0              4
  CLUS_3            1              7
  CLUS_4            0              6
  CLUS_5            0              8
  CLUS_6            4              2
  CLUS_7            2             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        1      4      1      1
  KRAS WILD-TYPE     10     18      3     18
D5V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1             10
  CLUS_2            4             18
  CLUS_3            1              3
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        1      0      5      1
  KRAS WILD-TYPE     23      8     13      5
D5V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1             23
  CLUS_2            0              8
  CLUS_3            5             13
  CLUS_4            1              5
[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
  KRAS MUTATED        1      5      0      1
  KRAS WILD-TYPE     10     18      5     16
D5V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1             10
  CLUS_2            5             18
  CLUS_3            0              5
  CLUS_4            1             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        0      0      1      1      4      1
  KRAS WILD-TYPE     10      7     14      9      5      4
D5V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             10
  CLUS_2            0              7
  CLUS_3            1             14
  CLUS_4            1              9
  CLUS_5            4              5
  CLUS_6            1              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = ZBTB7B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZBTB7B MUTATED        3      1      1
  ZBTB7B WILD-TYPE     19     23      9
D6V1, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              3               19
  CLUS_2              1               23
  CLUS_3              1                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  ZBTB7B MUTATED        2      1      1      1      1
  ZBTB7B WILD-TYPE     10      8      9     12     12
D6V2, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              2               10
  CLUS_2              1                8
  CLUS_3              1                9
  CLUS_4              1               12
  CLUS_5              1               12
[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
  ZBTB7B MUTATED        2      2      1      1
  ZBTB7B WILD-TYPE     13     18     11      9
D6V3, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              2               13
  CLUS_2              2               18
  CLUS_3              1               11
  CLUS_4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZBTB7B MUTATED        2      0      0      0      1      1      2
  ZBTB7B WILD-TYPE      9      4      8      6      7      5     12
D6V4, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              2                9
  CLUS_2              0                4
  CLUS_3              0                8
  CLUS_4              0                6
  CLUS_5              1                7
  CLUS_6              1                5
  CLUS_7              2               12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZBTB7B MUTATED        1      1      2      2
  ZBTB7B WILD-TYPE     10     21      2     17
D6V5, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               21
  CLUS_3              2                2
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZBTB7B MUTATED        5      1      0      0
  ZBTB7B WILD-TYPE     19      7     18      6
D6V6, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              5               19
  CLUS_2              1                7
  CLUS_3              0               18
  CLUS_4              0                6
[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
  ZBTB7B MUTATED        1      1      2      2
  ZBTB7B WILD-TYPE     10     22      3     15
D6V7, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              1               10
  CLUS_2              1               22
  CLUS_3              2                3
  CLUS_4              2               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZBTB7B MUTATED        1      1      4      0      0      0
  ZBTB7B WILD-TYPE      9      6     11     10      9      5
D6V8, multiclass
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  CLUS_1              1                9
  CLUS_2              1                6
  CLUS_3              4               11
  CLUS_4              0               10
  CLUS_5              0                9
  CLUS_6              0                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = CHD4 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD4 MUTATED        2      7      1
  CHD4 WILD-TYPE     20     17      9
D7V1, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            7             17
  CLUS_3            1              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  CHD4 MUTATED        0      4      4      1      1
  CHD4 WILD-TYPE     12      5      6     12     12
D7V2, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            0             12
  CLUS_2            4              5
  CLUS_3            4              6
  CLUS_4            1             12
  CLUS_5            1             12
[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
  CHD4 MUTATED        2      5      0      3
  CHD4 WILD-TYPE     13     15     12      7
D7V3, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            5             15
  CLUS_3            0             12
  CLUS_4            3              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CHD4 MUTATED        0      2      4      0      3      0      1
  CHD4 WILD-TYPE     11      2      4      6      5      6     13
D7V4, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            2              2
  CLUS_3            4              4
  CLUS_4            0              6
  CLUS_5            3              5
  CLUS_6            0              6
  CLUS_7            1             13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHD4 MUTATED        3      2      1      3
  CHD4 WILD-TYPE      8     20      3     16
D7V5, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            2             20
  CLUS_3            1              3
  CLUS_4            3             16
[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
  CHD4 MUTATED        6      0      2      1
  CHD4 WILD-TYPE     18      8     16      5
D7V6, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            6             18
  CLUS_2            0              8
  CLUS_3            2             16
  CLUS_4            1              5
[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
  CHD4 MUTATED        3      2      1      3
  CHD4 WILD-TYPE      8     21      4     14
D7V7, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            2             21
  CLUS_3            1              4
  CLUS_4            3             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CHD4 MUTATED        2      0      4      2      0      1
  CHD4 WILD-TYPE      8      7     11      8      9      4
D7V8, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0              7
  CLUS_3            4             11
  CLUS_4            2              8
  CLUS_5            0              9
  CLUS_6            1              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = PIK3R1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        3      2      1
  PIK3R1 WILD-TYPE     19     22      9
D8V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               19
  CLUS_2              2               22
  CLUS_3              1                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  PIK3R1 MUTATED        2      1      1      1      1
  PIK3R1 WILD-TYPE     10      8      9     12     12
D8V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               10
  CLUS_2              1                8
  CLUS_3              1                9
  CLUS_4              1               12
  CLUS_5              1               12
[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
  PIK3R1 MUTATED        3      2      1      0
  PIK3R1 WILD-TYPE     12     18     11     10
D8V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               12
  CLUS_2              2               18
  CLUS_3              1               11
  CLUS_4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PIK3R1 MUTATED        2      1      1      0      0      1      1
  PIK3R1 WILD-TYPE      9      3      7      6      8      5     13
D8V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              1                3
  CLUS_3              1                7
  CLUS_4              0                6
  CLUS_5              0                8
  CLUS_6              1                5
  CLUS_7              1               13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED        2      2      1      1
  PIK3R1 WILD-TYPE      9     20      3     18
D8V5, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              2               20
  CLUS_3              1                3
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED        2      2      2      0
  PIK3R1 WILD-TYPE     22      6     16      6
D8V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               22
  CLUS_2              2                6
  CLUS_3              2               16
  CLUS_4              0                6
[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
  PIK3R1 MUTATED        2      3      0      1
  PIK3R1 WILD-TYPE      9     20      5     16
D8V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                9
  CLUS_2              3               20
  CLUS_3              0                5
  CLUS_4              1               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PIK3R1 MUTATED        1      2      1      1      1      0
  PIK3R1 WILD-TYPE      9      5     14      9      8      5
D8V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1                9
  CLUS_2              2                5
  CLUS_3              1               14
  CLUS_4              1                9
  CLUS_5              1                8
  CLUS_6              0                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = ARHGAP35 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  ARHGAP35 MUTATED        2      3      1
  ARHGAP35 WILD-TYPE     20     21      9
D9V1, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                3                 21
  CLUS_3                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  ARHGAP35 MUTATED        2      0      2      0      2
  ARHGAP35 WILD-TYPE     10      9      8     13     11
D9V2, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                  9
  CLUS_3                2                  8
  CLUS_4                0                 13
  CLUS_5                2                 11
[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
  ARHGAP35 MUTATED        2      2      1      1
  ARHGAP35 WILD-TYPE     13     18     11      9
D9V3, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 18
  CLUS_3                1                 11
  CLUS_4                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ARHGAP35 MUTATED        2      0      2      0      1      1      0
  ARHGAP35 WILD-TYPE      9      4      6      6      7      5     14
D9V4, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                0                  4
  CLUS_3                2                  6
  CLUS_4                0                  6
  CLUS_5                1                  7
  CLUS_6                1                  5
  CLUS_7                0                 14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARHGAP35 MUTATED        1      2      0      2
  ARHGAP35 WILD-TYPE     10     20      4     17
D9V5, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 20
  CLUS_3                0                  4
  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARHGAP35 MUTATED        1      2      1      1
  ARHGAP35 WILD-TYPE     23      6     17      5
D9V6, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                2                  6
  CLUS_3                1                 17
  CLUS_4                1                  5
[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
  ARHGAP35 MUTATED        1      2      0      2
  ARHGAP35 WILD-TYPE     10     21      5     15
D9V7, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 21
  CLUS_3                0                  5
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARHGAP35 MUTATED        0      2      1      1      0      1
  ARHGAP35 WILD-TYPE     10      5     14      9      9      4
D9V8, multiclass
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  CLUS_1                0                 10
  CLUS_2                2                  5
  CLUS_3                1                 14
  CLUS_4                1                  9
  CLUS_5                0                  9
  CLUS_6                1                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        5     11      3
  PIK3CA WILD-TYPE     17     13      7
D10V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               17
  CLUS_2             11               13
  CLUS_3              3                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        4      3      5      4      4
  PIK3CA WILD-TYPE      8      6      5      9      9
D10V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4                8
  CLUS_2              3                6
  CLUS_3              5                5
  CLUS_4              4                9
  CLUS_5              4                9
[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
  PIK3CA MUTATED        5     10      3      2
  PIK3CA WILD-TYPE     10     10      9      8
D10V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               10
  CLUS_2             10               10
  CLUS_3              3                9
  CLUS_4              2                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PIK3CA MUTATED        3      3      4      2      1      1      6
  PIK3CA WILD-TYPE      8      1      4      4      7      5      8
D10V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3                8
  CLUS_2              3                1
  CLUS_3              4                4
  CLUS_4              2                4
  CLUS_5              1                7
  CLUS_6              1                5
  CLUS_7              6                8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        4      4      2     10
  PIK3CA WILD-TYPE      7     18      2      9
D10V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4                7
  CLUS_2              4               18
  CLUS_3              2                2
  CLUS_4             10                9
[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
  PIK3CA MUTATED       11      2      4      3
  PIK3CA WILD-TYPE     13      6     14      3
D10V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               13
  CLUS_2              2                6
  CLUS_3              4               14
  CLUS_4              3                3
[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
  PIK3CA MUTATED        5      5      1      9
  PIK3CA WILD-TYPE      6     18      4      8
D10V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5                6
  CLUS_2              5               18
  CLUS_3              1                4
  CLUS_4              9                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PIK3CA MUTATED        3      1      9      3      1      3
  PIK3CA WILD-TYPE      7      6      6      7      8      2
D10V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3                7
  CLUS_2              1                6
  CLUS_3              9                6
  CLUS_4              3                7
  CLUS_5              1                8
  CLUS_6              3                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MAMLD1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAMLD1 MUTATED        1      2      1
  MAMLD1 WILD-TYPE     21     22      9
D11V1, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              1               21
  CLUS_2              2               22
  CLUS_3              1                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  MAMLD1 MUTATED        0      1      1      1      1
  MAMLD1 WILD-TYPE     12      8      9     12     12
D11V2, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              0               12
  CLUS_2              1                8
  CLUS_3              1                9
  CLUS_4              1               12
  CLUS_5              1               12
[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
  MAMLD1 MUTATED        0      2      1      1
  MAMLD1 WILD-TYPE     15     18     11      9
D11V3, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              0               15
  CLUS_2              2               18
  CLUS_3              1               11
  CLUS_4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MAMLD1 MUTATED        0      0      1      1      1      0      1
  MAMLD1 WILD-TYPE     11      4      7      5      7      6     13
D11V4, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              0                4
  CLUS_3              1                7
  CLUS_4              1                5
  CLUS_5              1                7
  CLUS_6              0                6
  CLUS_7              1               13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAMLD1 MUTATED        0      0      1      3
  MAMLD1 WILD-TYPE     11     22      3     16
D11V5, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              0               22
  CLUS_3              1                3
  CLUS_4              3               16
[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
  MAMLD1 MUTATED        2      0      1      1
  MAMLD1 WILD-TYPE     22      8     17      5
D11V6, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              2               22
  CLUS_2              0                8
  CLUS_3              1               17
  CLUS_4              1                5
[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
  MAMLD1 MUTATED        1      0      1      2
  MAMLD1 WILD-TYPE     10     23      4     15
D11V7, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              0               23
  CLUS_3              1                4
  CLUS_4              2               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MAMLD1 MUTATED        1      0      2      0      0      1
  MAMLD1 WILD-TYPE      9      7     13     10      9      4
D11V8, multiclass
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  CLUS_1              1                9
  CLUS_2              0                7
  CLUS_3              2               13
  CLUS_4              0               10
  CLUS_5              0                9
  CLUS_6              1                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      4      0
  RB1 WILD-TYPE     20     20     10
D12V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            20
  CLUS_2           4            20
  CLUS_3           0            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  RB1 MUTATED        0      1      3      2      0
  RB1 WILD-TYPE     12      8      7     11     13
D12V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            12
  CLUS_2           1             8
  CLUS_3           3             7
  CLUS_4           2            11
  CLUS_5           0            13
[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
  RB1 MUTATED        0      4      0      2
  RB1 WILD-TYPE     15     16     12      8
D12V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            15
  CLUS_2           4            16
  CLUS_3           0            12
  CLUS_4           2             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RB1 MUTATED        0      0      2      0      3      0      1
  RB1 WILD-TYPE     11      4      6      6      5      6     13
D12V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            11
  CLUS_2           0             4
  CLUS_3           2             6
  CLUS_4           0             6
  CLUS_5           3             5
  CLUS_6           0             6
  CLUS_7           1            13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      2      0      2
  RB1 WILD-TYPE      9     20      4     17
D12V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2             9
  CLUS_2           2            20
  CLUS_3           0             4
  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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        3      0      2      1
  RB1 WILD-TYPE     21      8     16      5
D12V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            21
  CLUS_2           0             8
  CLUS_3           2            16
  CLUS_4           1             5
[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
  RB1 MUTATED        1      2      1      2
  RB1 WILD-TYPE     10     21      4     15
D12V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            10
  CLUS_2           2            21
  CLUS_3           1             4
  CLUS_4           2            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RB1 MUTATED        1      0      2      2      0      1
  RB1 WILD-TYPE      9      7     13      8      9      4
D12V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1             9
  CLUS_2           0             7
  CLUS_3           2            13
  CLUS_4           2             8
  CLUS_5           0             9
  CLUS_6           1             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = LYPLA2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LYPLA2 MUTATED        1      2      0
  LYPLA2 WILD-TYPE     21     22     10
D13V1, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              1               21
  CLUS_2              2               22
  CLUS_3              0               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  LYPLA2 MUTATED        0      1      1      0      1
  LYPLA2 WILD-TYPE     12      8      9     13     12
D13V2, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               12
  CLUS_2              1                8
  CLUS_3              1                9
  CLUS_4              0               13
  CLUS_5              1               12
[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
  LYPLA2 MUTATED        0      1      1      1
  LYPLA2 WILD-TYPE     15     19     11      9
D13V3, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               15
  CLUS_2              1               19
  CLUS_3              1               11
  CLUS_4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LYPLA2 MUTATED        0      0      1      0      1      1      0
  LYPLA2 WILD-TYPE     11      4      7      6      7      5     14
D13V4, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              0                4
  CLUS_3              1                7
  CLUS_4              0                6
  CLUS_5              1                7
  CLUS_6              1                5
  CLUS_7              0               14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LYPLA2 MUTATED        0      1      1      1
  LYPLA2 WILD-TYPE     11     21      3     18
D13V5, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              1               21
  CLUS_3              1                3
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LYPLA2 MUTATED        1      0      1      1
  LYPLA2 WILD-TYPE     23      8     17      5
D13V6, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              1               23
  CLUS_2              0                8
  CLUS_3              1               17
  CLUS_4              1                5
[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
  LYPLA2 MUTATED        0      1      1      1
  LYPLA2 WILD-TYPE     11     22      4     16
D13V7, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              1               22
  CLUS_3              1                4
  CLUS_4              1               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LYPLA2 MUTATED        0      0      1      0      1      1
  LYPLA2 WILD-TYPE     10      7     14     10      8      4
D13V8, multiclass
        clus
vv       LYPLA2 MUTATED LYPLA2 WILD-TYPE
  CLUS_1              0               10
  CLUS_2              0                7
  CLUS_3              1               14
  CLUS_4              0               10
  CLUS_5              1                8
  CLUS_6              1                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
