[1] "ofn"       "-oTUVM-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/UVM-TP/19785804/UVM-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/19894046/transformed.cor.cli.txt"

nPatients in clinical file=80, in cluster file=80, common to both=80
[1] "Reduce the number of clustering variables from 10 to 8."
[1]  8 80
[1] "GNAQ MUTATION ANALYSIS"
[1] 3
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
[1] "GNA11 MUTATION ANALYSIS"
[1] 3
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
[1] "PRMT8 MUTATION ANALYSIS"
[1] 3
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              5              75 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              5              75 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            12             68 
  BAP1 MUTATED BAP1 WILD-TYPE 
            12             68 
[1] "SFRS2 MUTATION ANALYSIS"
[1] 3
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3              77 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3              77 
[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 80 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	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 80 columns, 0 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = GNAQ MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GNAQ MUTATED        8     24      8
  GNAQ WILD-TYPE     14     12     14
D1V1, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            8             14
  CLUS_2           24             12
  CLUS_3            8             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GNAQ MUTATED       13      7     20
  GNAQ WILD-TYPE     20     11      9
D1V2, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           13             20
  CLUS_2            7             11
  CLUS_3           20              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
  GNAQ MUTATED       12      5     23
  GNAQ WILD-TYPE     18     10     12
D1V3, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           12             18
  CLUS_2            5             10
  CLUS_3           23             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GNAQ MUTATED       10     22      8
  GNAQ WILD-TYPE     19     11     10
D1V4, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           10             19
  CLUS_2           22             11
  CLUS_3            8             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
  GNAQ MUTATED       13      7     20
  GNAQ WILD-TYPE     21     10      9
D1V5, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           13             21
  CLUS_2            7             10
  CLUS_3           20              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
  GNAQ MUTATED        5      8     18      9
  GNAQ WILD-TYPE     12      5     10     13
D1V6, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            5             12
  CLUS_2            8              5
  CLUS_3           18             10
  CLUS_4            9             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
  GNAQ MUTATED       12     19      6
  GNAQ WILD-TYPE     20      9      8
D1V7, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           12             20
  CLUS_2           19              9
  CLUS_3            6              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  GNAQ MUTATED        1      2     11     12      5      6
  GNAQ WILD-TYPE      4     10      5      4     10      4
D1V8, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            1              4
  CLUS_2            2             10
  CLUS_3           11              5
  CLUS_4           12              4
  CLUS_5            5             10
  CLUS_6            6              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(2) Variable = GNA11 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GNA11 MUTATED       14     12     10
  GNA11 WILD-TYPE      8     24     12
D2V1, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            14               8
  CLUS_2            12              24
  CLUS_3            10              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GNA11 MUTATED       18     10      8
  GNA11 WILD-TYPE     15      8     21
D2V2, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            18              15
  CLUS_2            10               8
  CLUS_3             8              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GNA11 MUTATED       17      7     12
  GNA11 WILD-TYPE     13      8     23
D2V3, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            17              13
  CLUS_2             7               8
  CLUS_3            12              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GNA11 MUTATED       17     11      8
  GNA11 WILD-TYPE     12     22     10
D2V4, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            17              12
  CLUS_2            11              22
  CLUS_3             8              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
  GNA11 MUTATED       17     10      9
  GNA11 WILD-TYPE     17      7     20
D2V5, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            17              17
  CLUS_2            10               7
  CLUS_3             9              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GNA11 MUTATED       10      4     10     12
  GNA11 WILD-TYPE      7      9     18     10
D2V6, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            10               7
  CLUS_2             4               9
  CLUS_3            10              18
  CLUS_4            12              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
  GNA11 MUTATED       16      9      8
  GNA11 WILD-TYPE     16     19      6
D2V7, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            16              16
  CLUS_2             9              19
  CLUS_3             8               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  GNA11 MUTATED        4      7      6      5      8      3
  GNA11 WILD-TYPE      1      5     10     11      7      7
D2V8, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1             4               1
  CLUS_2             7               5
  CLUS_3             6              10
  CLUS_4             5              11
  CLUS_5             8               7
  CLUS_6             3               7
[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 = EIF1AX MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0     10      0
  EIF1AX WILD-TYPE     22     26     22
D3V1, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               22
  CLUS_2             10               26
  CLUS_3              0               22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      2      8
  EIF1AX WILD-TYPE     33     16     21
D3V2, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               33
  CLUS_2              2               16
  CLUS_3              8               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      2      8
  EIF1AX WILD-TYPE     30     13     27
D3V3, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               30
  CLUS_2              2               13
  CLUS_3              8               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
  EIF1AX MUTATED        0      8      2
  EIF1AX WILD-TYPE     29     25     16
D3V4, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               29
  CLUS_2              8               25
  CLUS_3              2               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      3      7
  EIF1AX WILD-TYPE     34     14     22
D3V5, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               34
  CLUS_2              3               14
  CLUS_3              7               22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        0      3      7      0
  EIF1AX WILD-TYPE     17     10     21     22
D3V6, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               17
  CLUS_2              3               10
  CLUS_3              7               21
  CLUS_4              0               22
[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
  EIF1AX MUTATED        1      6      1
  EIF1AX WILD-TYPE     31     22     13
D3V7, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              1               31
  CLUS_2              6               22
  CLUS_3              1               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  EIF1AX MUTATED        0      1      4      3      0      0
  EIF1AX WILD-TYPE      5     11     12     13     15     10
D3V8, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0                5
  CLUS_2              1               11
  CLUS_3              4               12
  CLUS_4              3               13
  CLUS_5              0               15
  CLUS_6              0               10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = SF3B1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SF3B1 MUTATED        0     14      4
  SF3B1 WILD-TYPE     22     22     18
D4V1, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             0              22
  CLUS_2            14              22
  CLUS_3             4              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SF3B1 MUTATED        1      6     11
  SF3B1 WILD-TYPE     32     12     18
D4V2, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1              32
  CLUS_2             6              12
  CLUS_3            11              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SF3B1 MUTATED        3      0     15
  SF3B1 WILD-TYPE     27     15     20
D4V3, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             0              15
  CLUS_3            15              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SF3B1 MUTATED        2     14      2
  SF3B1 WILD-TYPE     27     19     16
D4V4, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             2              27
  CLUS_2            14              19
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SF3B1 MUTATED        1      5     12
  SF3B1 WILD-TYPE     33     12     17
D4V5, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1              33
  CLUS_2             5              12
  CLUS_3            12              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SF3B1 MUTATED        1      5     10      2
  SF3B1 WILD-TYPE     16      8     18     20
D4V6, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             5               8
  CLUS_3            10              18
  CLUS_4             2              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
  SF3B1 MUTATED        1     11      5
  SF3B1 WILD-TYPE     31     17      9
D4V7, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1              31
  CLUS_2            11              17
  CLUS_3             5               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 CLUS_6
  SF3B1 MUTATED        0      1      6      8      2      0
  SF3B1 WILD-TYPE      5     11     10      8     13     10
D4V8, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1              11
  CLUS_3             6              10
  CLUS_4             8               8
  CLUS_5             2              13
  CLUS_6             0              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = PRMT8 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRMT8 MUTATED        1      2      2
  PRMT8 WILD-TYPE     21     34     20
D5V1, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             2              34
  CLUS_3             2              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRMT8 MUTATED        3      0      2
  PRMT8 WILD-TYPE     30     18     27
D5V2, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             3              30
  CLUS_2             0              18
  CLUS_3             2              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
  PRMT8 MUTATED        3      1      1
  PRMT8 WILD-TYPE     27     14     34
D5V3, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             1              14
  CLUS_3             1              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRMT8 MUTATED        3      1      1
  PRMT8 WILD-TYPE     26     32     17
D5V4, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             3              26
  CLUS_2             1              32
  CLUS_3             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRMT8 MUTATED        2      1      2
  PRMT8 WILD-TYPE     32     16     27
D5V5, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             2              32
  CLUS_2             1              16
  CLUS_3             2              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
  PRMT8 MUTATED        1      0      2      2
  PRMT8 WILD-TYPE     16     13     26     20
D5V6, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             0              13
  CLUS_3             2              26
  CLUS_4             2              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
  PRMT8 MUTATED        3      0      2
  PRMT8 WILD-TYPE     29     28     12
D5V7, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             3              29
  CLUS_2             0              28
  CLUS_3             2              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  PRMT8 MUTATED        0      1      1      1      1      1
  PRMT8 WILD-TYPE      5     11     15     15     14      9
D5V8, multiclass
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             1              11
  CLUS_3             1              15
  CLUS_4             1              15
  CLUS_5             1              14
  CLUS_6             1               9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = CYSLTR2 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYSLTR2 MUTATED        0      0      3
  CYSLTR2 WILD-TYPE     22     36     19
D6V1, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               0                22
  CLUS_2               0                36
  CLUS_3               3                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYSLTR2 MUTATED        1      1      1
  CYSLTR2 WILD-TYPE     32     17     28
D6V2, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                32
  CLUS_2               1                17
  CLUS_3               1                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
  CYSLTR2 MUTATED        1      2      0
  CYSLTR2 WILD-TYPE     29     13     35
D6V3, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                29
  CLUS_2               2                13
  CLUS_3               0                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYSLTR2 MUTATED        1      0      2
  CYSLTR2 WILD-TYPE     28     33     16
D6V4, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                28
  CLUS_2               0                33
  CLUS_3               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYSLTR2 MUTATED        2      0      1
  CYSLTR2 WILD-TYPE     32     17     28
D6V5, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               2                32
  CLUS_2               0                17
  CLUS_3               1                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 CLUS_4
  CYSLTR2 MUTATED        2      0      1      0
  CYSLTR2 WILD-TYPE     15     13     27     22
D6V6, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               2                15
  CLUS_2               0                13
  CLUS_3               1                27
  CLUS_4               0                22
[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
  CYSLTR2 MUTATED        2      1      0
  CYSLTR2 WILD-TYPE     30     27     14
D6V7, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               2                30
  CLUS_2               1                27
  CLUS_3               0                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  CYSLTR2 MUTATED        0      1      0      0      1      1
  CYSLTR2 WILD-TYPE      5     11     16     16     14      9
D6V8, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                11
  CLUS_3               0                16
  CLUS_4               0                16
  CLUS_5               1                14
  CLUS_6               1                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        6      0      6
  BAP1 WILD-TYPE     16     36     16
D7V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            6             16
  CLUS_2            0             36
  CLUS_3            6             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        9      3      0
  BAP1 WILD-TYPE     24     15     29
D7V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            9             24
  CLUS_2            3             15
  CLUS_3            0             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        7      4      1
  BAP1 WILD-TYPE     23     11     34
D7V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            7             23
  CLUS_2            4             11
  CLUS_3            1             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        6      0      6
  BAP1 WILD-TYPE     23     33     12
D7V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            6             23
  CLUS_2            0             33
  CLUS_3            6             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        9      2      1
  BAP1 WILD-TYPE     25     15     28
D7V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            9             25
  CLUS_2            2             15
  CLUS_3            1             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 CLUS_4
  BAP1 MUTATED        5      0      1      6
  BAP1 WILD-TYPE     12     13     27     16
D7V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            5             12
  CLUS_2            0             13
  CLUS_3            1             27
  CLUS_4            6             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
  BAP1 MUTATED        8      1      2
  BAP1 WILD-TYPE     24     27     12
D7V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            8             24
  CLUS_2            1             27
  CLUS_3            2             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BAP1 MUTATED        1      3      2      0      1      4
  BAP1 WILD-TYPE      4      9     14     16     14      6
D7V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            3              9
  CLUS_3            2             14
  CLUS_4            0             16
  CLUS_5            1             14
  CLUS_6            4              6
[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 = SFRS2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SFRS2 MUTATED        1      1      1
  SFRS2 WILD-TYPE     21     35     21
D8V1, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             1              35
  CLUS_3             1              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SFRS2 MUTATED        1      2      0
  SFRS2 WILD-TYPE     32     16     29
D8V2, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              32
  CLUS_2             2              16
  CLUS_3             0              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SFRS2 MUTATED        1      2      0
  SFRS2 WILD-TYPE     29     13     35
D8V3, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             2              13
  CLUS_3             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SFRS2 MUTATED        1      0      2
  SFRS2 WILD-TYPE     28     33     16
D8V4, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             0              33
  CLUS_3             2              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SFRS2 MUTATED        3      0      0
  SFRS2 WILD-TYPE     31     17     29
D8V5, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             3              31
  CLUS_2             0              17
  CLUS_3             0              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SFRS2 MUTATED        1      1      0      1
  SFRS2 WILD-TYPE     16     12     28     21
D8V6, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              12
  CLUS_3             0              28
  CLUS_4             1              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
  SFRS2 MUTATED        2      1      0
  SFRS2 WILD-TYPE     30     27     14
D8V7, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             2              30
  CLUS_2             1              27
  CLUS_3             0              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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
  SFRS2 MUTATED        0      2      0      0      1      0
  SFRS2 WILD-TYPE      5     10     16     16     14     10
D8V8, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2              10
  CLUS_3             0              16
  CLUS_4             0              16
  CLUS_5             1              14
  CLUS_6             0              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
