[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/22542449/UVM-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/22572046/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 9 to 7."
[1]  7 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] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            22             58 
  BAP1 MUTATED BAP1 WILD-TYPE 
            22             58 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
[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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 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=6, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = GNAQ MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GNAQ MUTATED       10      2      4     20      3      1
  GNAQ WILD-TYPE     12      5      6     11      3      3
D1V1, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           10             12
  CLUS_2            2              5
  CLUS_3            4              6
  CLUS_4           20             11
  CLUS_5            3              3
  CLUS_6            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GNAQ MUTATED       11      8      7     14
  GNAQ WILD-TYPE     17      6      7     10
D1V2, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1           11             17
  CLUS_2            8              6
  CLUS_3            7              7
  CLUS_4           14             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
  GNAQ MUTATED        8      5     21      6
  GNAQ WILD-TYPE     10     10     11      9
D1V3, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            8             10
  CLUS_2            5             10
  CLUS_3           21             11
  CLUS_4            6              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
  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 CLUS_4 CLUS_5 CLUS_6
  GNAQ MUTATED        2      1      7     17     10      3
  GNAQ WILD-TYPE      6      7      4      8     13      2
D1V5, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            2              6
  CLUS_2            1              7
  CLUS_3            7              4
  CLUS_4           17              8
  CLUS_5           10             13
  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"
                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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GNAQ MUTATED        9      0     11      5      4      5      3
  GNAQ WILD-TYPE     11      7      6      4      4      2      3
D1V7, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            9             11
  CLUS_2            0              7
  CLUS_3           11              6
  CLUS_4            5              4
  CLUS_5            4              4
  CLUS_6            5              2
  CLUS_7            3              3
[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
  GNAQ MUTATED        7     20      5      5
  GNAQ WILD-TYPE     11      8     11      7
D1V8, multiclass
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  CLUS_1            7             11
  CLUS_2           20              8
  CLUS_3            5             11
  CLUS_4            5              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"

Clustering(2) Variable = GNA11 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GNA11 MUTATED       12      5      3     11      2      3
  GNA11 WILD-TYPE     10      2      7     20      4      1
D2V1, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            12              10
  CLUS_2             5               2
  CLUS_3             3               7
  CLUS_4            11              20
  CLUS_5             2               4
  CLUS_6             3               1
[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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GNA11 MUTATED       15      6      6      9
  GNA11 WILD-TYPE     13      8      8     15
D2V2, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            15              13
  CLUS_2             6               8
  CLUS_3             6               8
  CLUS_4             9              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
  GNA11 MUTATED       11      7     11      7
  GNA11 WILD-TYPE      7      8     21      8
D2V3, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            11               7
  CLUS_2             7               8
  CLUS_3            11              21
  CLUS_4             7               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
  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 CLUS_4 CLUS_5 CLUS_6
  GNA11 MUTATED        5      5      4      9     11      2
  GNA11 WILD-TYPE      3      3      7     16     12      3
D2V5, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1             5               3
  CLUS_2             5               3
  CLUS_3             4               7
  CLUS_4             9              16
  CLUS_5            11              12
  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"
                 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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GNA11 MUTATED       10      6      6      3      4      2      2
  GNA11 WILD-TYPE     10      1     11      6      4      5      4
D2V7, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            10              10
  CLUS_2             6               1
  CLUS_3             6              11
  CLUS_4             3               6
  CLUS_5             4               4
  CLUS_6             2               5
  CLUS_7             2               4
[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
  GNA11 MUTATED       10      9      9      5
  GNA11 WILD-TYPE      8     19      7      7
D2V8, multiclass
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  CLUS_1            10               8
  CLUS_2             9              19
  CLUS_3             9               7
  CLUS_4             5               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"

Clustering(3) Variable = EIF1AX MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EIF1AX MUTATED        2      0      0      8      0      0
  EIF1AX WILD-TYPE     20      7     10     23      6      4
D3V1, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              2               20
  CLUS_2              0                7
  CLUS_3              0               10
  CLUS_4              8               23
  CLUS_5              0                6
  CLUS_6              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        0      6      0      4
  EIF1AX WILD-TYPE     28      8     14     20
D3V2, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               28
  CLUS_2              6                8
  CLUS_3              0               14
  CLUS_4              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        0      2      8      0
  EIF1AX WILD-TYPE     18     13     24     15
D3V3, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               18
  CLUS_2              2               13
  CLUS_3              8               24
  CLUS_4              0               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
  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 CLUS_4 CLUS_5 CLUS_6
  EIF1AX MUTATED        0      0      3      6      0      1
  EIF1AX WILD-TYPE      8      8      8     19     23      4
D3V5, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0                8
  CLUS_2              0                8
  CLUS_3              3                8
  CLUS_4              6               19
  CLUS_5              0               23
  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"
                  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  EIF1AX MUTATED        0      1      4      1      1      0      1
  EIF1AX WILD-TYPE     20      6     13      8      7      7      5
D3V7, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               20
  CLUS_2              1                6
  CLUS_3              4               13
  CLUS_4              1                8
  CLUS_5              1                7
  CLUS_6              0                7
  CLUS_7              1                5
[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
  EIF1AX MUTATED        0      6      0      2
  EIF1AX WILD-TYPE     18     22     16     10
D3V8, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               18
  CLUS_2              6               22
  CLUS_3              0               16
  CLUS_4              2               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"

Clustering(4) Variable = SF3B1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SF3B1 MUTATED        3      0      1     13      0      1
  SF3B1 WILD-TYPE     19      7      9     18      6      3
D4V1, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             0               7
  CLUS_3             1               9
  CLUS_4            13              18
  CLUS_5             0               6
  CLUS_6             1               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SF3B1 MUTATED        0      2      5     11
  SF3B1 WILD-TYPE     28     12      9     13
D4V2, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             0              28
  CLUS_2             2              12
  CLUS_3             5               9
  CLUS_4            11              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
  SF3B1 MUTATED        3      0     15      0
  SF3B1 WILD-TYPE     15     15     17     15
D4V3, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             3              15
  CLUS_2             0              15
  CLUS_3            15              17
  CLUS_4             0              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
  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 CLUS_4 CLUS_5 CLUS_6
  SF3B1 MUTATED        1      1      3     10      1      2
  SF3B1 WILD-TYPE      7      7      8     15     22      3
D4V5, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             1               7
  CLUS_3             3               8
  CLUS_4            10              15
  CLUS_5             1              22
  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"
                 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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SF3B1 MUTATED        0      0      7      3      3      2      2
  SF3B1 WILD-TYPE     20      7     10      6      5      5      4
D4V7, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             0               7
  CLUS_3             7              10
  CLUS_4             3               6
  CLUS_5             3               5
  CLUS_6             2               5
  CLUS_7             2               4
[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
  SF3B1 MUTATED        1     12      2      2
  SF3B1 WILD-TYPE     17     16     14     10
D4V8, multiclass
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  CLUS_1             1              17
  CLUS_2            12              16
  CLUS_3             2              14
  CLUS_4             2              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"

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BAP1 MUTATED        8      5      5      0      3      1
  BAP1 WILD-TYPE     14      2      5     31      3      3
D5V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            8             14
  CLUS_2            5              2
  CLUS_3            5              5
  CLUS_4            0             31
  CLUS_5            3              3
  CLUS_6            1              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED       14      1      7      0
  BAP1 WILD-TYPE     14     13      7     24
D5V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           14             14
  CLUS_2            1             13
  CLUS_3            7              7
  CLUS_4            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED       11      6      0      5
  BAP1 WILD-TYPE      7      9     32     10
D5V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           11              7
  CLUS_2            6              9
  CLUS_3            0             32
  CLUS_4            5             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
  BAP1 MUTATED       14      0      8
  BAP1 WILD-TYPE     15     33     10
D5V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           14             15
  CLUS_2            0             33
  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 CLUS_4 CLUS_5 CLUS_6
  BAP1 MUTATED        6      2      0      1     12      1
  BAP1 WILD-TYPE      2      6     11     24     11      4
D5V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            6              2
  CLUS_2            2              6
  CLUS_3            0             11
  CLUS_4            1             24
  CLUS_5           12             11
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED        9      0      1     12
  BAP1 WILD-TYPE      8     13     27     10
D5V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            9              8
  CLUS_2            0             13
  CLUS_3            1             27
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BAP1 MUTATED       10      3      0      4      3      1      0
  BAP1 WILD-TYPE     10      4     17      5      5      6      6
D5V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           10             10
  CLUS_2            3              4
  CLUS_3            0             17
  CLUS_4            4              5
  CLUS_5            3              5
  CLUS_6            1              6
  CLUS_7            0              6
[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
  BAP1 MUTATED       11      1      6      3
  BAP1 WILD-TYPE      7     27     10      9
D5V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           11              7
  CLUS_2            1             27
  CLUS_3            6             10
  CLUS_4            3              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"

Clustering(6) Variable = CYSLTR2 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CYSLTR2 MUTATED        0      0      2      0      1      0
  CYSLTR2 WILD-TYPE     22      7      8     31      5      4
D6V1, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               0                22
  CLUS_2               0                 7
  CLUS_3               2                 8
  CLUS_4               0                31
  CLUS_5               1                 5
  CLUS_6               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYSLTR2 MUTATED        1      0      1      1
  CYSLTR2 WILD-TYPE     27     14     13     23
D6V2, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                27
  CLUS_2               0                14
  CLUS_3               1                13
  CLUS_4               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYSLTR2 MUTATED        0      2      0      1
  CYSLTR2 WILD-TYPE     18     13     32     14
D6V3, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               0                18
  CLUS_2               2                13
  CLUS_3               0                32
  CLUS_4               1                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
  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 CLUS_4 CLUS_5 CLUS_6
  CYSLTR2 MUTATED        1      1      0      0      1      0
  CYSLTR2 WILD-TYPE      7      7     11     25     22      5
D6V5, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               1                 7
  CLUS_3               0                11
  CLUS_4               0                25
  CLUS_5               1                22
  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"
                   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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CYSLTR2 MUTATED        1      0      0      1      0      1      0
  CYSLTR2 WILD-TYPE     19      7     17      8      8      6      6
D6V7, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                19
  CLUS_2               0                 7
  CLUS_3               0                17
  CLUS_4               1                 8
  CLUS_5               0                 8
  CLUS_6               1                 6
  CLUS_7               0                 6
[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
  CYSLTR2 MUTATED        1      0      1      1
  CYSLTR2 WILD-TYPE     17     28     15     11
D6V8, multiclass
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                28
  CLUS_3               1                15
  CLUS_4               1                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"

Clustering(7) Variable = SFRS2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SFRS2 MUTATED        3      0      0      0      0      0
  SFRS2 WILD-TYPE     19      7     10     31      6      4
D7V1, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             0               7
  CLUS_3             0              10
  CLUS_4             0              31
  CLUS_5             0               6
  CLUS_6             0               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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SFRS2 MUTATED        1      2      0      0
  SFRS2 WILD-TYPE     27     12     14     24
D7V2, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              27
  CLUS_2             2              12
  CLUS_3             0              14
  CLUS_4             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SFRS2 MUTATED        0      2      0      1
  SFRS2 WILD-TYPE     18     13     32     14
D7V3, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             0              18
  CLUS_2             2              13
  CLUS_3             0              32
  CLUS_4             1              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
  SFRS2 MUTATED        1      0      2
  SFRS2 WILD-TYPE     28     33     16
D7V4, 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 CLUS_4 CLUS_5 CLUS_6
  SFRS2 MUTATED        1      0      1      0      1      0
  SFRS2 WILD-TYPE      7      8     10     25     22      5
D7V5, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             0               8
  CLUS_3             1              10
  CLUS_4             0              25
  CLUS_5             1              22
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SFRS2 MUTATED        1      1      0      1
  SFRS2 WILD-TYPE     16     12     28     21
D7V6, 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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SFRS2 MUTATED        1      1      1      0      0      0      0
  SFRS2 WILD-TYPE     19      6     16      9      8      7      6
D7V7, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1               6
  CLUS_3             1              16
  CLUS_4             0               9
  CLUS_5             0               8
  CLUS_6             0               7
  CLUS_7             0               6
[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
  SFRS2 MUTATED        0      0      1      2
  SFRS2 WILD-TYPE     18     28     15     10
D7V8, multiclass
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  CLUS_1             0              18
  CLUS_2             0              28
  CLUS_3             1              15
  CLUS_4             2              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"
