[1] "ofn"        "-oTCHOL-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/CHOL-TP/20125181/CHOL-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/19893431/transformed.cor.cli.txt"

nPatients in clinical file=36, in cluster file=35, common to both=35
[1] "Reduce the number of clustering variables from 17 to 15."
[1] 15 35
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              5              30 
  HLA-B MUTATED HLA-B WILD-TYPE 
              5              30 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
[1] "FTH1 MUTATION ANALYSIS"
[1] 3
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               30 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               30 
[1] "DDHD1 MUTATION ANALYSIS"
[1] 3
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              4              31 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              4              31 
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
[1] "MUC21 MUTATION ANALYSIS"
[1] 3
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
[1] "CLIP4 MUTATION ANALYSIS"
[1] 3
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              4              31 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              4              31 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             6             29 
  BAP1 MUTATED BAP1 WILD-TYPE 
             6             29 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              30 
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              30 
[1] "FAM35A MUTATION ANALYSIS"
[1] 3
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               32 
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               32 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 35 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=7,	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 35 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PBRM1 MUTATION ANALYSIS
D1V1, binary
                 cls
clus               0  1
  PBRM1 MUTATED    2  6
  PBRM1 WILD-TYPE 17 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      2    6
  PBRM1 WILD-TYPE   17   10
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             6              10
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED        0      2      6
  PBRM1 WILD-TYPE     13      7      7
D1V2, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             2               7
  CLUS_3             6               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
  PBRM1 MUTATED        2      1      3
  PBRM1 WILD-TYPE      8      7      8
D1V3, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             1               7
  CLUS_3             3               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
  PBRM1 MUTATED        2      1      3      0
  PBRM1 WILD-TYPE      4      6      5      8
D1V4, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             1               6
  CLUS_3             3               5
  CLUS_4             0               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
  PBRM1 MUTATED        1      5      2
  PBRM1 WILD-TYPE     11      9      7
D1V5, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1              11
  CLUS_2             5               9
  CLUS_3             2               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 CLUS_6 CLUS_7
  PBRM1 MUTATED        0      0      3      2      2      1      0
  PBRM1 WILD-TYPE      4      5      2      7      3      4      2
D1V6, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             3               2
  CLUS_4             2               7
  CLUS_5             2               3
  CLUS_6             1               4
  CLUS_7             0               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
  PBRM1 MUTATED        1      1      3      3
  PBRM1 WILD-TYPE      8      4      7      8
D1V7, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1               4
  CLUS_3             3               7
  CLUS_4             3               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
  PBRM1 MUTATED        0      3      2      1      2      0
  PBRM1 WILD-TYPE      8      7      2      3      3      4
D1V8, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             3               7
  CLUS_3             2               2
  CLUS_4             1               3
  CLUS_5             2               3
  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"
D1V9, binary
                 cls
clus               0  1
  PBRM1 MUTATED    3  5
  PBRM1 WILD-TYPE 12 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      3    5
  PBRM1 WILD-TYPE   12   15
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             5              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PBRM1 MUTATED        0      1      0      2      3      1      1
  PBRM1 WILD-TYPE      6      2      3      7      2      4      3
D1V10, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               2
  CLUS_3             0               3
  CLUS_4             2               7
  CLUS_5             3               2
  CLUS_6             1               4
  CLUS_7             1               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"

Clustering(2) Variable = HLA-B MUTATION ANALYSIS
D2V1, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  2
  HLA-B WILD-TYPE 16 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    2
  HLA-B WILD-TYPE   16   14
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              16
  CLUS_2             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-B MUTATED        1      4      0
  HLA-B WILD-TYPE     12      5     13
D2V2, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              12
  CLUS_2             4               5
  CLUS_3             0              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
  HLA-B MUTATED        1      1      3
  HLA-B WILD-TYPE      9      7      8
D2V3, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1               9
  CLUS_2             1               7
  CLUS_3             3               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
  HLA-B MUTATED        0      1      1      3
  HLA-B WILD-TYPE      6      6      7      5
D2V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               6
  CLUS_3             1               7
  CLUS_4             3               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
  HLA-B MUTATED        0      1      4
  HLA-B WILD-TYPE     12     13      5
D2V5, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              12
  CLUS_2             1              13
  CLUS_3             4               5
[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 CLUS_7
  HLA-B MUTATED        0      0      0      4      1      0      0
  HLA-B WILD-TYPE      4      5      5      5      4      5      2
D2V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             4               5
  CLUS_5             1               4
  CLUS_6             0               5
  CLUS_7             0               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
  HLA-B MUTATED        0      3      0      2
  HLA-B WILD-TYPE      9      2     10      9
D2V7, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3               2
  CLUS_3             0              10
  CLUS_4             2               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
  HLA-B MUTATED        0      0      0      2      1      2
  HLA-B WILD-TYPE      8     10      4      2      4      2
D2V8, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0              10
  CLUS_3             0               4
  CLUS_4             2               2
  CLUS_5             1               4
  CLUS_6             2               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"
D2V9, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  2
  HLA-B WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    2
  HLA-B WILD-TYPE   12   18
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              12
  CLUS_2             2              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  HLA-B MUTATED        0      0      0      2      0      2      1
  HLA-B WILD-TYPE      6      3      3      7      5      3      3
D2V10, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             2               7
  CLUS_5             0               5
  CLUS_6             2               3
  CLUS_7             1               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"

Clustering(3) Variable = MLL3 MUTATION ANALYSIS
D3V1, binary
                cls
clus              0  1
  MLL3 MUTATED    2  5
  MLL3 WILD-TYPE 17 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      2    5
  MLL3 WILD-TYPE   17   11
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            2             17
  CLUS_2            5             11
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL3 MUTATED        1      3      3
  MLL3 WILD-TYPE     12      6     10
D3V2, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            3              6
  CLUS_3            3             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
  MLL3 MUTATED        1      1      4
  MLL3 WILD-TYPE      9      7      7
D3V3, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            1              9
  CLUS_2            1              7
  CLUS_3            4              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
  MLL3 MUTATED        1      1      2      2
  MLL3 WILD-TYPE      5      6      6      6
D3V4, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            1              6
  CLUS_3            2              6
  CLUS_4            2              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
  MLL3 MUTATED        3      3      1
  MLL3 WILD-TYPE      9     11      8
D3V5, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            3              9
  CLUS_2            3             11
  CLUS_3            1              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 CLUS_7
  MLL3 MUTATED        1      1      1      1      2      1      0
  MLL3 WILD-TYPE      3      4      4      8      3      4      2
D3V6, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            1              4
  CLUS_3            1              4
  CLUS_4            1              8
  CLUS_5            2              3
  CLUS_6            1              4
  CLUS_7            0              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
  MLL3 MUTATED        3      1      0      3
  MLL3 WILD-TYPE      6      4     10      8
D3V7, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            3              6
  CLUS_2            1              4
  CLUS_3            0             10
  CLUS_4            3              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
  MLL3 MUTATED        2      1      1      1      2      0
  MLL3 WILD-TYPE      6      9      3      3      3      4
D3V8, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            1              9
  CLUS_3            1              3
  CLUS_4            1              3
  CLUS_5            2              3
  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"
D3V9, binary
                cls
clus              0  1
  MLL3 MUTATED    4  3
  MLL3 WILD-TYPE 11 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      4    3
  MLL3 WILD-TYPE   11   17
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            4             11
  CLUS_2            3             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MLL3 MUTATED        3      0      0      1      1      1      1
  MLL3 WILD-TYPE      3      3      3      8      4      4      3
D3V10, multiclass
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  CLUS_1            3              3
  CLUS_2            0              3
  CLUS_3            0              3
  CLUS_4            1              8
  CLUS_5            1              4
  CLUS_6            1              4
  CLUS_7            1              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"

Clustering(4) Variable = FTH1 MUTATION ANALYSIS
D4V1, binary
                cls
clus              0  1
  FTH1 MUTATED    1  2
  FTH1 WILD-TYPE 18 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      1    2
  FTH1 WILD-TYPE   18   14
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FTH1 MUTATED        0      0      3
  FTH1 WILD-TYPE     13      9     10
D4V2, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            0              9
  CLUS_3            3             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
  FTH1 MUTATED        0      0      3
  FTH1 WILD-TYPE     10      8      8
D4V3, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0             10
  CLUS_2            0              8
  CLUS_3            3              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
  FTH1 MUTATED        0      0      1      2
  FTH1 WILD-TYPE      6      7      7      6
D4V4, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            0              7
  CLUS_3            1              7
  CLUS_4            2              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
  FTH1 MUTATED        0      3      0
  FTH1 WILD-TYPE     12     11      9
D4V5, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0             12
  CLUS_2            3             11
  CLUS_3            0              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 CLUS_7
  FTH1 MUTATED        0      0      1      0      0      1      1
  FTH1 WILD-TYPE      4      5      4      9      5      4      1
D4V6, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              5
  CLUS_3            1              4
  CLUS_4            0              9
  CLUS_5            0              5
  CLUS_6            1              4
  CLUS_7            1              1
[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
  FTH1 MUTATED        0      0      1      2
  FTH1 WILD-TYPE      9      5      9      9
D4V7, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            0              5
  CLUS_3            1              9
  CLUS_4            2              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
  FTH1 MUTATED        0      1      1      0      1      0
  FTH1 WILD-TYPE      8      9      3      4      4      4
D4V8, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1              9
  CLUS_3            1              3
  CLUS_4            0              4
  CLUS_5            1              4
  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"
D4V9, binary
                cls
clus              0  1
  FTH1 MUTATED    2  1
  FTH1 WILD-TYPE 13 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    1
  FTH1 WILD-TYPE   13   19
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            1             19
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FTH1 MUTATED        1      0      0      1      1      0      0
  FTH1 WILD-TYPE      5      3      3      8      4      5      4
D4V10, multiclass
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            0              3
  CLUS_3            0              3
  CLUS_4            1              8
  CLUS_5            1              4
  CLUS_6            0              5
  CLUS_7            0              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"

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE 17 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE   17   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             17
  CLUS_2            3             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      1      2
  TP53 WILD-TYPE     11      8     11
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            1              8
  CLUS_3            2             11
[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
  TP53 MUTATED        2      0      2
  TP53 WILD-TYPE      8      8      9
D5V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0              8
  CLUS_3            2              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
  TP53 MUTATED        1      0      1      2
  TP53 WILD-TYPE      5      7      7      6
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            0              7
  CLUS_3            1              7
  CLUS_4            2              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
  TP53 MUTATED        2      2      1
  TP53 WILD-TYPE     10     12      8
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            2             12
  CLUS_3            1              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 CLUS_7
  TP53 MUTATED        1      0      1      1      1      1      0
  TP53 WILD-TYPE      3      5      4      8      4      4      2
D5V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            0              5
  CLUS_3            1              4
  CLUS_4            1              8
  CLUS_5            1              4
  CLUS_6            1              4
  CLUS_7            0              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        1      1      2      1
  TP53 WILD-TYPE      8      4      8     10
D5V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1              4
  CLUS_3            2              8
  CLUS_4            1             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
  TP53 MUTATED        1      2      1      1      0      0
  TP53 WILD-TYPE      7      8      3      3      5      4
D5V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2              8
  CLUS_3            1              3
  CLUS_4            1              3
  CLUS_5            0              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"
D5V9, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE   13   17
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            3             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        1      1      0      1      0      1      1
  TP53 WILD-TYPE      5      2      3      8      5      4      3
D5V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            1              2
  CLUS_3            0              3
  CLUS_4            1              8
  CLUS_5            0              5
  CLUS_6            1              4
  CLUS_7            1              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"

Clustering(6) Variable = ARID1A MUTATION ANALYSIS
D6V1, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  3
  ARID1A WILD-TYPE 17 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    3
  ARID1A WILD-TYPE   17   13
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               17
  CLUS_2              3               13
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      1      3
  ARID1A WILD-TYPE     12      8     10
D6V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1                8
  CLUS_3              3               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
  ARID1A MUTATED        2      0      2
  ARID1A WILD-TYPE      8      8      9
D6V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2                8
  CLUS_2              0                8
  CLUS_3              2                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
  ARID1A MUTATED        0      0      3      1
  ARID1A WILD-TYPE      6      7      5      7
D6V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0                7
  CLUS_3              3                5
  CLUS_4              1                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
  ARID1A MUTATED        0      3      2
  ARID1A WILD-TYPE     12     11      7
D6V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               12
  CLUS_2              3               11
  CLUS_3              2                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 CLUS_6 CLUS_7
  ARID1A MUTATED        0      0      2      2      1      0      0
  ARID1A WILD-TYPE      4      5      3      7      4      5      2
D6V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                5
  CLUS_3              2                3
  CLUS_4              2                7
  CLUS_5              1                4
  CLUS_6              0                5
  CLUS_7              0                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
  ARID1A MUTATED        1      1      1      2
  ARID1A WILD-TYPE      8      4      9      9
D6V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1                4
  CLUS_3              1                9
  CLUS_4              2                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
  ARID1A MUTATED        0      1      2      1      0      1
  ARID1A WILD-TYPE      8      9      2      3      5      3
D6V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                8
  CLUS_2              1                9
  CLUS_3              2                2
  CLUS_4              1                3
  CLUS_5              0                5
  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"
D6V9, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  2
  ARID1A WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    2
  ARID1A WILD-TYPE   12   18
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               12
  CLUS_2              2               18
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ARID1A MUTATED        0      0      0      3      1      1      0
  ARID1A WILD-TYPE      6      3      3      6      4      4      4
D6V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0                3
  CLUS_3              0                3
  CLUS_4              3                6
  CLUS_5              1                4
  CLUS_6              1                4
  CLUS_7              0                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"

Clustering(7) Variable = DDHD1 MUTATION ANALYSIS
D7V1, binary
                 cls
clus               0  1
  DDHD1 MUTATED    1  3
  DDHD1 WILD-TYPE 18 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      1    3
  DDHD1 WILD-TYPE   18   13
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             3              13
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DDHD1 MUTATED        1      1      2
  DDHD1 WILD-TYPE     12      8     11
D7V2, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             1               8
  CLUS_3             2              11
[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
  DDHD1 MUTATED        0      1      2
  DDHD1 WILD-TYPE     10      7      9
D7V3, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             0              10
  CLUS_2             1               7
  CLUS_3             2               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
  DDHD1 MUTATED        0      1      0      2
  DDHD1 WILD-TYPE      6      6      8      6
D7V4, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               6
  CLUS_3             0               8
  CLUS_4             2               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
  DDHD1 MUTATED        0      2      2
  DDHD1 WILD-TYPE     12     12      7
D7V5, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             0              12
  CLUS_2             2              12
  CLUS_3             2               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 CLUS_6 CLUS_7
  DDHD1 MUTATED        0      0      1      2      0      1      0
  DDHD1 WILD-TYPE      4      5      4      7      5      4      2
D7V6, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             2               7
  CLUS_5             0               5
  CLUS_6             1               4
  CLUS_7             0               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
  DDHD1 MUTATED        1      1      0      2
  DDHD1 WILD-TYPE      8      4     10      9
D7V7, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1               4
  CLUS_3             0              10
  CLUS_4             2               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
  DDHD1 MUTATED        0      0      1      1      1      1
  DDHD1 WILD-TYPE      8     10      3      3      4      3
D7V8, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0              10
  CLUS_3             1               3
  CLUS_4             1               3
  CLUS_5             1               4
  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"
D7V9, binary
                 cls
clus               0  1
  DDHD1 MUTATED    3  1
  DDHD1 WILD-TYPE 12 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      3    1
  DDHD1 WILD-TYPE   12   19
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             1              19
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DDHD1 MUTATED        1      0      0      1      0      2      0
  DDHD1 WILD-TYPE      5      3      3      8      5      3      4
D7V10, multiclass
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             1               8
  CLUS_5             0               5
  CLUS_6             2               3
  CLUS_7             0               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"

Clustering(8) Variable = MUC2 MUTATION ANALYSIS
D8V1, binary
                cls
clus              0  1
  MUC2 MUTATED    5  2
  MUC2 WILD-TYPE 14 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      5    2
  MUC2 WILD-TYPE   14   14
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            5             14
  CLUS_2            2             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC2 MUTATED        4      1      2
  MUC2 WILD-TYPE      9      8     11
D8V2, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            4              9
  CLUS_2            1              8
  CLUS_3            2             11
[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
  MUC2 MUTATED        3      0      1
  MUC2 WILD-TYPE      7      8     10
D8V3, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            3              7
  CLUS_2            0              8
  CLUS_3            1             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
  MUC2 MUTATED        2      0      1      1
  MUC2 WILD-TYPE      4      7      7      7
D8V4, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            0              7
  CLUS_3            1              7
  CLUS_4            1              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
  MUC2 MUTATED        4      1      2
  MUC2 WILD-TYPE      8     13      7
D8V5, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            4              8
  CLUS_2            1             13
  CLUS_3            2              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 CLUS_6 CLUS_7
  MUC2 MUTATED        3      1      0      2      1      0      0
  MUC2 WILD-TYPE      1      4      5      7      4      5      2
D8V6, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            3              1
  CLUS_2            1              4
  CLUS_3            0              5
  CLUS_4            2              7
  CLUS_5            1              4
  CLUS_6            0              5
  CLUS_7            0              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
  MUC2 MUTATED        3      1      1      2
  MUC2 WILD-TYPE      6      4      9      9
D8V7, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            3              6
  CLUS_2            1              4
  CLUS_3            1              9
  CLUS_4            2              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
  MUC2 MUTATED        4      1      1      1      0      0
  MUC2 WILD-TYPE      4      9      3      3      5      4
D8V8, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            4              4
  CLUS_2            1              9
  CLUS_3            1              3
  CLUS_4            1              3
  CLUS_5            0              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"
D8V9, binary
                cls
clus              0  1
  MUC2 MUTATED    4  3
  MUC2 WILD-TYPE 11 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      4    3
  MUC2 WILD-TYPE   11   17
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            4             11
  CLUS_2            3             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MUC2 MUTATED        2      1      1      2      0      1      0
  MUC2 WILD-TYPE      4      2      2      7      5      4      4
D8V10, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            1              2
  CLUS_3            1              2
  CLUS_4            2              7
  CLUS_5            0              5
  CLUS_6            1              4
  CLUS_7            0              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"

Clustering(9) Variable = IDH1 MUTATION ANALYSIS
D9V1, binary
                cls
clus              0  1
  IDH1 MUTATED    2  2
  IDH1 WILD-TYPE 17 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      2    2
  IDH1 WILD-TYPE   17   14
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            2             17
  CLUS_2            2             14
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      4      0
  IDH1 WILD-TYPE     13      5     13
D9V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            4              5
  CLUS_3            0             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
  IDH1 MUTATED        1      1      2
  IDH1 WILD-TYPE      9      7      9
D9V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1              9
  CLUS_2            1              7
  CLUS_3            2              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
  IDH1 MUTATED        1      1      0      2
  IDH1 WILD-TYPE      5      6      8      6
D9V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            1              6
  CLUS_3            0              8
  CLUS_4            2              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
  IDH1 MUTATED        0      1      3
  IDH1 WILD-TYPE     12     13      6
D9V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             12
  CLUS_2            1             13
  CLUS_3            3              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 CLUS_7
  IDH1 MUTATED        0      0      0      3      0      1      0
  IDH1 WILD-TYPE      4      5      5      6      5      4      2
D9V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              5
  CLUS_3            0              5
  CLUS_4            3              6
  CLUS_5            0              5
  CLUS_6            1              4
  CLUS_7            0              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
  IDH1 MUTATED        0      3      0      1
  IDH1 WILD-TYPE      9      2     10     10
D9V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            3              2
  CLUS_3            0             10
  CLUS_4            1             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
  IDH1 MUTATED        0      0      0      2      1      1
  IDH1 WILD-TYPE      8     10      4      2      4      3
D9V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0             10
  CLUS_3            0              4
  CLUS_4            2              2
  CLUS_5            1              4
  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"
D9V9, binary
                cls
clus              0  1
  IDH1 MUTATED    2  2
  IDH1 WILD-TYPE 13 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      2    2
  IDH1 WILD-TYPE   13   18
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            2             18
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  IDH1 MUTATED        0      0      0      2      0      2      0
  IDH1 WILD-TYPE      6      3      3      7      5      3      4
D9V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            0              3
  CLUS_3            0              3
  CLUS_4            2              7
  CLUS_5            0              5
  CLUS_6            2              3
  CLUS_7            0              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"

Clustering(10) Variable = MUC21 MUTATION ANALYSIS
D10V1, binary
                 cls
clus               0  1
  MUC21 MUTATED    2  1
  MUC21 WILD-TYPE 17 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      2    1
  MUC21 WILD-TYPE   17   15
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC21 MUTATED        2      0      1
  MUC21 WILD-TYPE     11      9     12
D10V2, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               9
  CLUS_3             1              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
  MUC21 MUTATED        1      0      1
  MUC21 WILD-TYPE      9      8     10
D10V3, multiclass
[1] "Remove cluster labels:" "MUC21 MUTATED"         
clus
  MUC21 MUTATED MUC21 WILD-TYPE 
              2              27 
     TCGA-3X-AAVA      TCGA-3X-AAVC      TCGA-W5-AA2G      TCGA-W5-AA2H 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA2I      TCGA-W5-AA2O      TCGA-W5-AA2Q      TCGA-W5-AA2R 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA2U      TCGA-W5-AA2W      TCGA-W5-AA2X      TCGA-W5-AA2Z 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA30      TCGA-W5-AA31      TCGA-W5-AA33      TCGA-W5-AA34 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA38      TCGA-W5-AA39      TCGA-W6-AA0S      TCGA-WD-A7RX 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-YR-A95A      TCGA-ZD-A8I3      TCGA-ZH-A8Y1      TCGA-ZH-A8Y2 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-ZH-A8Y5      TCGA-ZH-A8Y6      TCGA-ZH-A8Y8 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC21 MUTATED        1      0      1      0
  MUC21 WILD-TYPE      5      7      7      8
D10V4, multiclass
[1] "Remove cluster labels:" "MUC21 MUTATED"         
clus
  MUC21 MUTATED MUC21 WILD-TYPE 
              2              27 
     TCGA-3X-AAVA      TCGA-3X-AAVC      TCGA-W5-AA2G      TCGA-W5-AA2H 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA2I      TCGA-W5-AA2O      TCGA-W5-AA2Q      TCGA-W5-AA2R 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA2U      TCGA-W5-AA2W      TCGA-W5-AA2X      TCGA-W5-AA2Z 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA30      TCGA-W5-AA31      TCGA-W5-AA33      TCGA-W5-AA34 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-W5-AA38      TCGA-W5-AA39      TCGA-W6-AA0S      TCGA-WD-A7RX 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-YR-A95A      TCGA-ZD-A8I3      TCGA-ZH-A8Y1      TCGA-ZH-A8Y2 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
     TCGA-ZH-A8Y5      TCGA-ZH-A8Y6      TCGA-ZH-A8Y8 
"MUC21 WILD-TYPE" "MUC21 WILD-TYPE" "MUC21 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC21 MUTATED        2      1      0
  MUC21 WILD-TYPE     10     13      9
D10V5, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1              13
  CLUS_3             0               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 CLUS_7
  MUC21 MUTATED        2      0      1      0      0      0      0
  MUC21 WILD-TYPE      2      5      4      9      5      5      2
D10V6, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             0               9
  CLUS_5             0               5
  CLUS_6             0               5
  CLUS_7             0               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
  MUC21 MUTATED        1      0      1      1
  MUC21 WILD-TYPE      8      5      9     10
D10V7, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0               5
  CLUS_3             1               9
  CLUS_4             1              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
  MUC21 MUTATED        2      1      0      0      0      0
  MUC21 WILD-TYPE      6      9      4      4      5      4
D10V8, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2               6
  CLUS_2             1               9
  CLUS_3             0               4
  CLUS_4             0               4
  CLUS_5             0               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"
D10V9, binary
                 cls
clus               0  1
  MUC21 MUTATED    2  1
  MUC21 WILD-TYPE 13 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      2    1
  MUC21 WILD-TYPE   13   19
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             1              19
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MUC21 MUTATED        1      0      0      1      1      0      0
  MUC21 WILD-TYPE      5      3      3      8      4      5      4
D10V10, multiclass
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             1               8
  CLUS_5             1               4
  CLUS_6             0               5
  CLUS_7             0               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"

Clustering(11) Variable = CLIP4 MUTATION ANALYSIS
D11V1, binary
                 cls
clus               0  1
  CLIP4 MUTATED    2  2
  CLIP4 WILD-TYPE 17 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      2    2
  CLIP4 WILD-TYPE   17   14
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CLIP4 MUTATED        2      0      2
  CLIP4 WILD-TYPE     11      9     11
D11V2, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             0               9
  CLUS_3             2              11
[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
  CLIP4 MUTATED        1      2      1
  CLIP4 WILD-TYPE      9      6     10
D11V3, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             1               9
  CLUS_2             2               6
  CLUS_3             1              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
  CLIP4 MUTATED        0      1      1      2
  CLIP4 WILD-TYPE      6      6      7      6
D11V4, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               6
  CLUS_3             1               7
  CLUS_4             2               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
  CLIP4 MUTATED        1      1      2
  CLIP4 WILD-TYPE     11     13      7
D11V5, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             1              11
  CLUS_2             1              13
  CLUS_3             2               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 CLUS_6 CLUS_7
  CLIP4 MUTATED        0      0      1      2      0      1      0
  CLIP4 WILD-TYPE      4      5      4      7      5      4      2
D11V6, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             2               7
  CLUS_5             0               5
  CLUS_6             1               4
  CLUS_7             0               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
  CLIP4 MUTATED        1      0      2      1
  CLIP4 WILD-TYPE      8      5      8     10
D11V7, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0               5
  CLUS_3             2               8
  CLUS_4             1              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
  CLIP4 MUTATED        0      2      0      0      0      2
  CLIP4 WILD-TYPE      8      8      4      4      5      2
D11V8, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             2               8
  CLUS_3             0               4
  CLUS_4             0               4
  CLUS_5             0               5
  CLUS_6             2               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"
D11V9, binary
                 cls
clus               0  1
  CLIP4 MUTATED    2  2
  CLIP4 WILD-TYPE 13 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      2    2
  CLIP4 WILD-TYPE   13   18
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2              18
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CLIP4 MUTATED        0      0      0      1      1      1      1
  CLIP4 WILD-TYPE      6      3      3      8      4      4      3
D11V10, multiclass
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             1               8
  CLUS_5             1               4
  CLUS_6             1               4
  CLUS_7             1               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"

Clustering(12) Variable = BAP1 MUTATION ANALYSIS
D12V1, binary
                cls
clus              0  1
  BAP1 MUTATED    3  3
  BAP1 WILD-TYPE 16 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3    3
  BAP1 WILD-TYPE   16   13
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            3             16
  CLUS_2            3             13
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        2      0      4
  BAP1 WILD-TYPE     11      9      9
D12V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            2             11
  CLUS_2            0              9
  CLUS_3            4              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
  BAP1 MUTATED        1      0      2
  BAP1 WILD-TYPE      9      8      9
D12V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1              9
  CLUS_2            0              8
  CLUS_3            2              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
  BAP1 MUTATED        0      0      1      2
  BAP1 WILD-TYPE      6      7      7      6
D12V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            0              7
  CLUS_3            1              7
  CLUS_4            2              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
  BAP1 MUTATED        1      3      2
  BAP1 WILD-TYPE     11     11      7
D12V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             11
  CLUS_2            3             11
  CLUS_3            2              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 CLUS_6 CLUS_7
  BAP1 MUTATED        0      1      2      2      0      0      1
  BAP1 WILD-TYPE      4      4      3      7      5      5      1
D12V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            1              4
  CLUS_3            2              3
  CLUS_4            2              7
  CLUS_5            0              5
  CLUS_6            0              5
  CLUS_7            1              1
[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        1      0      2      3
  BAP1 WILD-TYPE      8      5      8      8
D12V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0              5
  CLUS_3            2              8
  CLUS_4            3              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
  BAP1 MUTATED        1      2      2      0      0      1
  BAP1 WILD-TYPE      7      8      2      4      5      3
D12V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2              8
  CLUS_3            2              2
  CLUS_4            0              4
  CLUS_5            0              5
  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"
D12V9, binary
                cls
clus              0  1
  BAP1 MUTATED    3  3
  BAP1 WILD-TYPE 12 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3    3
  BAP1 WILD-TYPE   12   17
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            3             12
  CLUS_2            3             17
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BAP1 MUTATED        0      1      1      3      1      0      0
  BAP1 WILD-TYPE      6      2      2      6      4      5      4
D12V10, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            1              2
  CLUS_3            1              2
  CLUS_4            3              6
  CLUS_5            1              4
  CLUS_6            0              5
  CLUS_7            0              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"

Clustering(13) Variable = CDC27 MUTATION ANALYSIS
D13V1, binary
                 cls
clus               0  1
  CDC27 MUTATED    4  1
  CDC27 WILD-TYPE 15 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      4    1
  CDC27 WILD-TYPE   15   15
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              15
  CLUS_2             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDC27 MUTATED        2      2      1
  CDC27 WILD-TYPE     11      7     12
D13V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              11
  CLUS_2             2               7
  CLUS_3             1              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
  CDC27 MUTATED        3      0      2
  CDC27 WILD-TYPE      7      8      9
D13V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3               7
  CLUS_2             0               8
  CLUS_3             2               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
  CDC27 MUTATED        2      0      0      3
  CDC27 WILD-TYPE      4      7      8      5
D13V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             0               7
  CLUS_3             0               8
  CLUS_4             3               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
  CDC27 MUTATED        1      2      2
  CDC27 WILD-TYPE     11     12      7
D13V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              11
  CLUS_2             2              12
  CLUS_3             2               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 CLUS_6 CLUS_7
  CDC27 MUTATED        1      0      0      2      0      1      1
  CDC27 WILD-TYPE      3      5      5      7      5      4      1
D13V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             2               7
  CLUS_5             0               5
  CLUS_6             1               4
  CLUS_7             1               1
[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
  CDC27 MUTATED        1      1      0      3
  CDC27 WILD-TYPE      8      4     10      8
D13V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1               4
  CLUS_3             0              10
  CLUS_4             3               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
  CDC27 MUTATED        1      0      1      0      1      2
  CDC27 WILD-TYPE      7     10      3      4      4      2
D13V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             0              10
  CLUS_3             1               3
  CLUS_4             0               4
  CLUS_5             1               4
  CLUS_6             2               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"
D13V9, binary
                 cls
clus               0  1
  CDC27 MUTATED    5  0
  CDC27 WILD-TYPE 10 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      5    0
  CDC27 WILD-TYPE   10   20
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             5              10
  CLUS_2             0              20
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CDC27 MUTATED        1      0      0      4      0      0      0
  CDC27 WILD-TYPE      5      3      3      5      5      5      4
D13V10, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             0               3
  CLUS_3             0               3
  CLUS_4             4               5
  CLUS_5             0               5
  CLUS_6             0               5
  CLUS_7             0               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"

Clustering(14) Variable = FAM35A MUTATION ANALYSIS
D14V1, binary
                  cls
clus                0  1
  FAM35A MUTATED    1  2
  FAM35A WILD-TYPE 18 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM35A MUTATED      1    2
  FAM35A WILD-TYPE   18   14
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              1               18
  CLUS_2              2               14
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM35A MUTATED        1      1      1
  FAM35A WILD-TYPE     12      8     12
D14V2, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1                8
  CLUS_3              1               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
  FAM35A MUTATED        1      0      1
  FAM35A WILD-TYPE      9      8     10
D14V3, multiclass
[1] "Remove cluster labels:" "FAM35A MUTATED"        
clus
  FAM35A MUTATED FAM35A WILD-TYPE 
               2               27 
      TCGA-3X-AAV9       TCGA-3X-AAVA       TCGA-3X-AAVC       TCGA-4G-AAZT 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2G       TCGA-W5-AA2H       TCGA-W5-AA2I       TCGA-W5-AA2O 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2Q       TCGA-W5-AA2R       TCGA-W5-AA2U       TCGA-W5-AA2W 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2Z       TCGA-W5-AA30       TCGA-W5-AA31       TCGA-W5-AA33 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA34       TCGA-W5-AA38       TCGA-W5-AA39       TCGA-W6-AA0S 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-WD-A7RX       TCGA-YR-A95A       TCGA-ZD-A8I3       TCGA-ZH-A8Y1 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-ZH-A8Y5       TCGA-ZH-A8Y6       TCGA-ZH-A8Y8 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM35A MUTATED        1      0      1      0
  FAM35A WILD-TYPE      5      7      7      8
D14V4, multiclass
[1] "Remove cluster labels:" "FAM35A MUTATED"        
clus
  FAM35A MUTATED FAM35A WILD-TYPE 
               2               27 
      TCGA-3X-AAV9       TCGA-3X-AAVA       TCGA-3X-AAVC       TCGA-4G-AAZT 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2G       TCGA-W5-AA2H       TCGA-W5-AA2I       TCGA-W5-AA2O 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2Q       TCGA-W5-AA2R       TCGA-W5-AA2U       TCGA-W5-AA2W 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA2Z       TCGA-W5-AA30       TCGA-W5-AA31       TCGA-W5-AA33 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-W5-AA34       TCGA-W5-AA38       TCGA-W5-AA39       TCGA-W6-AA0S 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-WD-A7RX       TCGA-YR-A95A       TCGA-ZD-A8I3       TCGA-ZH-A8Y1 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
      TCGA-ZH-A8Y5       TCGA-ZH-A8Y6       TCGA-ZH-A8Y8 
"FAM35A WILD-TYPE" "FAM35A WILD-TYPE" "FAM35A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM35A MUTATED        1      1      1
  FAM35A WILD-TYPE     11     13      8
D14V5, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              1               11
  CLUS_2              1               13
  CLUS_3              1                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 CLUS_7
  FAM35A MUTATED        1      0      0      1      1      0      0
  FAM35A WILD-TYPE      3      5      5      8      4      5      2
D14V6, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              1                3
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              1                8
  CLUS_5              1                4
  CLUS_6              0                5
  CLUS_7              0                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
  FAM35A MUTATED        0      0      2      1
  FAM35A WILD-TYPE      9      5      8     10
D14V7, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              0                9
  CLUS_2              0                5
  CLUS_3              2                8
  CLUS_4              1               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
  FAM35A MUTATED        0      2      0      0      1      0
  FAM35A WILD-TYPE      8      8      4      4      4      4
D14V8, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              0                8
  CLUS_2              2                8
  CLUS_3              0                4
  CLUS_4              0                4
  CLUS_5              1                4
  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"
D14V9, binary
                  cls
clus                0  1
  FAM35A MUTATED    1  2
  FAM35A WILD-TYPE 14 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM35A MUTATED      1    2
  FAM35A WILD-TYPE   14   18
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              1               14
  CLUS_2              2               18
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FAM35A MUTATED        0      2      0      0      0      0      1
  FAM35A WILD-TYPE      6      1      3      9      5      5      3
D14V10, multiclass
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                1
  CLUS_3              0                3
  CLUS_4              0                9
  CLUS_5              0                5
  CLUS_6              0                5
  CLUS_7              1                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"

Clustering(15) Variable = PAXIP1 MUTATION ANALYSIS
D15V1, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    3  1
  PAXIP1 WILD-TYPE 16 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      3    1
  PAXIP1 WILD-TYPE   16   15
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              3               16
  CLUS_2              1               15
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PAXIP1 MUTATED        1      1      2
  PAXIP1 WILD-TYPE     12      8     11
D15V2, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1               12
  CLUS_2              1                8
  CLUS_3              2               11
[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
  PAXIP1 MUTATED        1      1      1
  PAXIP1 WILD-TYPE      9      7     10
D15V3, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1                9
  CLUS_2              1                7
  CLUS_3              1               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
  PAXIP1 MUTATED        1      1      0      1
  PAXIP1 WILD-TYPE      5      6      8      7
D15V4, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              1                6
  CLUS_3              0                8
  CLUS_4              1                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
  PAXIP1 MUTATED        1      1      2
  PAXIP1 WILD-TYPE     11     13      7
D15V5, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1               11
  CLUS_2              1               13
  CLUS_3              2                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 CLUS_6 CLUS_7
  PAXIP1 MUTATED        1      0      0      2      0      0      1
  PAXIP1 WILD-TYPE      3      5      5      7      5      5      1
D15V6, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              2                7
  CLUS_5              0                5
  CLUS_6              0                5
  CLUS_7              1                1
[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
  PAXIP1 MUTATED        0      1      2      1
  PAXIP1 WILD-TYPE      9      4      8     10
D15V7, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1                4
  CLUS_3              2                8
  CLUS_4              1               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
  PAXIP1 MUTATED        0      2      1      1      0      0
  PAXIP1 WILD-TYPE      8      8      3      3      5      4
D15V8, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              2                8
  CLUS_3              1                3
  CLUS_4              1                3
  CLUS_5              0                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"
D15V9, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    1  3
  PAXIP1 WILD-TYPE 14 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      1    3
  PAXIP1 WILD-TYPE   14   17
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              3               17
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PAXIP1 MUTATED        0      2      0      1      0      1      0
  PAXIP1 WILD-TYPE      6      1      3      8      5      4      4
D15V10, multiclass
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                1
  CLUS_3              0                3
  CLUS_4              1                8
  CLUS_5              0                5
  CLUS_6              1                4
  CLUS_7              0                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"
