[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTDLBC-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/DLBC-TP/10668122/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/10013677/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=28, common to both=28
[1] "Reduce the number of clustering variables from 80 to 24."
[1] 24 28
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                24 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                24 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                23 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6                22 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6                22 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                25 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                20 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                20 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                21 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                21 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 25 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 25 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 24 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 24 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 20 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 25 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 25 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 24 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 24 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 24 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 24 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 24 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 24 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 23 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 23 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 22 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 22 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                25 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                25 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                25 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                25 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                25 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                25 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                24 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                24 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 23 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 24 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 24 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 25 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 25 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                25 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                25 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"            "MRNASEQ_CNMF"               
[3] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[5] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[7] "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 7 rows and 28 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"            "MRNASEQ_CNMF"               
[3] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[5] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[7] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 0 survival variables, and 7 non-survival variables.
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   13   11
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
D1V2, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   13   11
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        1      2      1
  1Q GAIN WILD-TYPE     12      8      4
D1V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                 8
  CLUS_3               1                 4
[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"
D1V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  3
  1Q GAIN WILD-TYPE 13 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    3
  1Q GAIN WILD-TYPE   13   10
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  1Q GAIN MUTATED        0      0      1      0      2      0      1      0
  1Q GAIN WILD-TYPE      2      2      4      4      3      3      2      3
D1V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               1                 4
  CLUS_4               0                 4
  CLUS_5               2                 3
  CLUS_6               0                 3
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        1      0      3
  1Q GAIN WILD-TYPE      8      9      6
D1V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                 9
  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 CLUS_8
  1Q GAIN MUTATED        0      0      1      0      0      0      2      1
  1Q GAIN WILD-TYPE      4      3      3      2      3      2      2      2
                   vv
clus                CLUS_9
  1Q GAIN MUTATED        0
  1Q GAIN WILD-TYPE      2
D1V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 3
  CLUS_3               1                 3
  CLUS_4               0                 2
  CLUS_5               0                 3
  CLUS_6               0                 2
  CLUS_7               2                 2
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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 = 3P GAIN MUTATION ANALYSIS
D2V1, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  2
  3P GAIN WILD-TYPE 12 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    2
  3P GAIN WILD-TYPE   12   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               2                11
[1] 2 2
[1] FALSE
D2V2, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  2
  3P GAIN WILD-TYPE 12 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    2
  3P GAIN WILD-TYPE   12   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        3      2      0
  3P GAIN WILD-TYPE     10      8      5
D2V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               2                 8
  CLUS_3               0                 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"
D2V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  2
  3P GAIN WILD-TYPE 11 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    2
  3P GAIN WILD-TYPE   11   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  3P GAIN MUTATED        0      0      2      2      0      1      0      0
  3P GAIN WILD-TYPE      2      2      3      2      5      2      3      3
D2V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               2                 3
  CLUS_4               2                 2
  CLUS_5               0                 5
  CLUS_6               1                 2
  CLUS_7               0                 3
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        2      2      1
  3P GAIN WILD-TYPE      7      7      8
D2V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 7
  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 CLUS_8
  3P GAIN MUTATED        1      0      1      2      0      1      0      0
  3P GAIN WILD-TYPE      3      3      3      0      3      1      4      3
                   vv
clus                CLUS_9
  3P GAIN MUTATED        0
  3P GAIN WILD-TYPE      2
D2V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 3
  CLUS_3               1                 3
  CLUS_4               2                 0
  CLUS_5               0                 3
  CLUS_6               1                 1
  CLUS_7               0                 4
  CLUS_8               0                 3
  CLUS_9               0                 2
[1] 9 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 = 3Q GAIN MUTATION ANALYSIS
D3V1, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  3
  3Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    3
  3Q GAIN WILD-TYPE   12   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               3                10
[1] 2 2
[1] FALSE
D3V2, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  3
  3Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    3
  3Q GAIN WILD-TYPE   12   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               3                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        3      3      0
  3Q GAIN WILD-TYPE     10      7      5
D3V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               3                 7
  CLUS_3               0                 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"
D3V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  3
  3Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    3
  3Q GAIN WILD-TYPE   11   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               3                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  3Q GAIN MUTATED        0      0      2      2      0      1      1      0
  3Q GAIN WILD-TYPE      2      2      3      2      5      2      2      3
D3V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               2                 3
  CLUS_4               2                 2
  CLUS_5               0                 5
  CLUS_6               1                 2
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        2      2      2
  3Q GAIN WILD-TYPE      7      7      7
D3V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 7
  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 CLUS_8
  3Q GAIN MUTATED        1      0      1      2      0      1      0      1
  3Q GAIN WILD-TYPE      3      3      3      0      3      1      4      2
                   vv
clus                CLUS_9
  3Q GAIN MUTATED        0
  3Q GAIN WILD-TYPE      2
D3V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 3
  CLUS_3               1                 3
  CLUS_4               2                 0
  CLUS_5               0                 3
  CLUS_6               1                 1
  CLUS_7               0                 4
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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 = 6P GAIN MUTATION ANALYSIS
D4V1, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  1
  6P GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    1
  6P GAIN WILD-TYPE   13   12
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
D4V2, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  1
  6P GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    1
  6P GAIN WILD-TYPE   13   12
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        2      1      0
  6P GAIN WILD-TYPE     11      9      5
D4V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                 9
  CLUS_3               0                 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"
D4V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  2
  6P GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    2
  6P GAIN WILD-TYPE   13   11
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  6P GAIN MUTATED        0      0      0      1      0      1      1      0
  6P GAIN WILD-TYPE      2      2      5      3      5      2      2      3
D4V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               0                 5
  CLUS_4               1                 3
  CLUS_5               0                 5
  CLUS_6               1                 2
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        0      1      2
  6P GAIN WILD-TYPE      9      8      7
D4V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                 8
  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 CLUS_8
  6P GAIN MUTATED        0      0      0      1      0      1      0      1
  6P GAIN WILD-TYPE      4      3      4      1      3      1      4      2
                   vv
clus                CLUS_9
  6P GAIN MUTATED        0
  6P GAIN WILD-TYPE      2
D4V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 3
  CLUS_3               0                 4
  CLUS_4               1                 1
  CLUS_5               0                 3
  CLUS_6               1                 1
  CLUS_7               0                 4
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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 = 7P GAIN MUTATION ANALYSIS
D5V1, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  3
  7P GAIN WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    3
  7P GAIN WILD-TYPE   10   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                10
  CLUS_2               3                10
[1] 2 2
[1] FALSE
D5V2, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  4
  7P GAIN WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    4
  7P GAIN WILD-TYPE   11    9
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                11
  CLUS_2               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2      4      2
  7P GAIN WILD-TYPE     11      6      3
D5V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               4                 6
  CLUS_3               2                 3
[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"
D5V4, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  4
  7P GAIN WILD-TYPE 10  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    4
  7P GAIN WILD-TYPE   10    9
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  7P GAIN MUTATED        0      0      2      2      2      2      0      0
  7P GAIN WILD-TYPE      2      2      3      2      3      1      3      3
D5V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               2                 3
  CLUS_4               2                 2
  CLUS_5               2                 3
  CLUS_6               2                 1
  CLUS_7               0                 3
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        3      2      3
  7P GAIN WILD-TYPE      6      7      6
D5V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               2                 7
  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 CLUS_8
  7P GAIN MUTATED        0      0      2      2      0      2      2      0
  7P GAIN WILD-TYPE      4      3      2      0      3      0      2      3
                   vv
clus                CLUS_9
  7P GAIN MUTATED        0
  7P GAIN WILD-TYPE      2
D5V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 3
  CLUS_3               2                 2
  CLUS_4               2                 0
  CLUS_5               0                 3
  CLUS_6               2                 0
  CLUS_7               2                 2
  CLUS_8               0                 3
  CLUS_9               0                 2
[1] 9 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 = 7Q GAIN MUTATION ANALYSIS
D6V1, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  3
  7Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE   11   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                11
  CLUS_2               3                10
[1] 2 2
[1] FALSE
D6V2, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  4
  7Q GAIN WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    4
  7Q GAIN WILD-TYPE   12    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        1      4      2
  7Q GAIN WILD-TYPE     12      6      3
D6V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               4                 6
  CLUS_3               2                 3
[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"
D6V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  4
  7Q GAIN WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    4
  7Q GAIN WILD-TYPE   11    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  7Q GAIN MUTATED        0      0      1      2      2      2      0      0
  7Q GAIN WILD-TYPE      2      2      4      2      3      1      3      3
D6V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               1                 4
  CLUS_4               2                 2
  CLUS_5               2                 3
  CLUS_6               2                 1
  CLUS_7               0                 3
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        2      2      3
  7Q GAIN WILD-TYPE      7      7      6
D6V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 7
  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 CLUS_8
  7Q GAIN MUTATED        0      0      1      2      0      2      2      0
  7Q GAIN WILD-TYPE      4      3      3      0      3      0      2      3
                   vv
clus                CLUS_9
  7Q GAIN MUTATED        0
  7Q GAIN WILD-TYPE      2
D6V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 3
  CLUS_3               1                 3
  CLUS_4               2                 0
  CLUS_5               0                 3
  CLUS_6               2                 0
  CLUS_7               2                 2
  CLUS_8               0                 3
  CLUS_9               0                 2
[1] 9 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 = 10P GAIN MUTATION ANALYSIS
D7V1, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  1
  10P GAIN WILD-TYPE 13 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    1
  10P GAIN WILD-TYPE   13   12
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
D7V2, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   14   11
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        1      1      1
  10P GAIN WILD-TYPE     12      9      4
D7V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                1                  4
[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"
D7V4, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   13   11
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  10P GAIN MUTATED        0      0      0      1      1      1      0      0
  10P GAIN WILD-TYPE      2      2      5      3      4      2      3      3
D7V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                0                  5
  CLUS_4                1                  3
  CLUS_5                1                  4
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        1      1      1
  10P GAIN WILD-TYPE      8      8      8
D7V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  8
  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 CLUS_8
  10P GAIN MUTATED        0      0      0      1      1      1      0      0
  10P GAIN WILD-TYPE      4      3      4      1      2      1      4      3
                    vv
clus                 CLUS_9
  10P GAIN MUTATED        0
  10P GAIN WILD-TYPE      2
D7V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  3
  CLUS_3                0                  4
  CLUS_4                1                  1
  CLUS_5                1                  2
  CLUS_6                1                  1
  CLUS_7                0                  4
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 11P GAIN MUTATION ANALYSIS
D8V1, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  3
  11P GAIN WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   14   10
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
D8V2, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  1
  11P GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    1
  11P GAIN WILD-TYPE   12   12
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        2      0      2
  11P GAIN WILD-TYPE     11     10      3
D8V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                0                 10
  CLUS_3                2                  3
[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"
D8V4, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  0
  11P GAIN WILD-TYPE 10 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    0
  11P GAIN WILD-TYPE   10   13
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  11P GAIN MUTATED        0      1      2      0      1      0      0      0
  11P GAIN WILD-TYPE      2      1      3      4      4      3      3      3
D8V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                1                  1
  CLUS_3                2                  3
  CLUS_4                0                  4
  CLUS_5                1                  4
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        2      1      1
  11P GAIN WILD-TYPE      7      8      8
D8V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  8
  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 CLUS_8
  11P GAIN MUTATED        1      1      1      0      0      0      1      0
  11P GAIN WILD-TYPE      3      2      3      2      3      2      3      3
                    vv
clus                 CLUS_9
  11P GAIN MUTATED        0
  11P GAIN WILD-TYPE      2
D8V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  2
  CLUS_3                1                  3
  CLUS_4                0                  2
  CLUS_5                0                  3
  CLUS_6                0                  2
  CLUS_7                1                  3
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 11Q GAIN MUTATION ANALYSIS
D9V1, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  5
  11Q GAIN WILD-TYPE 12  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    5
  11Q GAIN WILD-TYPE   12    8
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                5                  8
[1] 2 2
[1] FALSE
D9V2, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  3
  11Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    3
  11Q GAIN WILD-TYPE   10   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 10
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        4      1      3
  11Q GAIN WILD-TYPE      9      9      2
D9V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                1                  9
  CLUS_3                3                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  2
  11Q GAIN WILD-TYPE  9 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    2
  11Q GAIN WILD-TYPE    9   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  11Q GAIN MUTATED        0      1      3      0      3      0      0      0
  11Q GAIN WILD-TYPE      2      1      2      4      2      3      3      3
D9V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                1                  1
  CLUS_3                3                  2
  CLUS_4                0                  4
  CLUS_5                3                  2
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        3      1      3
  11Q GAIN WILD-TYPE      6      8      6
D9V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                1                  8
  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 CLUS_8
  11Q GAIN MUTATED        1      1      2      0      1      0      2      0
  11Q GAIN WILD-TYPE      3      2      2      2      2      2      2      3
                    vv
clus                 CLUS_9
  11Q GAIN MUTATED        0
  11Q GAIN WILD-TYPE      2
D9V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  2
  CLUS_3                2                  2
  CLUS_4                0                  2
  CLUS_5                1                  2
  CLUS_6                0                  2
  CLUS_7                2                  2
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 12P GAIN MUTATION ANALYSIS
D10V1, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  2
  12P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    2
  12P GAIN WILD-TYPE   14   11
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
D10V2, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  2
  12P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    2
  12P GAIN WILD-TYPE   14   11
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        1      0      2
  12P GAIN WILD-TYPE     12     10      3
D10V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                 10
  CLUS_3                2                  3
[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"
D10V4, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  1
  12P GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    1
  12P GAIN WILD-TYPE   12   12
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  12P GAIN MUTATED        0      1      1      0      1      0      0      0
  12P GAIN WILD-TYPE      2      1      4      4      4      3      3      3
D10V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                1                  1
  CLUS_3                1                  4
  CLUS_4                0                  4
  CLUS_5                1                  4
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        1      1      1
  12P GAIN WILD-TYPE      8      8      8
D10V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  8
  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 CLUS_8
  12P GAIN MUTATED        0      1      1      0      1      0      0      0
  12P GAIN WILD-TYPE      4      2      3      2      2      2      4      3
                    vv
clus                 CLUS_9
  12P GAIN MUTATED        0
  12P GAIN WILD-TYPE      2
D10V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  2
  CLUS_3                1                  3
  CLUS_4                0                  2
  CLUS_5                1                  2
  CLUS_6                0                  2
  CLUS_7                0                  4
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 12Q GAIN MUTATION ANALYSIS
D11V1, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE   14   10
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
D11V2, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   13   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        2      0      2
  12Q GAIN WILD-TYPE     11     10      3
D11V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                0                 10
  CLUS_3                2                  3
[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"
D11V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  1
  12Q GAIN WILD-TYPE 11 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    1
  12Q GAIN WILD-TYPE   11   12
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  12Q GAIN MUTATED        0      1      2      0      1      0      0      0
  12Q GAIN WILD-TYPE      2      1      3      4      4      3      3      3
D11V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                1                  1
  CLUS_3                2                  3
  CLUS_4                0                  4
  CLUS_5                1                  4
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        2      1      1
  12Q GAIN WILD-TYPE      7      8      8
D11V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  8
  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 CLUS_8
  12Q GAIN MUTATED        1      1      1      0      1      0      0      0
  12Q GAIN WILD-TYPE      3      2      3      2      2      2      4      3
                    vv
clus                 CLUS_9
  12Q GAIN MUTATED        0
  12Q GAIN WILD-TYPE      2
D11V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  2
  CLUS_3                1                  3
  CLUS_4                0                  2
  CLUS_5                1                  2
  CLUS_6                0                  2
  CLUS_7                0                  4
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 16P GAIN MUTATION ANALYSIS
D12V1, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    1  3
  16P GAIN WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    3
  16P GAIN WILD-TYPE   14   10
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
D12V2, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  1
  16P GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    1
  16P GAIN WILD-TYPE   12   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        1      1      2
  16P GAIN WILD-TYPE     12      9      3
D12V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                2                  3
[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"
D12V4, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  1
  16P GAIN WILD-TYPE 11 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    1
  16P GAIN WILD-TYPE   11   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  16P GAIN MUTATED        0      0      2      0      1      1      0      0
  16P GAIN WILD-TYPE      2      2      3      4      4      2      3      3
D12V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                2                  3
  CLUS_4                0                  4
  CLUS_5                1                  4
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        3      0      1
  16P GAIN WILD-TYPE      6      9      8
D12V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                0                  9
  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 CLUS_8
  16P GAIN MUTATED        1      0      1      0      0      1      1      0
  16P GAIN WILD-TYPE      3      3      3      2      3      1      3      3
                    vv
clus                 CLUS_9
  16P GAIN MUTATED        0
  16P GAIN WILD-TYPE      2
D12V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  3
  CLUS_3                1                  3
  CLUS_4                0                  2
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                1                  3
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 16Q GAIN MUTATION ANALYSIS
D13V1, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    0  4
  16Q GAIN WILD-TYPE 15  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    4
  16Q GAIN WILD-TYPE   15    9
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                4                  9
[1] 2 2
[1] FALSE
D13V2, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  1
  16Q GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    1
  16Q GAIN WILD-TYPE   12   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        2      1      1
  16Q GAIN WILD-TYPE     11      9      4
D13V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                1                  9
  CLUS_3                1                  4
[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"
D13V4, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  2
  16Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    2
  16Q GAIN WILD-TYPE   12   11
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  16Q GAIN MUTATED        0      0      2      0      1      0      0      1
  16Q GAIN WILD-TYPE      2      2      3      4      4      3      3      2
D13V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                2                  3
  CLUS_4                0                  4
  CLUS_5                1                  4
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                1                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        2      1      1
  16Q GAIN WILD-TYPE      7      8      8
D13V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  8
  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 CLUS_8
  16Q GAIN MUTATED        1      0      1      0      1      0      1      0
  16Q GAIN WILD-TYPE      3      3      3      2      2      2      3      3
                    vv
clus                 CLUS_9
  16Q GAIN MUTATED        0
  16Q GAIN WILD-TYPE      2
D13V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  3
  CLUS_3                1                  3
  CLUS_4                0                  2
  CLUS_5                1                  2
  CLUS_6                0                  2
  CLUS_7                1                  3
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 18P GAIN MUTATION ANALYSIS
D14V1, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  2
  18P GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    2
  18P GAIN WILD-TYPE   12   11
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
D14V2, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  2
  18P GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    2
  18P GAIN WILD-TYPE   12   11
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        3      2      0
  18P GAIN WILD-TYPE     10      8      5
D14V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                2                  8
  CLUS_3                0                  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"
D14V4, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  2
  18P GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    2
  18P GAIN WILD-TYPE   11   11
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  18P GAIN MUTATED        0      0      1      2      1      1      0      0
  18P GAIN WILD-TYPE      2      2      4      2      4      2      3      3
D14V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                1                  4
  CLUS_4                2                  2
  CLUS_5                1                  4
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        1      2      2
  18P GAIN WILD-TYPE      8      7      7
D14V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                  7
  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 CLUS_8
  18P GAIN MUTATED        0      0      1      2      0      1      1      0
  18P GAIN WILD-TYPE      4      3      3      0      3      1      3      3
                    vv
clus                 CLUS_9
  18P GAIN MUTATED        0
  18P GAIN WILD-TYPE      2
D14V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  3
  CLUS_3                1                  3
  CLUS_4                2                  0
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                1                  3
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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 = 18Q GAIN MUTATION ANALYSIS
D15V1, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  2
  18Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    2
  18Q GAIN WILD-TYPE   12   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
D15V2, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  2
  18Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    2
  18Q GAIN WILD-TYPE   12   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        3      2      0
  18Q GAIN WILD-TYPE     10      8      5
D15V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                2                  8
  CLUS_3                0                  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"
D15V4, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  2
  18Q GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    2
  18Q GAIN WILD-TYPE   11   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  18Q GAIN MUTATED        0      0      1      2      1      1      0      0
  18Q GAIN WILD-TYPE      2      2      4      2      4      2      3      3
D15V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                1                  4
  CLUS_4                2                  2
  CLUS_5                1                  4
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        1      2      2
  18Q GAIN WILD-TYPE      8      7      7
D15V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                  7
  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 CLUS_8
  18Q GAIN MUTATED        0      0      1      2      0      1      1      0
  18Q GAIN WILD-TYPE      4      3      3      0      3      1      3      3
                    vv
clus                 CLUS_9
  18Q GAIN MUTATED        0
  18Q GAIN WILD-TYPE      2
D15V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  3
  CLUS_3                1                  3
  CLUS_4                2                  0
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                1                  3
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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(16) Variable = 21Q GAIN MUTATION ANALYSIS
D16V1, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  3
  21Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    3
  21Q GAIN WILD-TYPE   12   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
D16V2, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  3
  21Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    3
  21Q GAIN WILD-TYPE   12   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        4      2      0
  21Q GAIN WILD-TYPE      9      8      5
D16V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                2                  8
  CLUS_3                0                  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"
D16V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  4
  21Q GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    4
  21Q GAIN WILD-TYPE   13    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  21Q GAIN MUTATED        0      1      0      0      3      0      0      1
  21Q GAIN WILD-TYPE      2      1      5      4      2      3      3      2
D16V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                1                  1
  CLUS_3                0                  5
  CLUS_4                0                  4
  CLUS_5                3                  2
  CLUS_6                0                  3
  CLUS_7                0                  3
  CLUS_8                1                  2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        0      2      3
  21Q GAIN WILD-TYPE      9      7      6
D16V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                  7
  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 CLUS_8
  21Q GAIN MUTATED        0      1      0      0      2      0      2      0
  21Q GAIN WILD-TYPE      4      2      4      2      1      2      2      3
                    vv
clus                 CLUS_9
  21Q GAIN MUTATED        0
  21Q GAIN WILD-TYPE      2
D16V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  2
  CLUS_3                0                  4
  CLUS_4                0                  2
  CLUS_5                2                  1
  CLUS_6                0                  2
  CLUS_7                2                  2
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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(17) Variable = XQ GAIN MUTATION ANALYSIS
D17V1, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  3
  XQ GAIN WILD-TYPE 15 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    3
  XQ GAIN WILD-TYPE   15   10
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               3                10
[1] 2 2
[1] FALSE
D17V2, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  1
  XQ GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    1
  XQ GAIN WILD-TYPE   13   12
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        2      0      1
  XQ GAIN WILD-TYPE     11     10      4
D17V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               0                10
  CLUS_3               1                 4
[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"
D17V4, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  1
  XQ GAIN WILD-TYPE 12 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    1
  XQ GAIN WILD-TYPE   12   12
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  XQ GAIN MUTATED        0      0      2      0      1      0      0      0
  XQ GAIN WILD-TYPE      2      2      3      4      4      3      3      3
D17V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               2                 3
  CLUS_4               0                 4
  CLUS_5               1                 4
  CLUS_6               0                 3
  CLUS_7               0                 3
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        2      0      1
  XQ GAIN WILD-TYPE      7      9      8
D17V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                 9
  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 CLUS_8
  XQ GAIN MUTATED        1      0      1      0      1      0      0      0
  XQ GAIN WILD-TYPE      3      3      3      2      2      2      4      3
                   vv
clus                CLUS_9
  XQ GAIN MUTATED        0
  XQ GAIN WILD-TYPE      2
D17V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 3
  CLUS_3               1                 3
  CLUS_4               0                 2
  CLUS_5               1                 2
  CLUS_6               0                 2
  CLUS_7               0                 4
  CLUS_8               0                 3
  CLUS_9               0                 2
[1] 9 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(18) Variable = 1P LOSS MUTATION ANALYSIS
D18V1, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   13   12
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
D18V2, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   13   12
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        2      1      0
  1P LOSS WILD-TYPE     11      9      5
D18V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                 9
  CLUS_3               0                 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"
D18V4, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   13   11
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  1P LOSS MUTATED        0      0      1      1      0      0      1      0
  1P LOSS WILD-TYPE      2      2      4      3      5      3      2      3
D18V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               1                 4
  CLUS_4               1                 3
  CLUS_5               0                 5
  CLUS_6               0                 3
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      1      1
  1P LOSS WILD-TYPE      8      8      8
D18V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 8
  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 CLUS_8
  1P LOSS MUTATED        1      0      0      1      0      0      0      1
  1P LOSS WILD-TYPE      3      3      4      1      3      2      4      2
                   vv
clus                CLUS_9
  1P LOSS MUTATED        0
  1P LOSS WILD-TYPE      2
D18V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 3
  CLUS_3               0                 4
  CLUS_4               1                 1
  CLUS_5               0                 3
  CLUS_6               0                 2
  CLUS_7               0                 4
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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(19) Variable = 6Q LOSS MUTATION ANALYSIS
D19V1, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  2
  6Q LOSS WILD-TYPE 14 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    2
  6Q LOSS WILD-TYPE   14   11
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               2                11
[1] 2 2
[1] FALSE
D19V2, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2  1
  6Q LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    1
  6Q LOSS WILD-TYPE   13   12
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        2      0      1
  6Q LOSS WILD-TYPE     11     10      4
D19V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               0                10
  CLUS_3               1                 4
[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"
D19V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    3  0
  6Q LOSS WILD-TYPE 11 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3    0
  6Q LOSS WILD-TYPE   11   13
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               0                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  6Q LOSS MUTATED        0      1      1      0      0      0      1      0
  6Q LOSS WILD-TYPE      2      1      4      4      5      3      2      3
D19V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               1                 1
  CLUS_3               1                 4
  CLUS_4               0                 4
  CLUS_5               0                 5
  CLUS_6               0                 3
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        1      1      1
  6Q LOSS WILD-TYPE      8      8      8
D19V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 8
  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 CLUS_8
  6Q LOSS MUTATED        1      1      0      0      0      0      0      1
  6Q LOSS WILD-TYPE      3      2      4      2      3      2      4      2
                   vv
clus                CLUS_9
  6Q LOSS MUTATED        0
  6Q LOSS WILD-TYPE      2
D19V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 2
  CLUS_3               0                 4
  CLUS_4               0                 2
  CLUS_5               0                 3
  CLUS_6               0                 2
  CLUS_7               0                 4
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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(20) Variable = 8P LOSS MUTATION ANALYSIS
D20V1, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2  2
  8P LOSS WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    2
  8P LOSS WILD-TYPE   13   11
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
D20V2, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE 14 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE   14   10
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               3                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        1      3      0
  8P LOSS WILD-TYPE     12      7      5
D20V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                 7
  CLUS_3               0                 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"
D20V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE 13 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE   13   10
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  8P LOSS MUTATED        0      0      1      2      0      0      1      0
  8P LOSS WILD-TYPE      2      2      4      2      5      3      2      3
D20V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               1                 4
  CLUS_4               2                 2
  CLUS_5               0                 5
  CLUS_6               0                 3
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        1      2      1
  8P LOSS WILD-TYPE      8      7      8
D20V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 7
  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 CLUS_8
  8P LOSS MUTATED        1      0      0      2      0      0      0      1
  8P LOSS WILD-TYPE      3      3      4      0      3      2      4      2
                   vv
clus                CLUS_9
  8P LOSS MUTATED        0
  8P LOSS WILD-TYPE      2
D20V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 3
  CLUS_3               0                 4
  CLUS_4               2                 0
  CLUS_5               0                 3
  CLUS_6               0                 2
  CLUS_7               0                 4
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 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(21) Variable = 15Q LOSS MUTATION ANALYSIS
D21V1, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  1
  15Q LOSS WILD-TYPE 11 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    1
  15Q LOSS WILD-TYPE   11   12
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
D21V2, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  3
  15Q LOSS WILD-TYPE 13 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    3
  15Q LOSS WILD-TYPE   13   10
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        1      3      1
  15Q LOSS WILD-TYPE     12      7      4
D21V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                  7
  CLUS_3                1                  4
[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"
D21V4, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  3
  15Q LOSS WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    3
  15Q LOSS WILD-TYPE   12   10
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  15Q LOSS MUTATED        0      0      0      2      2      1      0      0
  15Q LOSS WILD-TYPE      2      2      5      2      3      2      3      3
D21V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                0                  5
  CLUS_4                2                  2
  CLUS_5                2                  3
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        1      2      2
  15Q LOSS WILD-TYPE      8      7      7
D21V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                  7
  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 CLUS_8
  15Q LOSS MUTATED        0      0      0      2      0      1      2      0
  15Q LOSS WILD-TYPE      4      3      4      0      3      1      2      3
                    vv
clus                 CLUS_9
  15Q LOSS MUTATED        0
  15Q LOSS WILD-TYPE      2
D21V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  3
  CLUS_3                0                  4
  CLUS_4                2                  0
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                2                  2
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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(22) Variable = 16Q LOSS MUTATION ANALYSIS
D22V1, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   13   11
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
D22V2, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   13   11
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        1      2      1
  16Q LOSS WILD-TYPE     12      8      4
D22V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                  8
  CLUS_3                1                  4
[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"
D22V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   12   11
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  16Q LOSS MUTATED        0      0      0      1      1      1      1      0
  16Q LOSS WILD-TYPE      2      2      5      3      4      2      2      3
D22V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                0                  5
  CLUS_4                1                  3
  CLUS_5                1                  4
  CLUS_6                1                  2
  CLUS_7                1                  2
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        1      1      2
  16Q LOSS WILD-TYPE      8      8      7
D22V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  8
  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 CLUS_8
  16Q LOSS MUTATED        0      0      0      1      0      1      1      1
  16Q LOSS WILD-TYPE      4      3      4      1      3      1      3      2
                    vv
clus                 CLUS_9
  16Q LOSS MUTATED        0
  16Q LOSS WILD-TYPE      2
D22V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  3
  CLUS_3                0                  4
  CLUS_4                1                  1
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                1                  3
  CLUS_8                1                  2
  CLUS_9                0                  2
[1] 9 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(23) Variable = 17P LOSS MUTATION ANALYSIS
D23V1, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  1
  17P LOSS WILD-TYPE 13 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    1
  17P LOSS WILD-TYPE   13   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
D23V2, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  1
  17P LOSS WILD-TYPE 13 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    1
  17P LOSS WILD-TYPE   13   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        1      1      1
  17P LOSS WILD-TYPE     12      9      4
D23V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                1                  4
[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"
D23V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  1
  17P LOSS WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    1
  17P LOSS WILD-TYPE   12   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  17P LOSS MUTATED        0      0      1      1      0      1      0      0
  17P LOSS WILD-TYPE      2      2      4      3      5      2      3      3
D23V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                  2
  CLUS_2                0                  2
  CLUS_3                1                  4
  CLUS_4                1                  3
  CLUS_5                0                  5
  CLUS_6                1                  2
  CLUS_7                0                  3
  CLUS_8                0                  3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        2      1      0
  17P LOSS WILD-TYPE      7      8      9
D23V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  8
  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 CLUS_8
  17P LOSS MUTATED        1      0      0      1      0      1      0      0
  17P LOSS WILD-TYPE      3      3      4      1      3      1      4      3
                    vv
clus                 CLUS_9
  17P LOSS MUTATED        0
  17P LOSS WILD-TYPE      2
D23V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  3
  CLUS_3                0                  4
  CLUS_4                1                  1
  CLUS_5                0                  3
  CLUS_6                1                  1
  CLUS_7                0                  4
  CLUS_8                0                  3
  CLUS_9                0                  2
[1] 9 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(24) Variable = XQ LOSS MUTATION ANALYSIS
D24V1, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  3
  XQ LOSS WILD-TYPE 15 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    3
  XQ LOSS WILD-TYPE   15   10
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                15
  CLUS_2               3                10
[1] 2 2
[1] FALSE
D24V2, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  2
  XQ LOSS WILD-TYPE 14 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE   14   11
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        1      2      0
  XQ LOSS WILD-TYPE     12      8      5
D24V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                 8
  CLUS_3               0                 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"
D24V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  2
  XQ LOSS WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE   13   11
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  XQ LOSS MUTATED        0      0      0      0      2      0      1      0
  XQ LOSS WILD-TYPE      2      2      5      4      3      3      2      3
D24V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 2
  CLUS_2               0                 2
  CLUS_3               0                 5
  CLUS_4               0                 4
  CLUS_5               2                 3
  CLUS_6               0                 3
  CLUS_7               1                 2
  CLUS_8               0                 3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        0      0      3
  XQ LOSS WILD-TYPE      9      9      6
D24V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                 9
  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 CLUS_8
  XQ LOSS MUTATED        0      0      0      0      0      0      2      1
  XQ LOSS WILD-TYPE      4      3      4      2      3      2      2      2
                   vv
clus                CLUS_9
  XQ LOSS MUTATED        0
  XQ LOSS WILD-TYPE      2
D24V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 3
  CLUS_3               0                 4
  CLUS_4               0                 2
  CLUS_5               0                 3
  CLUS_6               0                 2
  CLUS_7               2                 2
  CLUS_8               1                 2
  CLUS_9               0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
