[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/20125263/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/19780780/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] "Reduce the number of clustering variables from 82 to 52."
[1] 52 48
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                42 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                42 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                42 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                42 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                42 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                42 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                38 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                38 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                35 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                35 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                41 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                42 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                42 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                42 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                42 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                44 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                44 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                33 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                33 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                35 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                35 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                41 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                40 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                40 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                41 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                41 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                41 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                41 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 44 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 44 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 44 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 44 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 39 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 39 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 35 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 35 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 41 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 41 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 39 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 39 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 43 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 43 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 41 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 41 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 41 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 45 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 45 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 35 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 35 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 34 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 34 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 45 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 45 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 45 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 45 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 43 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 43 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 44 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 44 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 38 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                42 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                42 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                42 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                42 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                45 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                45 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                43 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                43 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                44 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                44 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                45 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                45 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                44 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                44 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                41 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                40 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                40 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                44 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                44 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 45 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 45 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 41 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 41 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 44 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 44 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 39 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 39 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 44 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 44 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 43 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 43 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 44 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 44 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 45 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 45 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                43 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                43 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                44 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                44 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 48 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 48 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, 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  4
  1Q GAIN WILD-TYPE 27 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    4
  1Q GAIN WILD-TYPE   27   15
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                27
  CLUS_2               4                15
[1] 2 2
[1] FALSE
D1V2, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  4
  1Q GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    4
  1Q GAIN WILD-TYPE   22   20
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    3  0
  1Q GAIN WILD-TYPE 15 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    0
  1Q GAIN WILD-TYPE   15   15
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        0      3      0
  1Q GAIN WILD-TYPE      6     12     12
D1V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               3                12
  CLUS_3               0                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, 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
D1V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        2      0      1      3
  1Q GAIN WILD-TYPE     12     11      9      9
D1V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                11
  CLUS_3               1                 9
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q GAIN MUTATED        1      0      1      2      2
  1Q GAIN WILD-TYPE      8     12      7     10      4
D1V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                12
  CLUS_3               1                 7
  CLUS_4               2                10
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  3
  1Q GAIN WILD-TYPE 17 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    3
  1Q GAIN WILD-TYPE   17   20
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                20
[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        1      0      0      1      1      1      1      0
  1Q GAIN WILD-TYPE      3      5      6      5      7      2      4      2
                   vv
clus                CLUS_9
  1Q GAIN MUTATED        0
  1Q GAIN WILD-TYPE      3
D1V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               0                 6
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               1                 2
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               0                 3
[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 = 2P GAIN MUTATION ANALYSIS
D2V1, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE 26 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE   26   16
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                26
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D2V2, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  4
  2P GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    4
  2P GAIN WILD-TYPE   22   20
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D2V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  2
  2P GAIN WILD-TYPE 15 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    2
  2P GAIN WILD-TYPE   15   13
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        1      3      1
  2P GAIN WILD-TYPE      5     12     11
D2V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1  1
  2P GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    1
  2P GAIN WILD-TYPE   14   12
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        1      0      1
  2P GAIN WILD-TYPE     12     10      4
D2V6, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A6HN        TCGA-FA-A6HO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED        2      1      1      2
  2P GAIN WILD-TYPE     12     10      9     10
D2V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P GAIN MUTATED        0      2      2      1      1
  2P GAIN WILD-TYPE      9     10      6     11      5
D2V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               2                 6
  CLUS_4               1                11
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  2
  2P GAIN WILD-TYPE 17 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    2
  2P GAIN WILD-TYPE   17   21
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               2                21
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  2P GAIN MUTATED        1      0      1      0      0      1      0      0
  2P GAIN WILD-TYPE      3      5      5      6      8      2      5      2
                   vv
clus                CLUS_9
  2P GAIN MUTATED        1
  2P GAIN WILD-TYPE      2
D2V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               0                 6
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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 = 2Q GAIN MUTATION ANALYSIS
D3V1, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  3
  2Q GAIN WILD-TYPE 26 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE   26   16
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                26
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D3V2, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  4
  2Q GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    4
  2Q GAIN WILD-TYPE   22   20
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D3V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  2
  2Q GAIN WILD-TYPE 15 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    2
  2Q GAIN WILD-TYPE   15   13
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        1      3      1
  2Q GAIN WILD-TYPE      5     12     11
D3V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    1  1
  2Q GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1    1
  2Q GAIN WILD-TYPE   14   12
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        1      0      1
  2Q GAIN WILD-TYPE     12     10      4
D3V6, multiclass
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A6HN        TCGA-FA-A6HO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED        2      1      1      2
  2Q GAIN WILD-TYPE     12     10      9     10
D3V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q GAIN MUTATED        0      2      2      1      1
  2Q GAIN WILD-TYPE      9     10      6     11      5
D3V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               2                 6
  CLUS_4               1                11
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  2
  2Q GAIN WILD-TYPE 17 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    2
  2Q GAIN WILD-TYPE   17   21
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               2                21
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  2Q GAIN MUTATED        1      0      1      0      0      1      0      0
  2Q GAIN WILD-TYPE      3      5      5      6      8      2      5      2
                   vv
clus                CLUS_9
  2Q GAIN MUTATED        1
  2Q GAIN WILD-TYPE      2
D3V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               0                 6
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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 = 3P GAIN MUTATION ANALYSIS
D4V1, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  7
  3P GAIN WILD-TYPE 26 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    7
  3P GAIN WILD-TYPE   26   12
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                26
  CLUS_2               7                12
[1] 2 2
[1] FALSE
D4V2, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    7  3
  3P GAIN WILD-TYPE 17 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7    3
  3P GAIN WILD-TYPE   17   21
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7                17
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D4V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  4
  3P GAIN WILD-TYPE 14 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    4
  3P GAIN WILD-TYPE   14   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               4                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        1      2      5
  3P GAIN WILD-TYPE      5     13      7
D4V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                13
  CLUS_3               5                 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"
D4V5, 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
D4V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        4      3      2      1
  3P GAIN WILD-TYPE     10      8      8     11
D4V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               3                 8
  CLUS_3               2                 8
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED        1      2      3      4      0
  3P GAIN WILD-TYPE      8     10      5      8      6
D4V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                10
  CLUS_3               3                 5
  CLUS_4               4                 8
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    5  4
  3P GAIN WILD-TYPE 14 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    4
  3P GAIN WILD-TYPE   14   19
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               4                19
[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        1      0      3      1      1      0      1      0
  3P GAIN WILD-TYPE      3      5      3      5      7      3      4      2
                   vv
clus                CLUS_9
  3P GAIN MUTATED        2
  3P GAIN WILD-TYPE      1
D4V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               3                 3
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               0                 3
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               2                 1
[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 = 3Q GAIN MUTATION ANALYSIS
D5V1, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  9
  3Q GAIN WILD-TYPE 25 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    9
  3Q GAIN WILD-TYPE   25   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                25
  CLUS_2               9                10
[1] 2 2
[1] FALSE
D5V2, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    9  4
  3Q GAIN WILD-TYPE 15 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      9    4
  3Q GAIN WILD-TYPE   15   20
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9                15
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D5V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  6
  3Q GAIN WILD-TYPE 14  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    6
  3Q GAIN WILD-TYPE   14    9
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               6                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        1      2      7
  3Q GAIN WILD-TYPE      5     13      5
D5V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                13
  CLUS_3               7                 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"
D5V5, 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
D5V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        4      4      3      2
  3Q GAIN WILD-TYPE     10      7      7     10
D5V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               4                 7
  CLUS_3               3                 7
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q GAIN MUTATED        1      3      3      5      1
  3Q GAIN WILD-TYPE      8      9      5      7      5
D5V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               3                 9
  CLUS_3               3                 5
  CLUS_4               5                 7
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5  7
  3Q GAIN WILD-TYPE 14 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    7
  3Q GAIN WILD-TYPE   14   16
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               7                16
[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        1      1      3      1      2      0      1      0
  3Q GAIN WILD-TYPE      3      4      3      5      6      3      4      2
                   vv
clus                CLUS_9
  3Q GAIN MUTATED        3
  3Q GAIN WILD-TYPE      0
D5V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 4
  CLUS_3               3                 3
  CLUS_4               1                 5
  CLUS_5               2                 6
  CLUS_6               0                 3
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               3                 0
[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 = 5P GAIN MUTATION ANALYSIS
D6V1, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5  2
  5P GAIN WILD-TYPE 24 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    2
  5P GAIN WILD-TYPE   24   17
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5                24
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D6V2, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    3  4
  5P GAIN WILD-TYPE 21 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    4
  5P GAIN WILD-TYPE   21   20
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                21
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D6V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  3
  5P GAIN WILD-TYPE 16 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    3
  5P GAIN WILD-TYPE   16   12
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        0      3      2
  5P GAIN WILD-TYPE      6     12     10
D6V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               3                12
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    1  1
  5P GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    1
  5P GAIN WILD-TYPE   14   12
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        2      0      0
  5P GAIN WILD-TYPE     11     10      5
D6V6, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        1      1      1      4
  5P GAIN WILD-TYPE     13     10      9      8
D6V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P GAIN MUTATED        0      3      1      2      1
  5P GAIN WILD-TYPE      9      9      7     10      5
D6V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               3                 9
  CLUS_3               1                 7
  CLUS_4               2                10
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    1  4
  5P GAIN WILD-TYPE 18 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    4
  5P GAIN WILD-TYPE   18   19
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               4                19
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  5P GAIN MUTATED        0      0      1      0      1      2      0      0
  5P GAIN WILD-TYPE      4      5      5      6      7      1      5      2
                   vv
clus                CLUS_9
  5P GAIN MUTATED        1
  5P GAIN WILD-TYPE      2
D6V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               0                 6
  CLUS_5               1                 7
  CLUS_6               2                 1
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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 = 5Q GAIN MUTATION ANALYSIS
D7V1, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  2
  5Q GAIN WILD-TYPE 25 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    2
  5Q GAIN WILD-TYPE   25   17
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4                25
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D7V2, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  3
  5Q GAIN WILD-TYPE 21 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    3
  5Q GAIN WILD-TYPE   21   21
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                21
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D7V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  3
  5Q GAIN WILD-TYPE 16 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    3
  5Q GAIN WILD-TYPE   16   12
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        0      3      2
  5Q GAIN WILD-TYPE      6     12     10
D7V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               3                12
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    0  1
  5Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    1
  5Q GAIN WILD-TYPE   15   12
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        1      0      0
  5Q GAIN WILD-TYPE     12     10      5
D7V6, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                27 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED        1      1      1      3
  5Q GAIN WILD-TYPE     13     10      9      9
D7V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED        0      2      1      2      1
  5Q GAIN WILD-TYPE      9     10      7     10      5
D7V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               1                 7
  CLUS_4               2                10
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    1  3
  5Q GAIN WILD-TYPE 18 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    3
  5Q GAIN WILD-TYPE   18   20
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                20
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  5Q GAIN MUTATED        0      0      1      0      1      1      0      0
  5Q GAIN WILD-TYPE      4      5      5      6      7      2      5      2
                   vv
clus                CLUS_9
  5Q GAIN MUTATED        1
  5Q GAIN WILD-TYPE      2
D7V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               0                 6
  CLUS_5               1                 7
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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 = 6P GAIN MUTATION ANALYSIS
D8V1, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  4
  6P GAIN WILD-TYPE 27 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    4
  6P GAIN WILD-TYPE   27   15
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                27
  CLUS_2               4                15
[1] 2 2
[1] FALSE
D8V2, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    3  3
  6P GAIN WILD-TYPE 21 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    3
  6P GAIN WILD-TYPE   21   21
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                21
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D8V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4  1
  6P GAIN WILD-TYPE 14 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    1
  6P GAIN WILD-TYPE   14   14
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        1      3      1
  6P GAIN WILD-TYPE      5     12     11
D8V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, 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
D8V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        2      1      1      2
  6P GAIN WILD-TYPE     12     10      9     10
D8V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P GAIN MUTATED        2      1      1      2      0
  6P GAIN WILD-TYPE      7     11      7     10      6
D8V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               2                10
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    3  2
  6P GAIN WILD-TYPE 16 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    2
  6P GAIN WILD-TYPE   16   21
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               2                21
[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        1      0      1      1      1      1      0      0
  6P GAIN WILD-TYPE      3      5      5      5      7      2      5      2
                   vv
clus                CLUS_9
  6P GAIN MUTATED        0
  6P GAIN WILD-TYPE      3
D8V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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 = 6Q GAIN MUTATION ANALYSIS
D9V1, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0  4
  6Q GAIN WILD-TYPE 29 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    4
  6Q GAIN WILD-TYPE   29   15
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                29
  CLUS_2               4                15
[1] 2 2
[1] FALSE
D9V2, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  3
  6Q GAIN WILD-TYPE 23 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    3
  6Q GAIN WILD-TYPE   23   21
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                23
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D9V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  1
  6Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    1
  6Q GAIN WILD-TYPE   16   14
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED        1      1      1
  6Q GAIN WILD-TYPE      5     14     11
D9V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               1                14
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  1
  6Q GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    1
  6Q GAIN WILD-TYPE   14   12
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED        1      1      0
  6Q GAIN WILD-TYPE     12      9      5
D9V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED        2      1      1      0
  6Q GAIN WILD-TYPE     12     10      9     12
D9V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6Q GAIN MUTATED        1      1      1      1      0
  6Q GAIN WILD-TYPE      8     11      7     11      6
D9V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               1                11
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3  0
  6Q GAIN WILD-TYPE 16 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    0
  6Q GAIN WILD-TYPE   16   23
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               0                23
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  6Q GAIN MUTATED        1      0      0      1      1      0      0      0
  6Q GAIN WILD-TYPE      3      5      6      5      7      3      5      2
                   vv
clus                CLUS_9
  6Q GAIN MUTATED        0
  6Q GAIN WILD-TYPE      3
D9V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               0                 6
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               0                 3
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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 = 7P GAIN MUTATION ANALYSIS
D10V1, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    2 13
  7P GAIN WILD-TYPE 27  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   13
  7P GAIN WILD-TYPE   27    6
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                27
  CLUS_2              13                 6
[1] 2 2
[1] FALSE
D10V2, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9  6
  7P GAIN WILD-TYPE 15 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    6
  7P GAIN WILD-TYPE   15   18
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               9                15
  CLUS_2               6                18
[1] 2 2
[1] FALSE
D10V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  3
  7P GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    3
  7P GAIN WILD-TYPE   13   12
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        1      3      4
  7P GAIN WILD-TYPE      5     12      8
D10V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               4                 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"
D10V5, 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
D10V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        4      3      4      4
  7P GAIN WILD-TYPE     10      8      6      8
D10V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               3                 8
  CLUS_3               4                 6
  CLUS_4               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P GAIN MUTATED        2      3      3      5      2
  7P GAIN WILD-TYPE      7      9      5      7      4
D10V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                 9
  CLUS_3               3                 5
  CLUS_4               5                 7
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6  7
  7P GAIN WILD-TYPE 13 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6    7
  7P GAIN WILD-TYPE   13   16
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                13
  CLUS_2               7                16
[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        1      0      2      2      2      0      3      0
  7P GAIN WILD-TYPE      3      5      4      4      6      3      2      2
                   vv
clus                CLUS_9
  7P GAIN MUTATED        3
  7P GAIN WILD-TYPE      0
D10V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               2                 4
  CLUS_4               2                 4
  CLUS_5               2                 6
  CLUS_6               0                 3
  CLUS_7               3                 2
  CLUS_8               0                 2
  CLUS_9               3                 0
[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 = 7Q GAIN MUTATION ANALYSIS
D11V1, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    1 12
  7Q GAIN WILD-TYPE 28  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   12
  7Q GAIN WILD-TYPE   28    7
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                28
  CLUS_2              12                 7
[1] 2 2
[1] FALSE
D11V2, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  6
  7Q GAIN WILD-TYPE 17 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    6
  7Q GAIN WILD-TYPE   17   18
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                17
  CLUS_2               6                18
[1] 2 2
[1] FALSE
D11V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  3
  7Q GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE   14   12
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        1      3      3
  7Q GAIN WILD-TYPE      5     12      9
D11V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               3                 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"
D11V5, 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
D11V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        3      2      4      4
  7Q GAIN WILD-TYPE     11      9      6      8
D11V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               2                 9
  CLUS_3               4                 6
  CLUS_4               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q GAIN MUTATED        2      3      2      4      2
  7Q GAIN WILD-TYPE      7      9      6      8      4
D11V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                 9
  CLUS_3               2                 6
  CLUS_4               4                 8
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5  6
  7Q GAIN WILD-TYPE 14 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    6
  7Q GAIN WILD-TYPE   14   17
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               6                17
[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        1      0      1      2      2      0      3      0
  7Q GAIN WILD-TYPE      3      5      5      4      6      3      2      2
                   vv
clus                CLUS_9
  7Q GAIN MUTATED        2
  7Q GAIN WILD-TYPE      1
D11V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               2                 4
  CLUS_5               2                 6
  CLUS_6               0                 3
  CLUS_7               3                 2
  CLUS_8               0                 2
  CLUS_9               2                 1
[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 = 8P GAIN MUTATION ANALYSIS
D12V1, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 24 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   24   17
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                24
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D12V2, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 19 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   19   22
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                19
  CLUS_2               2                22
[1] 2 2
[1] FALSE
D12V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  2
  8P GAIN WILD-TYPE 16 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    2
  8P GAIN WILD-TYPE   16   13
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        1      2      1
  8P GAIN WILD-TYPE      5     13     11
D12V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                13
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    0  2
  8P GAIN WILD-TYPE 15 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    2
  8P GAIN WILD-TYPE   15   11
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        1      1      0
  8P GAIN WILD-TYPE     12      9      5
D12V6, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        0      1      3      3
  8P GAIN WILD-TYPE     14     10      7      9
D12V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                10
  CLUS_3               3                 7
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P GAIN MUTATED        0      0      0      5      2
  8P GAIN WILD-TYPE      9     12      8      7      4
D12V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                12
  CLUS_3               0                 8
  CLUS_4               5                 7
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  5
  8P GAIN WILD-TYPE 17 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    5
  8P GAIN WILD-TYPE   17   18
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               5                18
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  8P GAIN MUTATED        0      0      2      1      1      1      0      0
  8P GAIN WILD-TYPE      4      5      4      5      7      2      5      2
                   vv
clus                CLUS_9
  8P GAIN MUTATED        2
  8P GAIN WILD-TYPE      1
D12V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               2                 4
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               2                 1
[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 = 8Q GAIN MUTATION ANALYSIS
D13V1, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE 23 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE   23   17
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                23
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D13V2, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE 18 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE   18   22
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                18
  CLUS_2               2                22
[1] 2 2
[1] FALSE
D13V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2  3
  8Q GAIN WILD-TYPE 16 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    3
  8Q GAIN WILD-TYPE   16   12
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        1      3      1
  8Q GAIN WILD-TYPE      5     12     11
D13V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               3                12
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    0  2
  8Q GAIN WILD-TYPE 15 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    2
  8Q GAIN WILD-TYPE   15   11
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        1      1      0
  8Q GAIN WILD-TYPE     12      9      5
D13V6, multiclass
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        0      2      3      3
  8Q GAIN WILD-TYPE     14      9      7      9
D13V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                 9
  CLUS_3               3                 7
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED        0      1      0      5      2
  8Q GAIN WILD-TYPE      9     11      8      7      4
D13V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                11
  CLUS_3               0                 8
  CLUS_4               5                 7
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2  5
  8Q GAIN WILD-TYPE 17 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    5
  8Q GAIN WILD-TYPE   17   18
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               5                18
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  8Q GAIN MUTATED        0      0      2      1      1      1      0      0
  8Q GAIN WILD-TYPE      4      5      4      5      7      2      5      2
                   vv
clus                CLUS_9
  8Q GAIN MUTATED        2
  8Q GAIN WILD-TYPE      1
D13V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               2                 4
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               2                 1
[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 = 9P GAIN MUTATION ANALYSIS
D14V1, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  2
  9P GAIN WILD-TYPE 24 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    2
  9P GAIN WILD-TYPE   24   17
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               5                24
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D14V2, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  3
  9P GAIN WILD-TYPE 20 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    3
  9P GAIN WILD-TYPE   20   21
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                20
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D14V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  3
  9P GAIN WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    3
  9P GAIN WILD-TYPE   15   12
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        0      4      2
  9P GAIN WILD-TYPE      6     11     10
D14V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               4                11
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    1  1
  9P GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    1
  9P GAIN WILD-TYPE   14   12
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      0      1
  9P GAIN WILD-TYPE     12     10      4
D14V6, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A6HN        TCGA-FA-A6HO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        1      2      2      2
  9P GAIN WILD-TYPE     13      9      8     10
D14V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 9
  CLUS_3               2                 8
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        0      2      1      3      1
  9P GAIN WILD-TYPE      9     10      7      9      5
D14V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               1                 7
  CLUS_4               3                 9
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  3
  9P GAIN WILD-TYPE 17 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    3
  9P GAIN WILD-TYPE   17   20
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                20
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  9P GAIN MUTATED        0      1      2      1      0      1      0      0
  9P GAIN WILD-TYPE      4      4      4      5      8      2      5      2
                   vv
clus                CLUS_9
  9P GAIN MUTATED        0
  9P GAIN WILD-TYPE      3
D14V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               2                 4
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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 = 9Q GAIN MUTATION ANALYSIS
D15V1, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    5  2
  9Q GAIN WILD-TYPE 24 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    2
  9Q GAIN WILD-TYPE   24   17
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5                24
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D15V2, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  3
  9Q GAIN WILD-TYPE 20 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    3
  9Q GAIN WILD-TYPE   20   21
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                20
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D15V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  3
  9Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    3
  9Q GAIN WILD-TYPE   15   12
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        0      4      2
  9Q GAIN WILD-TYPE      6     11     10
D15V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               4                11
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  1
  9Q GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    1
  9Q GAIN WILD-TYPE   14   12
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      0      1
  9Q GAIN WILD-TYPE     12     10      4
D15V6, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A6HN        TCGA-FA-A6HO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        1      1      3      2
  9Q GAIN WILD-TYPE     13     10      7     10
D15V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               3                 7
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        0      1      1      4      1
  9Q GAIN WILD-TYPE      9     11      7      8      5
D15V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               4                 8
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  3
  9Q GAIN WILD-TYPE 17 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    3
  9Q GAIN WILD-TYPE   17   20
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                20
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  9Q GAIN MUTATED        0      0      2      1      0      1      0      0
  9Q GAIN WILD-TYPE      4      5      4      5      8      2      5      2
                   vv
clus                CLUS_9
  9Q GAIN MUTATED        1
  9Q GAIN WILD-TYPE      2
D15V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               2                 4
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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 = 10P GAIN MUTATION ANALYSIS
D16V1, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    0  4
  10P GAIN WILD-TYPE 29 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    4
  10P GAIN WILD-TYPE   29   15
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 29
  CLUS_2                4                 15
[1] 2 2
[1] FALSE
D16V2, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  2
  10P GAIN WILD-TYPE 22 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    2
  10P GAIN WILD-TYPE   22   22
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D16V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  1
  10P GAIN WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    1
  10P GAIN WILD-TYPE   17   14
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        1      0      1
  10P GAIN WILD-TYPE      5     15     11
D16V4, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 31 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FA-A86F         TCGA-FF-8041         TCGA-FF-8042 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GS-A9TT         TCGA-GS-A9TV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-VB-A8QN 
"10P GAIN WILD-TYPE" 
D16V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  1
  10P GAIN WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    1
  10P GAIN WILD-TYPE   14   12
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        0      1      1
  10P GAIN WILD-TYPE     13      9      4
D16V6, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 26 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED        1      1      1      1
  10P GAIN WILD-TYPE     13     10      9     11
D16V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                1                  9
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P GAIN MUTATED        1      1      1      1      0
  10P GAIN WILD-TYPE      8     11      7     11      6
D16V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  1
  10P GAIN WILD-TYPE 17 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    1
  10P GAIN WILD-TYPE   17   22
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 22
[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        1      0      0      1      0      0      1      0
  10P GAIN WILD-TYPE      3      5      6      5      8      3      4      2
                    vv
clus                 CLUS_9
  10P GAIN MUTATED        0
  10P GAIN WILD-TYPE      3
D16V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                0                  6
  CLUS_4                1                  5
  CLUS_5                0                  8
  CLUS_6                0                  3
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 10Q GAIN MUTATION ANALYSIS
D17V1, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  3
  10Q GAIN WILD-TYPE 28 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    3
  10Q GAIN WILD-TYPE   28   16
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D17V2, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  3
  10Q GAIN WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    3
  10Q GAIN WILD-TYPE   23   21
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                3                 21
[1] 2 2
[1] FALSE
D17V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  1
  10Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE   16   14
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        1      1      1
  10Q GAIN WILD-TYPE      5     14     11
D17V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 14
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    0  1
  10Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    1
  10Q GAIN WILD-TYPE   15   12
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        0      1      0
  10Q GAIN WILD-TYPE     13      9      5
D17V6, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        1      1      2      0
  10Q GAIN WILD-TYPE     13     10      8     12
D17V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                2                  8
  CLUS_4                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q GAIN MUTATED        0      1      1      2      0
  10Q GAIN WILD-TYPE      9     11      7     10      6
D17V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                2                 10
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  0
  10Q GAIN WILD-TYPE 16 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE   16   23
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 23
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  10Q GAIN MUTATED        1      0      0      2      0      0      0      0
  10Q GAIN WILD-TYPE      3      5      6      4      8      3      5      2
                    vv
clus                 CLUS_9
  10Q GAIN MUTATED        0
  10Q GAIN WILD-TYPE      3
D17V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                0                  6
  CLUS_4                2                  4
  CLUS_5                0                  8
  CLUS_6                0                  3
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 11P GAIN MUTATION ANALYSIS
D18V1, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  5
  11P GAIN WILD-TYPE 25 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    5
  11P GAIN WILD-TYPE   25   14
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 25
  CLUS_2                5                 14
[1] 2 2
[1] FALSE
D18V2, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  6
  11P GAIN WILD-TYPE 21 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    6
  11P GAIN WILD-TYPE   21   18
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                6                 18
[1] 2 2
[1] FALSE
D18V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE   15   13
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        2      2      1
  11P GAIN WILD-TYPE      4     13     11
D18V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                2                 13
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, 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
D18V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        4      1      2      2
  11P GAIN WILD-TYPE     10     10      8     10
D18V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 10
  CLUS_3                2                  8
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED        0      1      3      4      1
  11P GAIN WILD-TYPE      9     11      5      8      5
D18V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                3                  5
  CLUS_4                4                  8
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  3
  11P GAIN WILD-TYPE 14 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    3
  11P GAIN WILD-TYPE   14   20
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                 14
  CLUS_2                3                 20
[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        1      1      4      1      1      0      0      0
  11P GAIN WILD-TYPE      3      4      2      5      7      3      5      2
                    vv
clus                 CLUS_9
  11P GAIN MUTATED        0
  11P GAIN WILD-TYPE      3
D18V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  4
  CLUS_3                4                  2
  CLUS_4                1                  5
  CLUS_5                1                  7
  CLUS_6                0                  3
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 11Q GAIN MUTATION ANALYSIS
D19V1, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  8
  11Q GAIN WILD-TYPE 24 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    8
  11Q GAIN WILD-TYPE   24   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 24
  CLUS_2                8                 11
[1] 2 2
[1] FALSE
D19V2, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  9
  11Q GAIN WILD-TYPE 20 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    9
  11Q GAIN WILD-TYPE   20   15
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 20
  CLUS_2                9                 15
[1] 2 2
[1] FALSE
D19V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  2
  11Q GAIN WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    2
  11Q GAIN WILD-TYPE   14   13
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        2      3      1
  11Q GAIN WILD-TYPE      4     12     11
D19V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                3                 12
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, 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
D19V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        5      1      2      4
  11Q GAIN WILD-TYPE      9     10      8      8
D19V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                1                 10
  CLUS_3                2                  8
  CLUS_4                4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        0      2      4      3      3
  11Q GAIN WILD-TYPE      9     10      4      9      3
D19V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                4                  4
  CLUS_4                3                  9
  CLUS_5                3                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  4
  11Q GAIN WILD-TYPE 13 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    4
  11Q GAIN WILD-TYPE   13   19
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                 13
  CLUS_2                4                 19
[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        1      1      4      1      2      1      0      0
  11Q GAIN WILD-TYPE      3      4      2      5      6      2      5      2
                    vv
clus                 CLUS_9
  11Q GAIN MUTATED        0
  11Q GAIN WILD-TYPE      3
D19V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  4
  CLUS_3                4                  2
  CLUS_4                1                  5
  CLUS_5                2                  6
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 12P GAIN MUTATION ANALYSIS
D20V1, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    4  3
  12P GAIN WILD-TYPE 25 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    3
  12P GAIN WILD-TYPE   25   16
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 25
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D20V2, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  5
  12P GAIN WILD-TYPE 22 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    5
  12P GAIN WILD-TYPE   22   19
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                5                 19
[1] 2 2
[1] FALSE
D20V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  2
  12P GAIN WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    2
  12P GAIN WILD-TYPE   15   13
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        0      4      1
  12P GAIN WILD-TYPE      6     11     11
D20V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                4                 11
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, 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
D20V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED        3      2      1      1
  12P GAIN WILD-TYPE     11      9      9     11
D20V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                  9
  CLUS_3                1                  9
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED        0      2      3      1      1
  12P GAIN WILD-TYPE      9     10      5     11      5
D20V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                3                  5
  CLUS_4                1                 11
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    4  2
  12P GAIN WILD-TYPE 15 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    2
  12P GAIN WILD-TYPE   15   21
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                2                 21
[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      2      1      1      1      0      0
  12P GAIN WILD-TYPE      4      4      4      5      7      2      5      2
                    vv
clus                 CLUS_9
  12P GAIN MUTATED        0
  12P GAIN WILD-TYPE      3
D20V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  4
  CLUS_3                2                  4
  CLUS_4                1                  5
  CLUS_5                1                  7
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 12Q GAIN MUTATION ANALYSIS
D21V1, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    5  4
  12Q GAIN WILD-TYPE 24 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5    4
  12Q GAIN WILD-TYPE   24   15
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 24
  CLUS_2                4                 15
[1] 2 2
[1] FALSE
D21V2, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  7
  12Q GAIN WILD-TYPE 22 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    7
  12Q GAIN WILD-TYPE   22   17
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                7                 17
[1] 2 2
[1] FALSE
D21V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  4
  12Q GAIN WILD-TYPE 15 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    4
  12Q GAIN WILD-TYPE   15   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                4                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        0      4      3
  12Q GAIN WILD-TYPE      6     11      9
D21V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                4                 11
  CLUS_3                3                  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"
D21V5, 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
D21V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED        4      2      2      1
  12Q GAIN WILD-TYPE     10      9      8     11
D21V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                2                  9
  CLUS_3                2                  8
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q GAIN MUTATED        0      2      4      2      1
  12Q GAIN WILD-TYPE      9     10      4     10      5
D21V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                4                  4
  CLUS_4                2                 10
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    5  3
  12Q GAIN WILD-TYPE 14 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5    3
  12Q GAIN WILD-TYPE   14   20
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 14
  CLUS_2                3                 20
[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      3      2      1      1      0      0
  12Q GAIN WILD-TYPE      4      4      3      4      7      2      5      2
                    vv
clus                 CLUS_9
  12Q GAIN MUTATED        0
  12Q GAIN WILD-TYPE      3
D21V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  4
  CLUS_3                3                  3
  CLUS_4                2                  4
  CLUS_5                1                  7
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 13Q GAIN MUTATION ANALYSIS
D22V1, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  2
  13Q GAIN WILD-TYPE 26 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE   26   17
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 26
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D22V2, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  2
  13Q GAIN WILD-TYPE 21 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE   21   22
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D22V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  2
  13Q GAIN WILD-TYPE 16 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    2
  13Q GAIN WILD-TYPE   16   13
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        1      2      1
  13Q GAIN WILD-TYPE      5     13     11
D22V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                2                 13
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    0  2
  13Q GAIN WILD-TYPE 15 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    2
  13Q GAIN WILD-TYPE   15   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        0      2      0
  13Q GAIN WILD-TYPE     13      8      5
D22V6, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 26 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        1      1      3      0
  13Q GAIN WILD-TYPE     13     10      7     12
D22V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                3                  7
  CLUS_4                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q GAIN MUTATED        2      1      0      2      0
  13Q GAIN WILD-TYPE      7     11      8     10      6
D22V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                 11
  CLUS_3                0                  8
  CLUS_4                2                 10
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  0
  13Q GAIN WILD-TYPE 15 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE   15   23
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                0                 23
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  13Q GAIN MUTATED        0      0      1      2      1      0      0      0
  13Q GAIN WILD-TYPE      4      5      5      4      7      3      5      2
                    vv
clus                 CLUS_9
  13Q GAIN MUTATED        0
  13Q GAIN WILD-TYPE      3
D22V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                1                  5
  CLUS_4                2                  4
  CLUS_5                1                  7
  CLUS_6                0                  3
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 16P GAIN MUTATION ANALYSIS
D23V1, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    1  6
  16P GAIN WILD-TYPE 28 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    6
  16P GAIN WILD-TYPE   28   13
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                6                 13
[1] 2 2
[1] FALSE
D23V2, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  5
  16P GAIN WILD-TYPE 22 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    5
  16P GAIN WILD-TYPE   22   19
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                5                 19
[1] 2 2
[1] FALSE
D23V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  3
  16P GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    3
  16P GAIN WILD-TYPE   15   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        1      3      2
  16P GAIN WILD-TYPE      5     12     10
D23V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                3                 12
  CLUS_3                2                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, 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
D23V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        4      1      0      2
  16P GAIN WILD-TYPE     10     10     10     10
D23V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 10
  CLUS_3                0                 10
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED        1      1      4      0      1
  16P GAIN WILD-TYPE      8     11      4     12      5
D23V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                 11
  CLUS_3                4                  4
  CLUS_4                0                 12
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  2
  16P GAIN WILD-TYPE 15 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    2
  16P GAIN WILD-TYPE   15   21
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                2                 21
[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        1      0      2      0      1      0      2      0
  16P GAIN WILD-TYPE      3      5      4      6      7      3      3      2
                    vv
clus                 CLUS_9
  16P GAIN MUTATED        0
  16P GAIN WILD-TYPE      3
D23V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                2                  4
  CLUS_4                0                  6
  CLUS_5                1                  7
  CLUS_6                0                  3
  CLUS_7                2                  3
  CLUS_8                0                  2
  CLUS_9                0                  3
[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 = 16Q GAIN MUTATION ANALYSIS
D24V1, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  5
  16Q GAIN WILD-TYPE 27 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    5
  16Q GAIN WILD-TYPE   27   14
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 27
  CLUS_2                5                 14
[1] 2 2
[1] FALSE
D24V2, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  6
  16Q GAIN WILD-TYPE 23 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    6
  16Q GAIN WILD-TYPE   23   18
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                6                 18
[1] 2 2
[1] FALSE
D24V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    3
  16Q GAIN WILD-TYPE   15   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        1      3      2
  16Q GAIN WILD-TYPE      5     12     10
D24V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                3                 12
  CLUS_3                2                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, 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
D24V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        4      1      0      2
  16Q GAIN WILD-TYPE     10     10     10     10
D24V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 10
  CLUS_3                0                 10
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        0      2      4      0      1
  16Q GAIN WILD-TYPE      9     10      4     12      5
D24V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                4                  4
  CLUS_4                0                 12
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  2
  16Q GAIN WILD-TYPE 15 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    2
  16Q GAIN WILD-TYPE   15   21
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                2                 21
[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        1      0      2      0      1      1      1      0
  16Q GAIN WILD-TYPE      3      5      4      6      7      2      4      2
                    vv
clus                 CLUS_9
  16Q GAIN MUTATED        0
  16Q GAIN WILD-TYPE      3
D24V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                2                  4
  CLUS_4                0                  6
  CLUS_5                1                  7
  CLUS_6                1                  2
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(25) Variable = 17Q GAIN MUTATION ANALYSIS
D25V1, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  2
  17Q GAIN WILD-TYPE 28 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    2
  17Q GAIN WILD-TYPE   28   17
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D25V2, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  3
  17Q GAIN WILD-TYPE 24 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    3
  17Q GAIN WILD-TYPE   24   21
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 24
  CLUS_2                3                 21
[1] 2 2
[1] FALSE
D25V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2  1
  17Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    1
  17Q GAIN WILD-TYPE   16   14
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      1      1
  17Q GAIN WILD-TYPE      5     14     11
D25V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 14
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  1
  17Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    1
  17Q GAIN WILD-TYPE   15   12
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      0      0
  17Q GAIN WILD-TYPE     12     10      5
D25V6, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8042 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        2      0      0      1
  17Q GAIN WILD-TYPE     12     11     10     11
D25V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 11
  CLUS_3                0                 10
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED        0      0      2      0      1
  17Q GAIN WILD-TYPE      9     12      6     12      5
D25V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                0                 12
  CLUS_3                2                  6
  CLUS_4                0                 12
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2  1
  17Q GAIN WILD-TYPE 17 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    1
  17Q GAIN WILD-TYPE   17   22
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  17Q GAIN MUTATED        1      0      0      0      1      1      0      0
  17Q GAIN WILD-TYPE      3      5      6      6      7      2      5      2
                    vv
clus                 CLUS_9
  17Q GAIN MUTATED        0
  17Q GAIN WILD-TYPE      3
D25V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                0                  6
  CLUS_4                0                  6
  CLUS_5                1                  7
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(26) Variable = 18P GAIN MUTATION ANALYSIS
D26V1, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  8
  18P GAIN WILD-TYPE 24 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    8
  18P GAIN WILD-TYPE   24   11
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 24
  CLUS_2                8                 11
[1] 2 2
[1] FALSE
D26V2, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  6
  18P GAIN WILD-TYPE 17 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    6
  18P GAIN WILD-TYPE   17   18
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 17
  CLUS_2                6                 18
[1] 2 2
[1] FALSE
D26V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  2
  18P GAIN WILD-TYPE 11 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    2
  18P GAIN WILD-TYPE   11   13
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        1      5      3
  18P GAIN WILD-TYPE      5     10      9
D26V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                5                 10
  CLUS_3                3                  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"
D26V5, 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
D26V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        3      3      5      2
  18P GAIN WILD-TYPE     11      8      5     10
D26V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                3                  8
  CLUS_3                5                  5
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P GAIN MUTATED        1      2      2      7      1
  18P GAIN WILD-TYPE      8     10      6      5      5
D26V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
  CLUS_3                2                  6
  CLUS_4                7                  5
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  5
  18P GAIN WILD-TYPE 13 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    5
  18P GAIN WILD-TYPE   13   18
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                 13
  CLUS_2                5                 18
[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        1      0      2      3      2      0      1      0
  18P GAIN WILD-TYPE      3      5      4      3      6      3      4      2
                    vv
clus                 CLUS_9
  18P GAIN MUTATED        2
  18P GAIN WILD-TYPE      1
D26V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                2                  4
  CLUS_4                3                  3
  CLUS_5                2                  6
  CLUS_6                0                  3
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                2                  1
[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(27) Variable = 18Q GAIN MUTATION ANALYSIS
D27V1, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  9
  18Q GAIN WILD-TYPE 24 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    9
  18Q GAIN WILD-TYPE   24   10
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                 24
  CLUS_2                9                 10
[1] 2 2
[1] FALSE
D27V2, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  7
  18Q GAIN WILD-TYPE 17 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    7
  18Q GAIN WILD-TYPE   17   17
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                 17
  CLUS_2                7                 17
[1] 2 2
[1] FALSE
D27V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    8  2
  18Q GAIN WILD-TYPE 10 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      8    2
  18Q GAIN WILD-TYPE   10   13
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        1      6      3
  18Q GAIN WILD-TYPE      5      9      9
D27V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                6                  9
  CLUS_3                3                  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"
D27V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  2
  18Q GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    2
  18Q GAIN WILD-TYPE   11   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        3      2      1
  18Q GAIN WILD-TYPE     10      8      4
D27V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 10
  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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        4      3      5      2
  18Q GAIN WILD-TYPE     10      8      5     10
D27V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                3                  8
  CLUS_3                5                  5
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q GAIN MUTATED        1      2      3      7      1
  18Q GAIN WILD-TYPE      8     10      5      5      5
D27V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 10
  CLUS_3                3                  5
  CLUS_4                7                  5
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  5
  18Q GAIN WILD-TYPE 12 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    5
  18Q GAIN WILD-TYPE   12   18
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                 12
  CLUS_2                5                 18
[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        1      0      3      3      2      0      1      0
  18Q GAIN WILD-TYPE      3      5      3      3      6      3      4      2
                    vv
clus                 CLUS_9
  18Q GAIN MUTATED        2
  18Q GAIN WILD-TYPE      1
D27V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                3                  3
  CLUS_4                3                  3
  CLUS_5                2                  6
  CLUS_6                0                  3
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                2                  1
[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(28) Variable = 19P GAIN MUTATION ANALYSIS
D28V1, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  2
  19P GAIN WILD-TYPE 28 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    2
  19P GAIN WILD-TYPE   28   17
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D28V2, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  2
  19P GAIN WILD-TYPE 23 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    2
  19P GAIN WILD-TYPE   23   22
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D28V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  1
  19P GAIN WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    1
  19P GAIN WILD-TYPE   17   14
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      1      1
  19P GAIN WILD-TYPE      6     14     11
D28V4, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 31 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6325         TCGA-G8-6326 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6914         TCGA-GS-A9TV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-VB-A8QN 
"19P GAIN WILD-TYPE" 
D28V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  1
  19P GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    1
  19P GAIN WILD-TYPE   15   12
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      1      0
  19P GAIN WILD-TYPE     13      9      5
D28V6, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      1      1      1
  19P GAIN WILD-TYPE     14     10      9     11
D28V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                 10
  CLUS_3                1                  9
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED        0      2      0      1      0
  19P GAIN WILD-TYPE      9     10      8     11      6
D28V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                0                  8
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  0
  19P GAIN WILD-TYPE 18 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    0
  19P GAIN WILD-TYPE   18   23
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 23
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  19P GAIN MUTATED        0      0      0      1      0      0      0      0
  19P GAIN WILD-TYPE      4      5      6      5      8      3      5      2
                    vv
clus                 CLUS_9
  19P GAIN MUTATED        0
  19P GAIN WILD-TYPE      3
D28V10, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 41 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7353 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GS-A9TQ         TCGA-GS-A9TU         TCGA-GS-A9TV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9U3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 

Clustering(29) Variable = 19Q GAIN MUTATION ANALYSIS
D29V1, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 28 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    2
  19Q GAIN WILD-TYPE   28   17
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D29V2, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 23 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    2
  19Q GAIN WILD-TYPE   23   22
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D29V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  1
  19Q GAIN WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    1
  19Q GAIN WILD-TYPE   17   14
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      1      1
  19Q GAIN WILD-TYPE      6     14     11
D29V4, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 31 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6325         TCGA-G8-6326 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6914         TCGA-GS-A9TV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9TZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-VB-A8QN 
"19Q GAIN WILD-TYPE" 
D29V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0  1
  19Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    1
  19Q GAIN WILD-TYPE   15   12
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      1      0
  19Q GAIN WILD-TYPE     13      9      5
D29V6, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        0      1      1      1
  19Q GAIN WILD-TYPE     14     10      9     11
D29V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                 10
  CLUS_3                1                  9
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED        0      2      0      1      0
  19Q GAIN WILD-TYPE      9     10      8     11      6
D29V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                 10
  CLUS_3                0                  8
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  0
  19Q GAIN WILD-TYPE 18 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    0
  19Q GAIN WILD-TYPE   18   23
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 23
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  19Q GAIN MUTATED        0      0      0      1      0      0      0      0
  19Q GAIN WILD-TYPE      4      5      6      5      8      3      5      2
                    vv
clus                 CLUS_9
  19Q GAIN MUTATED        0
  19Q GAIN WILD-TYPE      3
D29V10, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 41 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7353 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GS-A9TQ         TCGA-GS-A9TU         TCGA-GS-A9TV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9U3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 

Clustering(30) Variable = 20P GAIN MUTATION ANALYSIS
D30V1, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  3
  20P GAIN WILD-TYPE 27 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    3
  20P GAIN WILD-TYPE   27   16
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 27
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D30V2, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  4
  20P GAIN WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    4
  20P GAIN WILD-TYPE   23   20
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                4                 20
[1] 2 2
[1] FALSE
D30V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3  1
  20P GAIN WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    1
  20P GAIN WILD-TYPE   15   14
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        2      2      0
  20P GAIN WILD-TYPE      4     13     12
D30V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                2                 13
  CLUS_3                0                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  1
  20P GAIN WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    1
  20P GAIN WILD-TYPE   14   12
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        2      0      0
  20P GAIN WILD-TYPE     11     10      5
D30V6, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 26 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8042 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        1      0      1      3
  20P GAIN WILD-TYPE     13     11      9      9
D30V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 11
  CLUS_3                1                  9
  CLUS_4                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P GAIN MUTATED        0      1      1      1      2
  20P GAIN WILD-TYPE      9     11      7     11      4
D30V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                1                 11
  CLUS_5                2                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  2
  20P GAIN WILD-TYPE 17 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    2
  20P GAIN WILD-TYPE   17   21
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                2                 21
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  20P GAIN MUTATED        1      0      1      0      1      1      0      0
  20P GAIN WILD-TYPE      3      5      5      6      7      2      5      2
                    vv
clus                 CLUS_9
  20P GAIN MUTATED        0
  20P GAIN WILD-TYPE      3
D30V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                1                  5
  CLUS_4                0                  6
  CLUS_5                1                  7
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(31) Variable = 20Q GAIN MUTATION ANALYSIS
D31V1, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  2
  20Q GAIN WILD-TYPE 27 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    2
  20Q GAIN WILD-TYPE   27   17
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 27
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D31V2, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    1  3
  20Q GAIN WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1    3
  20Q GAIN WILD-TYPE   23   21
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                3                 21
[1] 2 2
[1] FALSE
D31V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  1
  20Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    1
  20Q GAIN WILD-TYPE   16   14
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        2      1      0
  20Q GAIN WILD-TYPE      4     14     12
D31V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                1                 14
  CLUS_3                0                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    0  1
  20Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    1
  20Q GAIN WILD-TYPE   15   12
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        1      0      0
  20Q GAIN WILD-TYPE     12     10      5
D31V6, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8042 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6325         TCGA-G8-6326 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        1      0      1      2
  20Q GAIN WILD-TYPE     13     11      9     10
D31V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 11
  CLUS_3                1                  9
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q GAIN MUTATED        0      1      1      1      1
  20Q GAIN WILD-TYPE      9     11      7     11      5
D31V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                1                 11
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  1
  20Q GAIN WILD-TYPE 17 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    1
  20Q GAIN WILD-TYPE   17   22
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  20Q GAIN MUTATED        1      0      1      0      0      1      0      0
  20Q GAIN WILD-TYPE      3      5      5      6      8      2      5      2
                    vv
clus                 CLUS_9
  20Q GAIN MUTATED        0
  20Q GAIN WILD-TYPE      3
D31V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                1                  5
  CLUS_4                0                  6
  CLUS_5                0                  8
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(32) Variable = 21Q GAIN MUTATION ANALYSIS
D32V1, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6  4
  21Q GAIN WILD-TYPE 23 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6    4
  21Q GAIN WILD-TYPE   23   15
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                6                 23
  CLUS_2                4                 15
[1] 2 2
[1] FALSE
D32V2, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  5
  21Q GAIN WILD-TYPE 19 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    5
  21Q GAIN WILD-TYPE   19   19
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 19
  CLUS_2                5                 19
[1] 2 2
[1] FALSE
D32V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4  2
  21Q GAIN WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    2
  21Q GAIN WILD-TYPE   14   13
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        3      3      0
  21Q GAIN WILD-TYPE      3     12     12
D32V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                3                 12
  CLUS_3                0                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, 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
D32V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        1      1      1      6
  21Q GAIN WILD-TYPE     13     10      9      6
D32V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                1                  9
  CLUS_4                6                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        0      3      1      2      3
  21Q GAIN WILD-TYPE      9      9      7     10      3
D32V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                3                  9
  CLUS_3                1                  7
  CLUS_4                2                 10
  CLUS_5                3                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  6
  21Q GAIN WILD-TYPE 17 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    6
  21Q GAIN WILD-TYPE   17   17
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                6                 17
[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        1      1      2      0      2      2      0      0
  21Q GAIN WILD-TYPE      3      4      4      6      6      1      5      2
                    vv
clus                 CLUS_9
  21Q GAIN MUTATED        0
  21Q GAIN WILD-TYPE      3
D32V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  4
  CLUS_3                2                  4
  CLUS_4                0                  6
  CLUS_5                2                  6
  CLUS_6                2                  1
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(33) Variable = XP GAIN MUTATION ANALYSIS
D33V1, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    1  5
  XP GAIN WILD-TYPE 28 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    5
  XP GAIN WILD-TYPE   28   14
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                28
  CLUS_2               5                14
[1] 2 2
[1] FALSE
D33V2, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  4
  XP GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    4
  XP GAIN WILD-TYPE   22   20
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D33V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  2
  XP GAIN WILD-TYPE 16 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    2
  XP GAIN WILD-TYPE   16   13
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED        0      2      2
  XP GAIN WILD-TYPE      6     13     10
D33V4, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               2                13
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  0
  XP GAIN WILD-TYPE 13 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    0
  XP GAIN WILD-TYPE   13   13
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               0                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED        1      0      1
  XP GAIN WILD-TYPE     12     10      4
D33V6, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A6HN        TCGA-FA-A6HO 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A6JB 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        3      0      1      2
  XP GAIN WILD-TYPE     11     11      9     10
D33V7, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               0                11
  CLUS_3               1                 9
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP GAIN MUTATED        0      1      3      2      0
  XP GAIN WILD-TYPE      9     11      5     10      6
D33V8, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                11
  CLUS_3               3                 5
  CLUS_4               2                10
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    4  1
  XP GAIN WILD-TYPE 15 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    1
  XP GAIN WILD-TYPE   15   22
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               4                15
  CLUS_2               1                22
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  XP GAIN MUTATED        0      0      4      1      0      0      0      0
  XP GAIN WILD-TYPE      4      5      2      5      8      3      5      2
                   vv
clus                CLUS_9
  XP GAIN MUTATED        0
  XP GAIN WILD-TYPE      3
D33V10, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               4                 2
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               0                 3
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(34) Variable = XQ GAIN MUTATION ANALYSIS
D34V1, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE 27 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    4
  XQ GAIN WILD-TYPE   27   15
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                27
  CLUS_2               4                15
[1] 2 2
[1] FALSE
D34V2, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    4
  XQ GAIN WILD-TYPE   22   20
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D34V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 16 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    2
  XQ GAIN WILD-TYPE   16   13
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        0      2      2
  XQ GAIN WILD-TYPE      6     13     10
D34V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               2                13
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, 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
D34V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        3      1      1      1
  XQ GAIN WILD-TYPE     11     10      9     11
D34V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED        0      0      3      2      1
  XQ GAIN WILD-TYPE      9     12      5     10      5
D34V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                12
  CLUS_3               3                 5
  CLUS_4               2                10
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    4  2
  XQ GAIN WILD-TYPE 15 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    2
  XQ GAIN WILD-TYPE   15   21
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4                15
  CLUS_2               2                21
[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      3      1      0      1      0      0
  XQ GAIN WILD-TYPE      4      5      3      5      8      2      5      2
                   vv
clus                CLUS_9
  XQ GAIN MUTATED        1
  XQ GAIN WILD-TYPE      2
D34V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               3                 3
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               1                 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(35) Variable = 1P LOSS MUTATION ANALYSIS
D35V1, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 28 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   28   17
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                28
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D35V2, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 22 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   22   23
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               1                23
[1] 2 2
[1] FALSE
D35V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   17   13
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        0      1      2
  1P LOSS WILD-TYPE      6     14     10
D35V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                14
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, 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
D35V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        1      1      0      1
  1P LOSS WILD-TYPE     13     10     10     11
D35V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               0                10
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED        1      1      1      0      0
  1P LOSS WILD-TYPE      8     11      7     12      6
D35V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  1
  1P LOSS WILD-TYPE 18 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    1
  1P LOSS WILD-TYPE   18   22
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                22
[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      0      0      1      0      0
  1P LOSS WILD-TYPE      4      5      5      6      8      2      5      2
                   vv
clus                CLUS_9
  1P LOSS MUTATED        0
  1P LOSS WILD-TYPE      3
D35V10, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                40 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F        TCGA-FA-A86F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6324 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907        TCGA-G8-6909 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G8-6914        TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GR-A4D6        TCGA-GS-A9TQ        TCGA-GS-A9TT        TCGA-GS-A9TU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
D36V1, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 26 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE   26   17
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                26
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D36V2, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 21 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE   21   22
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                21
  CLUS_2               2                22
[1] 2 2
[1] FALSE
D36V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  2
  3P LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    2
  3P LOSS WILD-TYPE   17   13
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        0      2      1
  3P LOSS WILD-TYPE      6     13     11
D36V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               2                13
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  0
  3P LOSS WILD-TYPE 14 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    0
  3P LOSS WILD-TYPE   14   13
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               0                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        1      0      0
  3P LOSS WILD-TYPE     12     10      5
D36V6, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                27 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        1      2      1      1
  3P LOSS WILD-TYPE     13      9      9     11
D36V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 9
  CLUS_3               1                 9
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P LOSS MUTATED        1      2      1      1      0
  3P LOSS WILD-TYPE      8     10      7     11      6
D36V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                10
  CLUS_3               1                 7
  CLUS_4               1                11
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    2  2
  3P LOSS WILD-TYPE 17 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    2
  3P LOSS WILD-TYPE   17   21
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               2                21
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  3P LOSS MUTATED        0      1      1      1      0      1      0      0
  3P LOSS WILD-TYPE      4      4      5      5      8      2      5      2
                   vv
clus                CLUS_9
  3P LOSS MUTATED        0
  3P LOSS WILD-TYPE      3
D36V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               1                 5
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(37) Variable = 3Q LOSS MUTATION ANALYSIS
D37V1, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  2
  3Q LOSS WILD-TYPE 27 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE   27   17
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                27
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D37V2, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  2
  3Q LOSS WILD-TYPE 22 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE   22   22
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               2                22
[1] 2 2
[1] FALSE
D37V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  1
  3Q LOSS WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    1
  3Q LOSS WILD-TYPE   17   14
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        0      2      0
  3Q LOSS WILD-TYPE      6     13     12
D37V4, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D37V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  0
  3Q LOSS WILD-TYPE 14 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    0
  3Q LOSS WILD-TYPE   14   13
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               0                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        1      0      0
  3Q LOSS WILD-TYPE     12     10      5
D37V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                27 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        1      1      1      1
  3Q LOSS WILD-TYPE     13     10      9     11
D37V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q LOSS MUTATED        1      1      1      1      0
  3Q LOSS WILD-TYPE      8     11      7     11      6
D37V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               1                11
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 17 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   17   22
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               1                22
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  3Q LOSS MUTATED        0      0      1      1      0      1      0      0
  3Q LOSS WILD-TYPE      4      5      5      5      8      2      5      2
                   vv
clus                CLUS_9
  3Q LOSS MUTATED        0
  3Q LOSS WILD-TYPE      3
D37V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               1                 5
  CLUS_4               1                 5
  CLUS_5               0                 8
  CLUS_6               1                 2
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(38) Variable = 4P LOSS MUTATION ANALYSIS
D38V1, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1  2
  4P LOSS WILD-TYPE 28 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    2
  4P LOSS WILD-TYPE   28   17
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                28
  CLUS_2               2                17
[1] 2 2
[1] FALSE
D38V2, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    2  1
  4P LOSS WILD-TYPE 22 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    1
  4P LOSS WILD-TYPE   22   23
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               1                23
[1] 2 2
[1] FALSE
D38V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  2
  4P LOSS WILD-TYPE 18 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    2
  4P LOSS WILD-TYPE   18   13
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        0      0      2
  4P LOSS WILD-TYPE      6     15     10
D38V4, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F        TCGA-FF-8041 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR        TCGA-FF-A7CW 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6325        TCGA-G8-6326 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT        TCGA-GS-A9TV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ        TCGA-GS-A9U4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D38V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  1
  4P LOSS WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    1
  4P LOSS WILD-TYPE   15   12
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                15
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        0      1      0
  4P LOSS WILD-TYPE     13      9      5
D38V6, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                27 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A68N        TCGA-RQ-A6JB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        0      2      1      0
  4P LOSS WILD-TYPE     14      9      9     12
D38V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                 9
  CLUS_3               1                 9
  CLUS_4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P LOSS MUTATED        0      2      0      1      0
  4P LOSS WILD-TYPE      9     10      8     11      6
D38V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               0                 8
  CLUS_4               1                11
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1  1
  4P LOSS WILD-TYPE 18 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    1
  4P LOSS WILD-TYPE   18   22
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                22
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  4P LOSS MUTATED        0      1      0      1      0      0      0      0
  4P LOSS WILD-TYPE      4      4      6      5      8      3      5      2
                   vv
clus                CLUS_9
  4P LOSS MUTATED        0
  4P LOSS WILD-TYPE      3
D38V10, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                40 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F        TCGA-FF-8041 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR        TCGA-FF-A7CW 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6325 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907        TCGA-G8-6909 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G8-6914        TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GR-A4D6        TCGA-GS-A9TT        TCGA-GS-A9TU        TCGA-GS-A9TV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U3        TCGA-GS-A9U4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 

Clustering(39) Variable = 4Q LOSS MUTATION ANALYSIS
D39V1, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 28 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   28   16
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                28
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D39V2, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 23 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   23   21
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                23
  CLUS_2               3                21
[1] 2 2
[1] FALSE
D39V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  2
  4Q LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    2
  4Q LOSS WILD-TYPE   17   13
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        0      1      2
  4Q LOSS WILD-TYPE      6     14     10
D39V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                14
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  1
  4Q LOSS WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    1
  4Q LOSS WILD-TYPE   14   12
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        1      1      0
  4Q LOSS WILD-TYPE     12      9      5
D39V6, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8046 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6        TCGA-GR-A4D9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        0      1      1      2
  4Q LOSS WILD-TYPE     14     10      9     10
D39V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                10
  CLUS_3               1                 9
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q LOSS MUTATED        0      1      0      1      2
  4Q LOSS WILD-TYPE      9     11      8     11      4
D39V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                11
  CLUS_3               0                 8
  CLUS_4               1                11
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 18 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   18   20
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                20
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  4Q LOSS MUTATED        0      1      0      1      2      0      0      0
  4Q LOSS WILD-TYPE      4      4      6      5      6      3      5      2
                   vv
clus                CLUS_9
  4Q LOSS MUTATED        0
  4Q LOSS WILD-TYPE      3
D39V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               0                 6
  CLUS_4               1                 5
  CLUS_5               2                 6
  CLUS_6               0                 3
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(40) Variable = 6Q LOSS MUTATION ANALYSIS
D40V1, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE 25 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE   25   16
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                25
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D40V2, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2  5
  6Q LOSS WILD-TYPE 22 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    5
  6Q LOSS WILD-TYPE   22   19
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               5                19
[1] 2 2
[1] FALSE
D40V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2  2
  6Q LOSS WILD-TYPE 16 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    2
  6Q LOSS WILD-TYPE   16   13
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        1      2      1
  6Q LOSS WILD-TYPE      5     13     11
D40V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               2                13
  CLUS_3               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, 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
D40V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        3      1      2      1
  6Q LOSS WILD-TYPE     11     10      8     11
D40V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                10
  CLUS_3               2                 8
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6Q LOSS MUTATED        2      2      2      1      0
  6Q LOSS WILD-TYPE      7     10      6     11      6
D40V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                10
  CLUS_3               2                 6
  CLUS_4               1                11
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5  1
  6Q LOSS WILD-TYPE 14 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    1
  6Q LOSS WILD-TYPE   14   22
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                14
  CLUS_2               1                22
[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      3      1      1      0      0      0
  6Q LOSS WILD-TYPE      4      4      3      5      7      3      5      2
                   vv
clus                CLUS_9
  6Q LOSS MUTATED        0
  6Q LOSS WILD-TYPE      3
D40V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               3                 3
  CLUS_4               1                 5
  CLUS_5               1                 7
  CLUS_6               0                 3
  CLUS_7               0                 5
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(41) Variable = 8P LOSS MUTATION ANALYSIS
D41V1, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2  6
  8P LOSS WILD-TYPE 27 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    6
  8P LOSS WILD-TYPE   27   13
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                27
  CLUS_2               6                13
[1] 2 2
[1] FALSE
D41V2, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  4
  8P LOSS WILD-TYPE 20 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    4
  8P LOSS WILD-TYPE   20   20
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                20
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D41V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    0  6
  8P LOSS WILD-TYPE 18  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    6
  8P LOSS WILD-TYPE   18    9
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               6                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      1      5
  8P LOSS WILD-TYPE      6     14      7
D41V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                14
  CLUS_3               5                 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"
D41V5, 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
D41V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        2      4      0      2
  8P LOSS WILD-TYPE     12      7     10     10
D41V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               4                 7
  CLUS_3               0                10
  CLUS_4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P LOSS MUTATED        0      5      2      0      1
  8P LOSS WILD-TYPE      9      7      6     12      5
D41V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               5                 7
  CLUS_3               2                 6
  CLUS_4               0                12
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2  3
  8P LOSS WILD-TYPE 17 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    3
  8P LOSS WILD-TYPE   17   20
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                20
[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      1      1      0      2      0      1      0
  8P LOSS WILD-TYPE      4      4      5      6      6      3      4      2
                   vv
clus                CLUS_9
  8P LOSS MUTATED        0
  8P LOSS WILD-TYPE      3
D41V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 4
  CLUS_3               1                 5
  CLUS_4               0                 6
  CLUS_5               2                 6
  CLUS_6               0                 3
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               0                 3
[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(42) Variable = 8Q LOSS MUTATION ANALYSIS
D42V1, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  3
  8Q LOSS WILD-TYPE 28 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE   28   16
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                28
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D42V2, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  2
  8Q LOSS WILD-TYPE 22 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE   22   22
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               2                22
[1] 2 2
[1] FALSE
D42V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    0  3
  8Q LOSS WILD-TYPE 18 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    3
  8Q LOSS WILD-TYPE   18   12
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      0      3
  8Q LOSS WILD-TYPE      6     15      9
D42V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                15
  CLUS_3               3                 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"
D42V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  1
  8Q LOSS WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE   14   12
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        1      1      0
  8Q LOSS WILD-TYPE     12      9      5
D42V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                26 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GR-A4D9        TCGA-RQ-A6JB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        1      2      0      1
  8Q LOSS WILD-TYPE     13      9     10     11
D42V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 9
  CLUS_3               0                10
  CLUS_4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED        0      3      1      0      0
  8Q LOSS WILD-TYPE      9      9      7     12      6
D42V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               3                 9
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  1
  8Q LOSS WILD-TYPE 18 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE   18   22
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                22
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  8Q LOSS MUTATED        0      1      1      0      0      0      0      0
  8Q LOSS WILD-TYPE      4      4      5      6      8      3      5      2
                   vv
clus                CLUS_9
  8Q LOSS MUTATED        0
  8Q LOSS WILD-TYPE      3
D42V10, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                40 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F        TCGA-FF-8041 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046        TCGA-FF-8047 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR        TCGA-FF-A7CW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6325 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907        TCGA-G8-6909 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G8-6914        TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GR-A4D6        TCGA-GS-A9TQ        TCGA-GS-A9TT        TCGA-GS-A9TU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 

Clustering(43) Variable = 13Q LOSS MUTATION ANALYSIS
D43V1, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    1  2
  13Q LOSS WILD-TYPE 28 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    2
  13Q LOSS WILD-TYPE   28   17
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                2                 17
[1] 2 2
[1] FALSE
D43V2, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 22 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   22   23
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                1                 23
[1] 2 2
[1] FALSE
D43V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    0  1
  13Q LOSS WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    1
  13Q LOSS WILD-TYPE   18   14
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        0      1      0
  13Q LOSS WILD-TYPE      6     14     12
D43V4, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 32 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6325 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6914 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TV         TCGA-GS-A9TW 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9U4         TCGA-RQ-A68N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-VB-A8QN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D43V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    1  0
  13Q LOSS WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    0
  13Q LOSS WILD-TYPE   14   13
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        0      0      1
  13Q LOSS WILD-TYPE     13     10      4
D43V6, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GR-7353         TCGA-GR-A4D5         TCGA-GR-A4D6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        1      1      0      1
  13Q LOSS WILD-TYPE     13     10     10     11
D43V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                0                 10
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q LOSS MUTATED        1      1      1      0      0
  13Q LOSS WILD-TYPE      8     11      7     12      6
D43V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                0                 12
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    1  1
  13Q LOSS WILD-TYPE 18 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    1
  13Q LOSS WILD-TYPE   18   22
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  13Q LOSS MUTATED        0      0      1      0      0      0      1      0
  13Q LOSS WILD-TYPE      4      5      5      6      8      3      4      2
                    vv
clus                 CLUS_9
  13Q LOSS MUTATED        0
  13Q LOSS WILD-TYPE      3
D43V10, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 40 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FA-A86F         TCGA-FF-8041 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7353 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GS-A9TQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TU         TCGA-GS-A9TV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GS-A9TW         TCGA-GS-A9TX         TCGA-GS-A9U3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GS-A9U4         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-VB-A8QN 
"13Q LOSS WILD-TYPE" 

Clustering(44) Variable = 15Q LOSS MUTATION ANALYSIS
D44V1, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  6
  15Q LOSS WILD-TYPE 28 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    6
  15Q LOSS WILD-TYPE   28   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                6                 13
[1] 2 2
[1] FALSE
D44V2, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5  2
  15Q LOSS WILD-TYPE 19 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    2
  15Q LOSS WILD-TYPE   19   22
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                 19
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D44V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  2
  15Q LOSS WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    2
  15Q LOSS WILD-TYPE   17   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        0      1      2
  15Q LOSS WILD-TYPE      6     14     10
D44V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 14
  CLUS_3                2                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, 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
D44V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      3      1      3
  15Q LOSS WILD-TYPE     14      8      9      9
D44V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                  8
  CLUS_3                1                  9
  CLUS_4                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q LOSS MUTATED        1      3      0      1      2
  15Q LOSS WILD-TYPE      8      9      8     11      4
D44V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                3                  9
  CLUS_3                0                  8
  CLUS_4                1                 11
  CLUS_5                2                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  5
  15Q LOSS WILD-TYPE 18 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    5
  15Q LOSS WILD-TYPE   18   18
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                5                 18
[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      1      0      1      2      0      2      0
  15Q LOSS WILD-TYPE      4      4      6      5      6      3      3      2
                    vv
clus                 CLUS_9
  15Q LOSS MUTATED        0
  15Q LOSS WILD-TYPE      3
D44V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  4
  CLUS_3                0                  6
  CLUS_4                1                  5
  CLUS_5                2                  6
  CLUS_6                0                  3
  CLUS_7                2                  3
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(45) Variable = 16Q LOSS MUTATION ANALYSIS
D45V1, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    0  4
  16Q LOSS WILD-TYPE 29 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE   29   15
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 29
  CLUS_2                4                 15
[1] 2 2
[1] FALSE
D45V2, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 22 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   22   22
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D45V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE   17   13
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        0      1      2
  16Q LOSS WILD-TYPE      6     14     10
D45V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                1                 14
  CLUS_3                2                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, 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
D45V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      1      0      3
  16Q LOSS WILD-TYPE     14     10     10      9
D45V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                 10
  CLUS_3                0                 10
  CLUS_4                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q LOSS MUTATED        1      1      0      0      2
  16Q LOSS WILD-TYPE      8     11      8     12      4
D45V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                 11
  CLUS_3                0                  8
  CLUS_4                0                 12
  CLUS_5                2                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    0  3
  16Q LOSS WILD-TYPE 19 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    3
  16Q LOSS WILD-TYPE   19   20
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 20
[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      0      2      0      1      0
  16Q LOSS WILD-TYPE      4      5      6      6      6      3      4      2
                    vv
clus                 CLUS_9
  16Q LOSS MUTATED        0
  16Q LOSS WILD-TYPE      3
D45V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                0                  6
  CLUS_4                0                  6
  CLUS_5                2                  6
  CLUS_6                0                  3
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(46) Variable = 17P LOSS MUTATION ANALYSIS
D46V1, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  7
  17P LOSS WILD-TYPE 27 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    7
  17P LOSS WILD-TYPE   27   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 27
  CLUS_2                7                 12
[1] 2 2
[1] FALSE
D46V2, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4  5
  17P LOSS WILD-TYPE 20 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    5
  17P LOSS WILD-TYPE   20   19
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 20
  CLUS_2                5                 19
[1] 2 2
[1] FALSE
D46V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  3
  17P LOSS WILD-TYPE 16 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    3
  17P LOSS WILD-TYPE   16   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        1      2      2
  17P LOSS WILD-TYPE      5     13     10
D46V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                2                 13
  CLUS_3                2                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, 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
D46V6, 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        3      2      1      3
  17P LOSS WILD-TYPE     11      9      9      9
D46V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                  9
  CLUS_3                1                  9
  CLUS_4                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P LOSS MUTATED        1      3      3      2      0
  17P LOSS WILD-TYPE      8      9      5     10      6
D46V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                3                  9
  CLUS_3                3                  5
  CLUS_4                2                 10
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4  2
  17P LOSS WILD-TYPE 15 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    2
  17P LOSS WILD-TYPE   15   21
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                2                 21
[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        1      0      3      1      0      0      1      0
  17P LOSS WILD-TYPE      3      5      3      5      8      3      4      2
                    vv
clus                 CLUS_9
  17P LOSS MUTATED        0
  17P LOSS WILD-TYPE      3
D46V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  5
  CLUS_3                3                  3
  CLUS_4                1                  5
  CLUS_5                0                  8
  CLUS_6                0                  3
  CLUS_7                1                  4
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(47) Variable = 17Q LOSS MUTATION ANALYSIS
D47V1, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  3
  17Q LOSS WILD-TYPE 28 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    3
  17Q LOSS WILD-TYPE   28   16
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D47V2, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  3
  17Q LOSS WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    3
  17Q LOSS WILD-TYPE   23   21
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                3                 21
[1] 2 2
[1] FALSE
D47V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    0  2
  17Q LOSS WILD-TYPE 18 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    2
  17Q LOSS WILD-TYPE   18   13
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        0      1      1
  17Q LOSS WILD-TYPE      6     14     11
D47V4, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 31 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6325 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6914 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-GS-A9TV         TCGA-GS-A9TW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9U4         TCGA-RQ-A6JB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-VB-A8QN 
"17Q LOSS WILD-TYPE" 
D47V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  0
  17Q LOSS WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    0
  17Q LOSS WILD-TYPE   14   13
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        1      0      0
  17Q LOSS WILD-TYPE     12     10      5
D47V6, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GR-7353         TCGA-GR-A4D4         TCGA-GR-A4D5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GR-A4D6         TCGA-GR-A4D9         TCGA-RQ-A6JB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        2      1      1      0
  17Q LOSS WILD-TYPE     12     10      9     12
D47V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 10
  CLUS_3                1                  9
  CLUS_4                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        0      1      2      1      0
  17Q LOSS WILD-TYPE      9     11      6     11      6
D47V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                2                  6
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  0
  17Q LOSS WILD-TYPE 16 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    0
  17Q LOSS WILD-TYPE   16   23
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 23
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  17Q LOSS MUTATED        0      0      2      1      0      0      0      0
  17Q LOSS WILD-TYPE      4      5      4      5      8      3      5      2
                    vv
clus                 CLUS_9
  17Q LOSS MUTATED        0
  17Q LOSS WILD-TYPE      3
D47V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                2                  4
  CLUS_4                1                  5
  CLUS_5                0                  8
  CLUS_6                0                  3
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(48) Variable = 18P LOSS MUTATION ANALYSIS
D48V1, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 27 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   27   16
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 27
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D48V2, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  4
  18P LOSS WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    4
  18P LOSS WILD-TYPE   23   20
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                4                 20
[1] 2 2
[1] FALSE
D48V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    3  0
  18P LOSS WILD-TYPE 15 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    0
  18P LOSS WILD-TYPE   15   15
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        0      3      0
  18P LOSS WILD-TYPE      6     12     12
D48V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                3                 12
  CLUS_3                0                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  0
  18P LOSS WILD-TYPE 13 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    0
  18P LOSS WILD-TYPE   13   13
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      0      1
  18P LOSS WILD-TYPE     12     10      4
D48V6, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 26 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A6HN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FA-A6HO         TCGA-FF-8041         TCGA-FF-8042 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8046         TCGA-FF-8047 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FM-8000 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        2      0      2      1
  18P LOSS WILD-TYPE     12     11      8     11
D48V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 11
  CLUS_3                2                  8
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED        2      0      2      1      0
  18P LOSS WILD-TYPE      7     12      6     11      6
D48V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                0                 12
  CLUS_3                2                  6
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  1
  18P LOSS WILD-TYPE 15 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   15   22
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  18P LOSS MUTATED        0      0      2      2      0      1      0      0
  18P LOSS WILD-TYPE      4      5      4      4      8      2      5      2
                    vv
clus                 CLUS_9
  18P LOSS MUTATED        0
  18P LOSS WILD-TYPE      3
D48V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                2                  4
  CLUS_4                2                  4
  CLUS_5                0                  8
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(49) Variable = 18Q LOSS MUTATION ANALYSIS
D49V1, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    1  3
  18Q LOSS WILD-TYPE 28 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE   28   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D49V2, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    1  3
  18Q LOSS WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE   23   21
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                3                 21
[1] 2 2
[1] FALSE
D49V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    1  0
  18Q LOSS WILD-TYPE 17 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    0
  18Q LOSS WILD-TYPE   17   15
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        0      1      0
  18Q LOSS WILD-TYPE      6     14     12
D49V4, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                 32 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FA-A7DS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FA-A7Q1         TCGA-FA-A82F         TCGA-FA-A86F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6326 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6914         TCGA-GS-A9TT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GS-A9TV         TCGA-GS-A9TW         TCGA-GS-A9TX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GS-A9TZ         TCGA-GS-A9U4         TCGA-RQ-A68N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-VB-A8QN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D49V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    1  0
  18Q LOSS WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    0
  18Q LOSS WILD-TYPE   14   13
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      0      0
  18Q LOSS WILD-TYPE     12     10      5
D49V6, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                 27 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A6HO         TCGA-FF-8041 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8042         TCGA-FF-8043         TCGA-FF-8046 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6326 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G8-6906         TCGA-G8-6907         TCGA-G8-6909 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G8-6914         TCGA-GR-7351         TCGA-GR-7353 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        1      0      1      2
  18Q LOSS WILD-TYPE     13     11      9     10
D49V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 11
  CLUS_3                1                  9
  CLUS_4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q LOSS MUTATED        1      1      1      1      0
  18Q LOSS WILD-TYPE      8     11      7     11      6
D49V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                1                 11
  CLUS_5                0                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  1
  18Q LOSS WILD-TYPE 17 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    1
  18Q LOSS WILD-TYPE   17   22
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  18Q LOSS MUTATED        0      0      1      1      0      1      0      0
  18Q LOSS WILD-TYPE      4      5      5      5      8      2      5      2
                    vv
clus                 CLUS_9
  18Q LOSS MUTATED        0
  18Q LOSS WILD-TYPE      3
D49V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  5
  CLUS_3                1                  5
  CLUS_4                1                  5
  CLUS_5                0                  8
  CLUS_6                1                  2
  CLUS_7                0                  5
  CLUS_8                0                  2
  CLUS_9                0                  3
[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(50) Variable = 22Q LOSS MUTATION ANALYSIS
D50V1, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    0  3
  22Q LOSS WILD-TYPE 29 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0    3
  22Q LOSS WILD-TYPE   29   16
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 29
  CLUS_2                3                 16
[1] 2 2
[1] FALSE
D50V2, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    1  2
  22Q LOSS WILD-TYPE 23 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    2
  22Q LOSS WILD-TYPE   23   22
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                2                 22
[1] 2 2
[1] FALSE
D50V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    2  1
  22Q LOSS WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    1
  22Q LOSS WILD-TYPE   16   14
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        1      1      1
  22Q LOSS WILD-TYPE      5     14     11
D50V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                1                 14
  CLUS_3                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    1  1
  22Q LOSS WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    1
  22Q LOSS WILD-TYPE   14   12
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        1      1      0
  22Q LOSS WILD-TYPE     12      9      5
D50V6, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 26 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FF-8041         TCGA-FF-8042 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        1      1      0      1
  22Q LOSS WILD-TYPE     13     10     10     11
D50V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 10
  CLUS_3                0                 10
  CLUS_4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q LOSS MUTATED        0      1      1      0      1
  22Q LOSS WILD-TYPE      9     11      7     12      5
D50V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                 11
  CLUS_3                1                  7
  CLUS_4                0                 12
  CLUS_5                1                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    1  1
  22Q LOSS WILD-TYPE 18 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    1
  22Q LOSS WILD-TYPE   18   22
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                1                 22
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  22Q LOSS MUTATED        1      0      0      0      1      0      0      0
  22Q LOSS WILD-TYPE      3      5      6      6      7      3      5      2
                    vv
clus                 CLUS_9
  22Q LOSS MUTATED        0
  22Q LOSS WILD-TYPE      3
D50V10, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 40 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FA-A6HN         TCGA-FA-A7DS         TCGA-FA-A7Q1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FA-A86F         TCGA-FF-8041         TCGA-FF-8042 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-8046         TCGA-FF-8047         TCGA-FF-8061 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CR         TCGA-FF-A7CW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6324 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GR-7353         TCGA-GR-A4D4         TCGA-GR-A4D5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GR-A4D6         TCGA-GS-A9TQ         TCGA-GS-A9TT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GS-A9TU         TCGA-GS-A9TV         TCGA-GS-A9TW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GS-A9TX         TCGA-GS-A9U3         TCGA-GS-A9U4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-RQ-A68N         TCGA-RQ-A6JB         TCGA-RQ-AAAT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-VB-A8QN 
"22Q LOSS WILD-TYPE" 

Clustering(51) Variable = XP LOSS MUTATION ANALYSIS
D51V1, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2  3
  XP LOSS WILD-TYPE 27 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    3
  XP LOSS WILD-TYPE   27   16
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               2                27
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D51V2, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  4
  XP LOSS WILD-TYPE 23 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    4
  XP LOSS WILD-TYPE   23   20
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                23
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D51V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  2
  XP LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    2
  XP LOSS WILD-TYPE   17   13
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED        0      1      2
  XP LOSS WILD-TYPE      6     14     10
D51V4, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                14
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  2
  XP LOSS WILD-TYPE 14 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    2
  XP LOSS WILD-TYPE   14   11
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               2                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED        1      2      0
  XP LOSS WILD-TYPE     12      8      5
D51V6, multiclass
        clus
vv       XP LOSS MUTATED XP 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED        1      1      0      3
  XP LOSS WILD-TYPE     13     10     10      9
D51V7, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                10
  CLUS_3               0                10
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP LOSS MUTATED        0      0      1      1      3
  XP LOSS WILD-TYPE      9     12      7     11      3
D51V8, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                12
  CLUS_3               1                 7
  CLUS_4               1                11
  CLUS_5               3                 3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  4
  XP LOSS WILD-TYPE 18 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    4
  XP LOSS WILD-TYPE   18   19
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               4                19
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  XP LOSS MUTATED        0      0      0      0      3      0      1      0
  XP LOSS WILD-TYPE      4      5      6      6      5      3      4      2
                   vv
clus                CLUS_9
  XP LOSS MUTATED        1
  XP LOSS WILD-TYPE      2
D51V10, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               0                 6
  CLUS_4               0                 6
  CLUS_5               3                 5
  CLUS_6               0                 3
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               1                 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(52) Variable = XQ LOSS MUTATION ANALYSIS
D52V1, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  3
  XQ LOSS WILD-TYPE 28 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    3
  XQ LOSS WILD-TYPE   28   16
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                28
  CLUS_2               3                16
[1] 2 2
[1] FALSE
D52V2, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  4
  XQ LOSS WILD-TYPE 24 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    4
  XQ LOSS WILD-TYPE   24   20
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                24
  CLUS_2               4                20
[1] 2 2
[1] FALSE
D52V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  2
  XQ LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE   17   13
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        0      1      2
  XQ LOSS WILD-TYPE      6     14     10
D52V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               1                14
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, 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
D52V6, 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        1      0      0      3
  XQ LOSS WILD-TYPE     13     11     10      9
D52V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                11
  CLUS_3               0                10
  CLUS_4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED        0      0      1      0      3
  XQ LOSS WILD-TYPE      9     12      7     12      3
D52V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                12
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               3                 3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  3
  XQ LOSS WILD-TYPE 18 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    3
  XQ LOSS WILD-TYPE   18   20
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                20
[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      3      0      1      0
  XQ LOSS WILD-TYPE      4      5      6      6      5      3      4      2
                   vv
clus                CLUS_9
  XQ LOSS MUTATED        0
  XQ LOSS WILD-TYPE      3
D52V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 5
  CLUS_3               0                 6
  CLUS_4               0                 6
  CLUS_5               3                 5
  CLUS_6               0                 3
  CLUS_7               1                 4
  CLUS_8               0                 2
  CLUS_9               0                 3
[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"
