[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTMESO-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/MESO-TP/10668104/MESO-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/10013772/transformed.cor.cli.txt"

nPatients in clinical file=37, in cluster file=37, common to both=37
[1] "Reduce the number of clustering variables from 80 to 52."
[1] 52 37
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                34 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                34 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                27 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                27 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                29 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                28 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                28 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11                26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11                26 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                30 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                27 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                30 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                32 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                31 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                31 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                 31 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                 31 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 32 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 32 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 30 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                 30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                 30 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 32 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 32 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 8                 29 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 8                 29 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                 28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                 28 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 34 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 34 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 30 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 34 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 34 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 32 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 32 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 34 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 34 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                 34 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                 34 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 34 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 34 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                30 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                34 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                34 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                21 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                21 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                23 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                34 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                34 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                31 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                31 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                23 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                32 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                32 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15                22 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15                22 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                26 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                26 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 26 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 29 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 33 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 33 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                 19 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                 21 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                 21 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 31 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 31 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 34 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 34 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 33 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 33 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 28 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 28 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 34 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 34 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 32 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 32 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 28 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 28 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 34 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 34 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 30 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 34 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 34 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 31 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 31 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                29                  8 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                29                  8 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                30 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 37 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:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 37 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2  1
  1P GAIN WILD-TYPE 14 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE   14   20
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D1V2, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    0  3
  1P GAIN WILD-TYPE 20 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE   20   14
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               3                14
[1] 2 2
[1] FALSE
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    0  3
  1P GAIN WILD-TYPE 18 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE   18   15
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        0      1      2
  1P GAIN WILD-TYPE     13      9     11
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1                 9
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  1
  1P GAIN WILD-TYPE 15  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE   15    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P GAIN MUTATED        0      0      1      1      0      0      0
  1P GAIN WILD-TYPE      4      4      4      4      2      4      2
D1V6, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                24 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MQ-A6BR        TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SC-A6LM        TCGA-SC-A6LN        TCGA-SC-A6LR        TCGA-SH-A7BD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8        TCGA-TS-A7PB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  1
  1P GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE   13   11
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P GAIN MUTATED        0      0      1      1      0      0
  1P GAIN WILD-TYPE      3      4      6      5      2      4
D1V8, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                24 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MQ-A6BR        TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SC-A6LM        TCGA-SC-A6LN        TCGA-SC-A6LR        TCGA-SH-A7BD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8        TCGA-TS-A7PB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  4
  1Q GAIN WILD-TYPE 10 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    4
  1Q GAIN WILD-TYPE   10   17
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                10
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D2V2, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  4
  1Q GAIN WILD-TYPE 14 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    4
  1Q GAIN WILD-TYPE   14   13
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                14
  CLUS_2               4                13
[1] 2 2
[1] FALSE
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  4
  1Q GAIN WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    4
  1Q GAIN WILD-TYPE   12   14
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        2      4      4
  1Q GAIN WILD-TYPE     11      6      9
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               4                 6
  CLUS_3               4                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5  3
  1Q GAIN WILD-TYPE 11  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    3
  1Q GAIN WILD-TYPE   11    7
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q GAIN MUTATED        0      0      2      3      1      1      1
  1Q GAIN WILD-TYPE      4      4      3      2      1      3      1
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 4
  CLUS_3               2                 3
  CLUS_4               3                 2
  CLUS_5               1                 1
  CLUS_6               1                 3
  CLUS_7               1                 1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   5 3
  1Q GAIN WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    3
  1Q GAIN WILD-TYPE    9    9
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               3                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q GAIN MUTATED        0      0      3      4      1      0
  1Q GAIN WILD-TYPE      3      4      4      2      1      4
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               0                 4
  CLUS_3               3                 4
  CLUS_4               4                 2
  CLUS_5               1                 1
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 3P GAIN MUTATION ANALYSIS
D3V1, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    5  3
  3P GAIN WILD-TYPE 11 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    3
  3P GAIN WILD-TYPE   11   18
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D3V2, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  5
  3P GAIN WILD-TYPE 17 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    5
  3P GAIN WILD-TYPE   17   12
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               5                12
[1] 2 2
[1] FALSE
D3V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  4
  3P GAIN WILD-TYPE 14 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    4
  3P GAIN WILD-TYPE   14   14
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        2      3      3
  3P GAIN WILD-TYPE     11      7     10
D3V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               3                 7
  CLUS_3               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  3
  3P GAIN WILD-TYPE 13  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    3
  3P GAIN WILD-TYPE   13    7
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                13
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3P GAIN MUTATED        2      1      2      1      0      0      0
  3P GAIN WILD-TYPE      2      3      3      4      2      4      2
D3V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                 2
  CLUS_2               1                 3
  CLUS_3               2                 3
  CLUS_4               1                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  4
  3P GAIN WILD-TYPE 12  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    4
  3P GAIN WILD-TYPE   12    8
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               4                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P GAIN MUTATED        1      1      2      1      0      1
  3P GAIN WILD-TYPE      2      3      5      5      2      3
D3V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 2
  CLUS_2               1                 3
  CLUS_3               2                 5
  CLUS_4               1                 5
  CLUS_5               0                 2
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 3Q GAIN MUTATION ANALYSIS
D4V1, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    6  3
  3Q GAIN WILD-TYPE 10 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    3
  3Q GAIN WILD-TYPE   10   18
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                10
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D4V2, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  6
  3Q GAIN WILD-TYPE 17 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    6
  3Q GAIN WILD-TYPE   17   11
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               6                11
[1] 2 2
[1] FALSE
D4V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  5
  3Q GAIN WILD-TYPE 14 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    5
  3Q GAIN WILD-TYPE   14   13
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               5                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        3      3      3
  3Q GAIN WILD-TYPE     10      7     10
D4V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               3                 7
  CLUS_3               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  3
  3Q GAIN WILD-TYPE 12  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    3
  3Q GAIN WILD-TYPE   12    7
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3Q GAIN MUTATED        2      2      2      1      0      0      0
  3Q GAIN WILD-TYPE      2      2      3      4      2      4      2
D4V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 2
  CLUS_2               2                 2
  CLUS_3               2                 3
  CLUS_4               1                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  4
  3Q GAIN WILD-TYPE 11  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    4
  3Q GAIN WILD-TYPE   11    8
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               4                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q GAIN MUTATED        1      2      2      1      0      1
  3Q GAIN WILD-TYPE      2      2      5      5      2      3
D4V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 2
  CLUS_2               2                 2
  CLUS_3               2                 5
  CLUS_4               1                 5
  CLUS_5               0                 2
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 5P GAIN MUTATION ANALYSIS
D5V1, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7  4
  5P GAIN WILD-TYPE  9 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    4
  5P GAIN WILD-TYPE    9   17
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D5V2, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    6  5
  5P GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      6    5
  5P GAIN WILD-TYPE   14   12
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6                14
  CLUS_2               5                12
[1] 2 2
[1] FALSE
D5V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5  6
  5P GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    6
  5P GAIN WILD-TYPE   13   12
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               6                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        3      4      4
  5P GAIN WILD-TYPE     10      6      9
D5V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               4                 6
  CLUS_3               4                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                0 1
  5P GAIN MUTATED   8 1
  5P GAIN WILD-TYPE 8 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8    1
  5P GAIN WILD-TYPE    8    9
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                 8
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5P GAIN MUTATED        3      1      0      3      1      1      0
  5P GAIN WILD-TYPE      1      3      5      2      1      3      2
D5V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                 1
  CLUS_2               1                 3
  CLUS_3               0                 5
  CLUS_4               3                 2
  CLUS_5               1                 1
  CLUS_6               1                 3
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7  2
  5P GAIN WILD-TYPE  7 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    2
  5P GAIN WILD-TYPE    7   10
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7                 7
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P GAIN MUTATED        2      1      0      3      1      2
  5P GAIN WILD-TYPE      1      3      7      3      1      2
D5V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 1
  CLUS_2               1                 3
  CLUS_3               0                 7
  CLUS_4               3                 3
  CLUS_5               1                 1
  CLUS_6               2                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 5Q GAIN MUTATION ANALYSIS
D6V1, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  4
  5Q GAIN WILD-TYPE 13 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    4
  5Q GAIN WILD-TYPE   13   17
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                13
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D6V2, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  4
  5Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    4
  5Q GAIN WILD-TYPE   17   13
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               4                13
[1] 2 2
[1] FALSE
D6V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  4
  5Q GAIN WILD-TYPE 15 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    4
  5Q GAIN WILD-TYPE   15   14
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        1      3      3
  5Q GAIN WILD-TYPE     12      7     10
D6V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                 7
  CLUS_3               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5  0
  5Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    0
  5Q GAIN WILD-TYPE   11   10
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q GAIN MUTATED        2      0      0      2      1      0      0
  5Q GAIN WILD-TYPE      2      4      5      3      1      4      2
D6V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                 2
  CLUS_2               0                 4
  CLUS_3               0                 5
  CLUS_4               2                 3
  CLUS_5               1                 1
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  1
  5Q GAIN WILD-TYPE 10 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    1
  5Q GAIN WILD-TYPE   10   11
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q GAIN MUTATED        1      0      0      2      1      1
  5Q GAIN WILD-TYPE      2      4      7      4      1      3
D6V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                 2
  CLUS_2               0                 4
  CLUS_3               0                 7
  CLUS_4               2                 4
  CLUS_5               1                 1
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 7P GAIN MUTATION ANALYSIS
D7V1, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    7  3
  7P GAIN WILD-TYPE  9 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7    3
  7P GAIN WILD-TYPE    9   18
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D7V2, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  5
  7P GAIN WILD-TYPE 15 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    5
  7P GAIN WILD-TYPE   15   12
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                15
  CLUS_2               5                12
[1] 2 2
[1] FALSE
D7V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  5
  7P GAIN WILD-TYPE 13 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    5
  7P GAIN WILD-TYPE   13   13
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               5                13
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        4      4      2
  7P GAIN WILD-TYPE      9      6     11
D7V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               4                 6
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                0 1
  7P GAIN MUTATED   7 1
  7P GAIN WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7    1
  7P GAIN WILD-TYPE    9    9
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P GAIN MUTATED        3      1      1      3      0      0      0
  7P GAIN WILD-TYPE      1      3      4      2      2      4      2
D7V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 1
  CLUS_2               1                 3
  CLUS_3               1                 4
  CLUS_4               3                 2
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6  2
  7P GAIN WILD-TYPE  8 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6    2
  7P GAIN WILD-TYPE    8   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P GAIN MUTATED        2      1      1      3      0      1
  7P GAIN WILD-TYPE      1      3      6      3      2      3
D7V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 1
  CLUS_2               1                 3
  CLUS_3               1                 6
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 7Q GAIN MUTATION ANALYSIS
D8V1, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  3
  7Q GAIN WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE   12   18
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D8V2, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  4
  7Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    4
  7Q GAIN WILD-TYPE   17   13
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               4                13
[1] 2 2
[1] FALSE
D8V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  3
  7Q GAIN WILD-TYPE 14 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE   14   15
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        4      2      1
  7Q GAIN WILD-TYPE      9      8     12
D8V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               2                 8
  CLUS_3               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5  1
  7Q GAIN WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    1
  7Q GAIN WILD-TYPE   11    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7Q GAIN MUTATED        3      1      1      1      0      0      0
  7Q GAIN WILD-TYPE      1      3      4      4      2      4      2
D8V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 1
  CLUS_2               1                 3
  CLUS_3               1                 4
  CLUS_4               1                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  2
  7Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    2
  7Q GAIN WILD-TYPE   10   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q GAIN MUTATED        2      1      1      1      0      1
  7Q GAIN WILD-TYPE      1      3      6      5      2      3
D8V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 1
  CLUS_2               1                 3
  CLUS_3               1                 6
  CLUS_4               1                 5
  CLUS_5               0                 2
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 8P GAIN MUTATION ANALYSIS
D9V1, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  3
  8P GAIN WILD-TYPE 14 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    3
  8P GAIN WILD-TYPE   14   18
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D9V2, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    3  2
  8P GAIN WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    2
  8P GAIN WILD-TYPE   17   15
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               2                15
[1] 2 2
[1] FALSE
D9V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  3
  8P GAIN WILD-TYPE 16 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    3
  8P GAIN WILD-TYPE   16   15
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        1      2      2
  8P GAIN WILD-TYPE     12      8     11
D9V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                 8
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  1
  8P GAIN WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    1
  8P GAIN WILD-TYPE   12    9
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED        2      0      1      2      0      0      0
  8P GAIN WILD-TYPE      2      4      4      3      2      4      2
D9V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                 2
  CLUS_2               0                 4
  CLUS_3               1                 4
  CLUS_4               2                 3
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  1
  8P GAIN WILD-TYPE 10 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    1
  8P GAIN WILD-TYPE   10   11
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P GAIN MUTATED        2      0      1      2      0      0
  8P GAIN WILD-TYPE      1      4      6      4      2      4
D9V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                 1
  CLUS_2               0                 4
  CLUS_3               1                 6
  CLUS_4               2                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 8Q GAIN MUTATION ANALYSIS
D10V1, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2  4
  8Q GAIN WILD-TYPE 14 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    4
  8Q GAIN WILD-TYPE   14   17
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D10V2, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    3  3
  8Q GAIN WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    3
  8Q GAIN WILD-TYPE   17   14
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               3                14
[1] 2 2
[1] FALSE
D10V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2  4
  8Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    4
  8Q GAIN WILD-TYPE   16   14
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        1      2      3
  8Q GAIN WILD-TYPE     12      8     10
D10V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                 8
  CLUS_3               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4  2
  8Q GAIN WILD-TYPE 12  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    2
  8Q GAIN WILD-TYPE   12    8
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q GAIN MUTATED        2      0      2      2      0      0      0
  8Q GAIN WILD-TYPE      2      4      3      3      2      4      2
D10V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                 2
  CLUS_2               0                 4
  CLUS_3               2                 3
  CLUS_4               2                 3
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4  2
  8Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    2
  8Q GAIN WILD-TYPE   10   10
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q GAIN MUTATED        2      0      2      2      0      0
  8Q GAIN WILD-TYPE      1      4      5      4      2      4
D10V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                 1
  CLUS_2               0                 4
  CLUS_3               2                 5
  CLUS_4               2                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 11P GAIN MUTATION ANALYSIS
D11V1, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  2
  11P GAIN WILD-TYPE 12 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    2
  11P GAIN WILD-TYPE   12   19
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D11V2, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  3
  11P GAIN WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    3
  11P GAIN WILD-TYPE   17   14
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                3                 14
[1] 2 2
[1] FALSE
D11V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  2
  11P GAIN WILD-TYPE 14 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    2
  11P GAIN WILD-TYPE   14   16
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        2      3      1
  11P GAIN WILD-TYPE     11      7     12
D11V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                3                  7
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 13 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   13   10
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P GAIN MUTATED        2      0      0      1      0      0      0
  11P GAIN WILD-TYPE      2      4      5      4      2      4      2
D11V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                0                  4
  CLUS_3                0                  5
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  1
  11P GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    1
  11P GAIN WILD-TYPE   12   11
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P GAIN MUTATED        1      0      0      1      0      1
  11P GAIN WILD-TYPE      2      4      7      5      2      3
D11V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                0                  4
  CLUS_3                0                  7
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 11Q GAIN MUTATION ANALYSIS
D12V1, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 13 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE   13   19
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D12V2, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 17 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE   17   15
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D12V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 15 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE   15   16
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        1      4      0
  11Q GAIN WILD-TYPE     12      6     13
D12V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                4                  6
  CLUS_3                0                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  0
  11Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE   12   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q GAIN MUTATED        2      0      0      1      1      0      0
  11Q GAIN WILD-TYPE      2      4      5      4      1      4      2
D12V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                0                  4
  CLUS_3                0                  5
  CLUS_4                1                  4
  CLUS_5                1                  1
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  1
  11Q GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    1
  11Q GAIN WILD-TYPE   11   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q GAIN MUTATED        1      0      0      1      1      1
  11Q GAIN WILD-TYPE      2      4      7      5      1      3
D12V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                0                  4
  CLUS_3                0                  7
  CLUS_4                1                  5
  CLUS_5                1                  1
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 12P GAIN MUTATION ANALYSIS
D13V1, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    6  1
  12P GAIN WILD-TYPE 10 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6    1
  12P GAIN WILD-TYPE   10   20
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D13V2, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  4
  12P GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    4
  12P GAIN WILD-TYPE   17   13
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D13V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    4  3
  12P GAIN WILD-TYPE 14 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    3
  12P GAIN WILD-TYPE   14   15
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        4      2      1
  12P GAIN WILD-TYPE      9      8     12
D13V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                2                  8
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  2
  12P GAIN WILD-TYPE 14  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    2
  12P GAIN WILD-TYPE   14    8
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12P GAIN MUTATED        2      1      1      0      0      0      0
  12P GAIN WILD-TYPE      2      3      4      5      2      4      2
D13V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                0                  5
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  3
  12P GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    3
  12P GAIN WILD-TYPE   13    9
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P GAIN MUTATED        1      1      1      0      0      1
  12P GAIN WILD-TYPE      2      3      6      6      2      3
D13V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                0                  6
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 12Q GAIN MUTATION ANALYSIS
D14V1, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    6  1
  12Q GAIN WILD-TYPE 10 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6    1
  12Q GAIN WILD-TYPE   10   20
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D14V2, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  4
  12Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    4
  12Q GAIN WILD-TYPE   17   13
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D14V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    4  3
  12Q GAIN WILD-TYPE 14 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    3
  12Q GAIN WILD-TYPE   14   15
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        4      2      1
  12Q GAIN WILD-TYPE      9      8     12
D14V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                2                  8
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 14  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   14    8
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q GAIN MUTATED        2      1      1      0      0      0      0
  12Q GAIN WILD-TYPE      2      3      4      5      2      4      2
D14V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                0                  5
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE   13    9
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q GAIN MUTATED        1      1      1      0      0      1
  12Q GAIN WILD-TYPE      2      3      6      6      2      3
D14V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                0                  6
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 15Q GAIN MUTATION ANALYSIS
D15V1, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4  1
  15Q GAIN WILD-TYPE 12 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    1
  15Q GAIN WILD-TYPE   12   20
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D15V2, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4  1
  15Q GAIN WILD-TYPE 16 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    1
  15Q GAIN WILD-TYPE   16   16
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                1                 16
[1] 2 2
[1] FALSE
D15V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    2  3
  15Q GAIN WILD-TYPE 16 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    3
  15Q GAIN WILD-TYPE   16   15
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        0      4      1
  15Q GAIN WILD-TYPE     13      6     12
D15V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                  6
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  1
  15Q GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    1
  15Q GAIN WILD-TYPE   13    9
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q GAIN MUTATED        1      0      1      1      0      1      0
  15Q GAIN WILD-TYPE      3      4      4      4      2      3      2
D15V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  1
  15Q GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    1
  15Q GAIN WILD-TYPE   11   11
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q GAIN MUTATED        1      0      1      2      0      0
  15Q GAIN WILD-TYPE      2      4      6      4      2      4
D15V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                0                  4
  CLUS_3                1                  6
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 16P GAIN MUTATION ANALYSIS
D16V1, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  3
  16P GAIN WILD-TYPE 11 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    3
  16P GAIN WILD-TYPE   11   18
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                3                 18
[1] 2 2
[1] FALSE
D16V2, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  4
  16P GAIN WILD-TYPE 16 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    4
  16P GAIN WILD-TYPE   16   13
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D16V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  5
  16P GAIN WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    5
  16P GAIN WILD-TYPE   15   13
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        0      6      2
  16P GAIN WILD-TYPE     13      4     11
D16V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                6                  4
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE 11  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    2
  16P GAIN WILD-TYPE   11    8
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P GAIN MUTATED        1      0      2      3      1      0      0
  16P GAIN WILD-TYPE      3      4      3      2      1      4      2
D16V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                2                  3
  CLUS_4                3                  2
  CLUS_5                1                  1
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE  9 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    2
  16P GAIN WILD-TYPE    9   10
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P GAIN MUTATED        1      0      2      3      1      0
  16P GAIN WILD-TYPE      2      4      5      3      1      4
D16V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                0                  4
  CLUS_3                2                  5
  CLUS_4                3                  3
  CLUS_5                1                  1
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 16Q GAIN MUTATION ANALYSIS
D17V1, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6  3
  16Q GAIN WILD-TYPE 10 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    3
  16Q GAIN WILD-TYPE   10   18
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                3                 18
[1] 2 2
[1] FALSE
D17V2, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  5
  16Q GAIN WILD-TYPE 16 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    5
  16Q GAIN WILD-TYPE   16   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                5                 12
[1] 2 2
[1] FALSE
D17V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  6
  16Q GAIN WILD-TYPE 15 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    6
  16Q GAIN WILD-TYPE   15   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        1      6      2
  16Q GAIN WILD-TYPE     12      4     11
D17V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                6                  4
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6  2
  16Q GAIN WILD-TYPE 10  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    2
  16Q GAIN WILD-TYPE   10    8
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        1      1      2      3      1      0      0
  16Q GAIN WILD-TYPE      3      3      3      2      1      4      2
D17V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  3
  CLUS_3                2                  3
  CLUS_4                3                  2
  CLUS_5                1                  1
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6  2
  16Q GAIN WILD-TYPE  8 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    2
  16Q GAIN WILD-TYPE    8   10
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q GAIN MUTATED        1      1      2      3      1      0
  16Q GAIN WILD-TYPE      2      3      5      3      1      4
D17V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                1                  3
  CLUS_3                2                  5
  CLUS_4                3                  3
  CLUS_5                1                  1
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 17P GAIN MUTATION ANALYSIS
D18V1, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  0
  17P GAIN WILD-TYPE 13 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    0
  17P GAIN WILD-TYPE   13   21
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                0                 21
[1] 2 2
[1] FALSE
D18V2, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  3
  17P GAIN WILD-TYPE 20 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    3
  17P GAIN WILD-TYPE   20   14
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                3                 14
[1] 2 2
[1] FALSE
D18V3, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  3
  17P GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    3
  17P GAIN WILD-TYPE   18   15
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        0      2      1
  17P GAIN WILD-TYPE     13      8     12
D18V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                  8
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  1
  17P GAIN WILD-TYPE 16  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    1
  17P GAIN WILD-TYPE   16    9
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P GAIN MUTATED        0      0      1      0      0      0      0
  17P GAIN WILD-TYPE      4      4      4      5      2      4      2
D18V6, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 25 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-NQ-A638         TCGA-SC-A6LM         TCGA-SC-A6LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BD         TCGA-SH-A7BH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-TS-A7OY         TCGA-TS-A7P0         TCGA-TS-A7P8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-TS-A7PB 
"17P GAIN WILD-TYPE" 
D18V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  1
  17P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    1
  17P GAIN WILD-TYPE   14   11
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P GAIN MUTATED        0      0      1      0      0      0
  17P GAIN WILD-TYPE      3      4      6      6      2      4
D18V8, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 25 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-NQ-A638         TCGA-SC-A6LM         TCGA-SC-A6LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BD         TCGA-SH-A7BH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-TS-A7OY         TCGA-TS-A7P0         TCGA-TS-A7P8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-TS-A7PB 
"17P GAIN WILD-TYPE" 

Clustering(19) Variable = 17Q GAIN MUTATION ANALYSIS
D19V1, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    6  1
  17Q GAIN WILD-TYPE 10 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    1
  17Q GAIN WILD-TYPE   10   20
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D19V2, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4  3
  17Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    3
  17Q GAIN WILD-TYPE   16   14
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                3                 14
[1] 2 2
[1] FALSE
D19V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4  3
  17Q GAIN WILD-TYPE 14 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    3
  17Q GAIN WILD-TYPE   14   15
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      5      1
  17Q GAIN WILD-TYPE     12      5     12
D19V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                5                  5
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  1
  17Q GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    1
  17Q GAIN WILD-TYPE   13    9
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q GAIN MUTATED        2      0      1      1      0      0      0
  17Q GAIN WILD-TYPE      2      4      4      4      2      4      2
D19V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                0                  4
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  1
  17Q GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    1
  17Q GAIN WILD-TYPE   11   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q GAIN MUTATED        2      0      1      1      0      0
  17Q GAIN WILD-TYPE      1      4      6      5      2      4
D19V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                  1
  CLUS_2                0                  4
  CLUS_3                1                  6
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 18P GAIN MUTATION ANALYSIS
D20V1, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  1
  18P GAIN WILD-TYPE 14 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE   14   20
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D20V2, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   19   15
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D20V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    0  3
  18P GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    3
  18P GAIN WILD-TYPE   18   15
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        0      1      2
  18P GAIN WILD-TYPE     13      9     11
D20V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  0
  18P GAIN WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    0
  18P GAIN WILD-TYPE   14   10
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P GAIN MUTATED        0      0      0      2      0      0      0
  18P GAIN WILD-TYPE      4      4      5      3      2      4      2
D20V6, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-NQ-A638         TCGA-SC-A6LM         TCGA-SC-A6LN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BC         TCGA-SH-A7BD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-TS-A7OY         TCGA-TS-A7P8         TCGA-TS-A7PB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D20V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  0
  18P GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    0
  18P GAIN WILD-TYPE   12   12
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P GAIN MUTATED        0      0      0      2      0      0
  18P GAIN WILD-TYPE      3      4      7      4      2      4
D20V8, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-NQ-A638         TCGA-SC-A6LM         TCGA-SC-A6LN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BC         TCGA-SH-A7BD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-TS-A7OY         TCGA-TS-A7P8         TCGA-TS-A7PB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 

Clustering(21) Variable = 19P GAIN MUTATION ANALYSIS
D21V1, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  2
  19P GAIN WILD-TYPE 13 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    2
  19P GAIN WILD-TYPE   13   19
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D21V2, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  2
  19P GAIN WILD-TYPE 17 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    2
  19P GAIN WILD-TYPE   17   15
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D21V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  3
  19P GAIN WILD-TYPE 16 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    3
  19P GAIN WILD-TYPE   16   15
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      2      3
  19P GAIN WILD-TYPE     13      8     10
D21V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                  8
  CLUS_3                3                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  1
  19P GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    1
  19P GAIN WILD-TYPE   13    9
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P GAIN MUTATED        1      0      0      2      0      1      0
  19P GAIN WILD-TYPE      3      4      5      3      2      3      2
D21V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                0                  5
  CLUS_4                2                  3
  CLUS_5                0                  2
  CLUS_6                1                  3
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  1
  19P GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    1
  19P GAIN WILD-TYPE   11   11
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P GAIN MUTATED        1      0      0      2      0      1
  19P GAIN WILD-TYPE      2      4      7      4      2      3
D21V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                0                  4
  CLUS_3                0                  7
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 19Q GAIN MUTATION ANALYSIS
D22V1, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 14 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   14   20
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D22V2, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    2
  19Q GAIN WILD-TYPE   19   15
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D22V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 17 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    2
  19Q GAIN WILD-TYPE   17   16
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      1      2
  19Q GAIN WILD-TYPE     13      9     11
D22V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  0
  19Q GAIN WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    0
  19Q GAIN WILD-TYPE   14   10
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q GAIN MUTATED        0      0      0      2      0      0      0
  19Q GAIN WILD-TYPE      4      4      5      3      2      4      2
D22V6, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-TS-A7OY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D22V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  0
  19Q GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    0
  19Q GAIN WILD-TYPE   12   12
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q GAIN MUTATED        0      0      0      2      0      0
  19Q GAIN WILD-TYPE      3      4      7      4      2      4
D22V8, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-NQ-A57I 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-TS-A7OY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 

Clustering(23) Variable = 20P GAIN MUTATION ANALYSIS
D23V1, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  2
  20P GAIN WILD-TYPE 15 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    2
  20P GAIN WILD-TYPE   15   19
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D23V2, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  2
  20P GAIN WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    2
  20P GAIN WILD-TYPE   19   15
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D23V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  2
  20P GAIN WILD-TYPE 17 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    2
  20P GAIN WILD-TYPE   17   16
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        0      1      2
  20P GAIN WILD-TYPE     13      9     11
D23V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  1
  20P GAIN WILD-TYPE 15  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    1
  20P GAIN WILD-TYPE   15    9
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P GAIN MUTATED        0      1      1      0      0      0      0
  20P GAIN WILD-TYPE      4      3      4      5      2      4      2
D23V6, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BR 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A6BS         TCGA-NQ-A638         TCGA-SC-A6LM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
D23V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  1
  20P GAIN WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    1
  20P GAIN WILD-TYPE   13   11
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P GAIN MUTATED        0      1      1      0      0      0
  20P GAIN WILD-TYPE      3      3      6      6      2      4
D23V8, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BR 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MQ-A6BS         TCGA-NQ-A638         TCGA-SC-A6LM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 

Clustering(24) Variable = 20Q GAIN MUTATION ANALYSIS
D24V1, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    1  2
  20Q GAIN WILD-TYPE 15 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1    2
  20Q GAIN WILD-TYPE   15   19
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D24V2, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    1  2
  20Q GAIN WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1    2
  20Q GAIN WILD-TYPE   19   15
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D24V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    0  3
  20Q GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    3
  20Q GAIN WILD-TYPE   18   15
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        0      1      2
  20Q GAIN WILD-TYPE     13      9     11
D24V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  1
  20Q GAIN WILD-TYPE 14  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    1
  20Q GAIN WILD-TYPE   14    9
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q GAIN MUTATED        0      1      1      1      0      0      0
  20Q GAIN WILD-TYPE      4      3      4      4      2      4      2
D24V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  1
  20Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    1
  20Q GAIN WILD-TYPE   12   11
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q GAIN MUTATED        0      1      1      1      0      0
  20Q GAIN WILD-TYPE      3      3      6      5      2      4
D24V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 1P LOSS MUTATION ANALYSIS
D25V1, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    5  2
  1P LOSS WILD-TYPE 11 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    2
  1P LOSS WILD-TYPE   11   19
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               2                19
[1] 2 2
[1] FALSE
D25V2, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  3
  1P LOSS WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    3
  1P LOSS WILD-TYPE   16   14
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                16
  CLUS_2               3                14
[1] 2 2
[1] FALSE
D25V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  3
  1P LOSS WILD-TYPE 14 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    3
  1P LOSS WILD-TYPE   14   15
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      3      3
  1P LOSS WILD-TYPE     12      7     10
D25V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                 7
  CLUS_3               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    5  1
  1P LOSS WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    1
  1P LOSS WILD-TYPE   11    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P LOSS MUTATED        1      1      1      2      0      1      0
  1P LOSS WILD-TYPE      3      3      4      3      2      3      2
D25V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 3
  CLUS_3               1                 4
  CLUS_4               2                 3
  CLUS_5               0                 2
  CLUS_6               1                 3
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  2
  1P LOSS WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    2
  1P LOSS WILD-TYPE   10   10
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P LOSS MUTATED        0      1      1      3      0      1
  1P LOSS WILD-TYPE      3      3      6      3      2      3
D25V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               1                 3
  CLUS_3               1                 6
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 2Q LOSS MUTATION ANALYSIS
D26V1, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  1
  2Q LOSS WILD-TYPE 14 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    1
  2Q LOSS WILD-TYPE   14   20
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D26V2, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  2
  2Q LOSS WILD-TYPE 19 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   19   15
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                15
[1] 2 2
[1] FALSE
D26V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  2
  2Q LOSS WILD-TYPE 17 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   17   16
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        1      1      1
  2Q LOSS WILD-TYPE     12      9     12
D26V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                 9
  CLUS_3               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE 13 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE   13   10
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2Q LOSS MUTATED        0      1      0      2      0      0      0
  2Q LOSS WILD-TYPE      4      3      5      3      2      4      2
D26V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                 3
  CLUS_3               0                 5
  CLUS_4               2                 3
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE 11 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE   11   12
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               0                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q LOSS MUTATED        0      1      0      2      0      0
  2Q LOSS WILD-TYPE      3      3      7      4      2      4
D26V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               1                 3
  CLUS_3               0                 7
  CLUS_4               2                 4
  CLUS_5               0                 2
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 4P LOSS MUTATION ANALYSIS
D27V1, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   10  6
  4P LOSS WILD-TYPE  6 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10    6
  4P LOSS WILD-TYPE    6   15
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              10                 6
  CLUS_2               6                15
[1] 2 2
[1] FALSE
D27V2, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  8
  4P LOSS WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    8
  4P LOSS WILD-TYPE   12    9
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               8                12
  CLUS_2               8                 9
[1] 2 2
[1] FALSE
D27V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    6 10
  4P LOSS WILD-TYPE 12  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   10
  4P LOSS WILD-TYPE   12    8
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                12
  CLUS_2              10                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        2      6      8
  4P LOSS WILD-TYPE     11      4      5
D27V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               6                 4
  CLUS_3               8                 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"
D27V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   10  4
  4P LOSS WILD-TYPE  6  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10    4
  4P LOSS WILD-TYPE    6    6
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              10                 6
  CLUS_2               4                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4P LOSS MUTATED        1      3      2      5      1      2      0
  4P LOSS WILD-TYPE      3      1      3      0      1      2      2
D27V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               3                 1
  CLUS_3               2                 3
  CLUS_4               5                 0
  CLUS_5               1                 1
  CLUS_6               2                 2
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                   cls
clus                0 1
  4P LOSS MUTATED   9 5
  4P LOSS WILD-TYPE 5 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9    5
  4P LOSS WILD-TYPE    5    7
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                 5
  CLUS_2               5                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P LOSS MUTATED        0      3      2      6      1      2
  4P LOSS WILD-TYPE      3      1      5      0      1      2
D27V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               3                 1
  CLUS_3               2                 5
  CLUS_4               6                 0
  CLUS_5               1                 1
  CLUS_6               2                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 4Q LOSS MUTATION ANALYSIS
D28V1, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8  6
  4Q LOSS WILD-TYPE  8 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    6
  4Q LOSS WILD-TYPE    8   15
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                 8
  CLUS_2               6                15
[1] 2 2
[1] FALSE
D28V2, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    6  8
  4Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6    8
  4Q LOSS WILD-TYPE   14    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               6                14
  CLUS_2               8                 9
[1] 2 2
[1] FALSE
D28V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4 10
  4Q LOSS WILD-TYPE 14  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   10
  4Q LOSS WILD-TYPE   14    8
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2              10                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        1      5      8
  4Q LOSS WILD-TYPE     12      5      5
D28V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               5                 5
  CLUS_3               8                 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"
D28V5, binary
                   cls
clus                0 1
  4Q LOSS MUTATED   8 4
  4Q LOSS WILD-TYPE 8 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    4
  4Q LOSS WILD-TYPE    8    6
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                 8
  CLUS_2               4                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4Q LOSS MUTATED        0      3      2      4      1      2      0
  4Q LOSS WILD-TYPE      4      1      3      1      1      2      2
D28V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               3                 1
  CLUS_3               2                 3
  CLUS_4               4                 1
  CLUS_5               1                 1
  CLUS_6               2                 2
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                   cls
clus                0 1
  4Q LOSS MUTATED   8 4
  4Q LOSS WILD-TYPE 6 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    4
  4Q LOSS WILD-TYPE    6    8
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2               4                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q LOSS MUTATED        0      3      2      5      1      1
  4Q LOSS WILD-TYPE      3      1      5      1      1      3
D28V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               3                 1
  CLUS_3               2                 5
  CLUS_4               5                 1
  CLUS_5               1                 1
  CLUS_6               1                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 5Q LOSS MUTATION ANALYSIS
D29V1, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  1
  5Q LOSS WILD-TYPE 14 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    1
  5Q LOSS WILD-TYPE   14   20
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D29V2, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  2
  5Q LOSS WILD-TYPE 19 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    2
  5Q LOSS WILD-TYPE   19   15
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                15
[1] 2 2
[1] FALSE
D29V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  2
  5Q LOSS WILD-TYPE 17 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    2
  5Q LOSS WILD-TYPE   17   16
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        1      0      2
  5Q LOSS WILD-TYPE     12     10     11
D29V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                10
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  1
  5Q LOSS WILD-TYPE 15  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    1
  5Q LOSS WILD-TYPE   15    9
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q LOSS MUTATED        0      0      1      0      0      1      0
  5Q LOSS WILD-TYPE      4      4      4      5      2      3      2
D29V6, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                24 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A6BL        TCGA-MQ-A6BR 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SC-A6LR        TCGA-SH-A7BC        TCGA-SH-A7BD        TCGA-SH-A7BH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8        TCGA-TS-A7PB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D29V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  1
  5Q LOSS WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    1
  5Q LOSS WILD-TYPE   13   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q LOSS MUTATED        0      0      1      1      0      0
  5Q LOSS WILD-TYPE      3      4      6      5      2      4
D29V8, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                24 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A6BL        TCGA-MQ-A6BR 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SC-A6LR        TCGA-SH-A7BC        TCGA-SH-A7BD        TCGA-SH-A7BH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8        TCGA-TS-A7PB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 

Clustering(30) Variable = 6P LOSS MUTATION ANALYSIS
D30V1, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5  1
  6P LOSS WILD-TYPE 11 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    1
  6P LOSS WILD-TYPE   11   20
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D30V2, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3  3
  6P LOSS WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    3
  6P LOSS WILD-TYPE   17   14
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                17
  CLUS_2               3                14
[1] 2 2
[1] FALSE
D30V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2  4
  6P LOSS WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    4
  6P LOSS WILD-TYPE   16   14
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        0      4      2
  6P LOSS WILD-TYPE     13      6     11
D30V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               4                 6
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3  1
  6P LOSS WILD-TYPE 13  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    1
  6P LOSS WILD-TYPE   13    9
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6P LOSS MUTATED        0      0      1      3      0      0      0
  6P LOSS WILD-TYPE      4      4      4      2      2      4      2
D30V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 4
  CLUS_3               1                 4
  CLUS_4               3                 2
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3  1
  6P LOSS WILD-TYPE 11 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    1
  6P LOSS WILD-TYPE   11   11
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                11
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P LOSS MUTATED        0      0      1      3      0      0
  6P LOSS WILD-TYPE      3      4      6      3      2      4
D30V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               0                 4
  CLUS_3               1                 6
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 6Q LOSS MUTATION ANALYSIS
D31V1, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    7  7
  6Q LOSS WILD-TYPE  9 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7    7
  6Q LOSS WILD-TYPE    9   14
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               7                14
[1] 2 2
[1] FALSE
D31V2, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    6  8
  6Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6    8
  6Q LOSS WILD-TYPE   14    9
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                14
  CLUS_2               8                 9
[1] 2 2
[1] FALSE
D31V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    6  8
  6Q LOSS WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6    8
  6Q LOSS WILD-TYPE   12   10
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                12
  CLUS_2               8                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        5      5      4
  6Q LOSS WILD-TYPE      8      5      9
D31V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                 8
  CLUS_2               5                 5
  CLUS_3               4                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5  3
  6Q LOSS WILD-TYPE 11  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    3
  6Q LOSS WILD-TYPE   11    7
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED        0      2      3      3      0      0      0
  6Q LOSS WILD-TYPE      4      2      2      2      2      4      2
D31V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 2
  CLUS_3               3                 2
  CLUS_4               3                 2
  CLUS_5               0                 2
  CLUS_6               0                 4
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                   cls
clus                0 1
  6Q LOSS MUTATED   5 3
  6Q LOSS WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    3
  6Q LOSS WILD-TYPE    9    9
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               3                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q LOSS MUTATED        0      2      3      3      0      0
  6Q LOSS WILD-TYPE      3      2      4      3      2      4
D31V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               2                 2
  CLUS_3               3                 4
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               0                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 8P LOSS MUTATION ANALYSIS
D32V1, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2  3
  8P LOSS WILD-TYPE 14 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    3
  8P LOSS WILD-TYPE   14   18
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                18
[1] 2 2
[1] FALSE
D32V2, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  2
  8P LOSS WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    2
  8P LOSS WILD-TYPE   17   15
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                17
  CLUS_2               2                15
[1] 2 2
[1] FALSE
D32V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  1
  8P LOSS WILD-TYPE 14 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    1
  8P LOSS WILD-TYPE   14   17
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        3      1      1
  8P LOSS WILD-TYPE     10      9     12
D32V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                 9
  CLUS_3               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  0
  8P LOSS WILD-TYPE 15 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    0
  8P LOSS WILD-TYPE   15   10
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P LOSS MUTATED        0      0      0      1      0      0      0
  8P LOSS WILD-TYPE      4      4      5      4      2      4      2
D32V6, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                25 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LJ        TCGA-MQ-A4LM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL        TCGA-MQ-A6BR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LR        TCGA-SH-A7BC        TCGA-SH-A7BD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SH-A7BH        TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-TS-A7PB 
"8P LOSS WILD-TYPE" 
D32V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  0
  8P LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    0
  8P LOSS WILD-TYPE   13   12
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                12
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P LOSS MUTATED        0      0      0      1      0      0
  8P LOSS WILD-TYPE      3      4      7      5      2      4
D32V8, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                25 
       TCGA-LK-A4NW        TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-LK-A4O6        TCGA-LK-A4O7        TCGA-MQ-A4LJ        TCGA-MQ-A4LM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL        TCGA-MQ-A6BR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LR        TCGA-SH-A7BC        TCGA-SH-A7BD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SH-A7BH        TCGA-TS-A7OY        TCGA-TS-A7P0        TCGA-TS-A7P8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-TS-A7PB 
"8P LOSS WILD-TYPE" 

Clustering(33) Variable = 9P LOSS MUTATION ANALYSIS
D33V1, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   11  4
  9P LOSS WILD-TYPE  5 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11    4
  9P LOSS WILD-TYPE    5   17
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                 5
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D33V2, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8  7
  9P LOSS WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8    7
  9P LOSS WILD-TYPE   12   10
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                12
  CLUS_2               7                10
[1] 2 2
[1] FALSE
D33V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    4 11
  9P LOSS WILD-TYPE 14  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4   11
  9P LOSS WILD-TYPE   14    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2              11                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        1      6      8
  9P LOSS WILD-TYPE     12      4      5
D33V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               6                 4
  CLUS_3               8                 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"
D33V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  6
  9P LOSS WILD-TYPE 10  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    6
  9P LOSS WILD-TYPE   10    4
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               6                10
  CLUS_2               6                 4
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P LOSS MUTATED        1      1      4      3      0      3      0
  9P LOSS WILD-TYPE      3      3      1      2      2      1      2
D33V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 3
  CLUS_3               4                 1
  CLUS_4               3                 2
  CLUS_5               0                 2
  CLUS_6               3                 1
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                   cls
clus                0 1
  9P LOSS MUTATED   5 7
  9P LOSS WILD-TYPE 9 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5    7
  9P LOSS WILD-TYPE    9    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               7                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P LOSS MUTATED        0      1      4      4      0      3
  9P LOSS WILD-TYPE      3      3      3      2      2      1
D33V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               1                 3
  CLUS_3               4                 3
  CLUS_4               4                 2
  CLUS_5               0                 2
  CLUS_6               3                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 9Q LOSS MUTATION ANALYSIS
D34V1, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    7  4
  9Q LOSS WILD-TYPE  9 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7    4
  9Q LOSS WILD-TYPE    9   17
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               4                17
[1] 2 2
[1] FALSE
D34V2, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5  6
  9Q LOSS WILD-TYPE 15 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    6
  9Q LOSS WILD-TYPE   15   11
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                15
  CLUS_2               6                11
[1] 2 2
[1] FALSE
D34V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3  8
  9Q LOSS WILD-TYPE 15 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    8
  9Q LOSS WILD-TYPE   15   10
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               8                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        1      4      6
  9Q LOSS WILD-TYPE     12      6      7
D34V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               4                 6
  CLUS_3               6                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5  5
  9Q LOSS WILD-TYPE 11  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    5
  9Q LOSS WILD-TYPE   11    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               5                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q LOSS MUTATED        1      1      4      3      0      1      0
  9Q LOSS WILD-TYPE      3      3      1      2      2      3      2
D34V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               1                 3
  CLUS_3               4                 1
  CLUS_4               3                 2
  CLUS_5               0                 2
  CLUS_6               1                 3
  CLUS_7               0                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4  6
  9Q LOSS WILD-TYPE 10  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    6
  9Q LOSS WILD-TYPE   10    6
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               6                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q LOSS MUTATED        0      1      4      3      0      2
  9Q LOSS WILD-TYPE      3      3      3      3      2      2
D34V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               1                 3
  CLUS_3               4                 3
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               2                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 10P LOSS MUTATION ANALYSIS
D35V1, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    7  4
  10P LOSS WILD-TYPE  9 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7    4
  10P LOSS WILD-TYPE    9   17
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                  9
  CLUS_2                4                 17
[1] 2 2
[1] FALSE
D35V2, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    6  5
  10P LOSS WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    5
  10P LOSS WILD-TYPE   14   12
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                 14
  CLUS_2                5                 12
[1] 2 2
[1] FALSE
D35V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    4  7
  10P LOSS WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    7
  10P LOSS WILD-TYPE   14   11
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        2      5      4
  10P LOSS WILD-TYPE     11      5      9
D35V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                5                  5
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    6  4
  10P LOSS WILD-TYPE 10  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    4
  10P LOSS WILD-TYPE   10    6
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                4                  6
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10P LOSS MUTATED        1      0      2      4      0      2      1
  10P LOSS WILD-TYPE      3      4      3      1      2      2      1
D35V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                2                  3
  CLUS_4                4                  1
  CLUS_5                0                  2
  CLUS_6                2                  2
  CLUS_7                1                  1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    4  6
  10P LOSS WILD-TYPE 10  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    6
  10P LOSS WILD-TYPE   10    6
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                6                  6
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P LOSS MUTATED        0      0      3      4      0      3
  10P LOSS WILD-TYPE      3      4      4      2      2      1
D35V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                3                  4
  CLUS_4                4                  2
  CLUS_5                0                  2
  CLUS_6                3                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 10Q LOSS MUTATION ANALYSIS
D36V1, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4  4
  10Q LOSS WILD-TYPE 12 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    4
  10Q LOSS WILD-TYPE   12   17
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                4                 17
[1] 2 2
[1] FALSE
D36V2, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4  4
  10Q LOSS WILD-TYPE 16 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    4
  10Q LOSS WILD-TYPE   16   13
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D36V3, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    3  5
  10Q LOSS WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    5
  10Q LOSS WILD-TYPE   15   13
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        2      2      4
  10Q LOSS WILD-TYPE     11      8      9
D36V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                2                  8
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4  3
  10Q LOSS WILD-TYPE 12  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    3
  10Q LOSS WILD-TYPE   12    7
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10Q LOSS MUTATED        1      0      1      2      0      2      1
  10Q LOSS WILD-TYPE      3      4      4      3      2      2      1
D36V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                1                  4
  CLUS_4                2                  3
  CLUS_5                0                  2
  CLUS_6                2                  2
  CLUS_7                1                  1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2  5
  10Q LOSS WILD-TYPE 12  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    5
  10Q LOSS WILD-TYPE   12    7
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                5                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q LOSS MUTATED        0      0      2      2      0      3
  10Q LOSS WILD-TYPE      3      4      5      4      2      1
D36V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                2                  5
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                3                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 11Q LOSS MUTATION ANALYSIS
D37V1, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  2
  11Q LOSS WILD-TYPE 14 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    2
  11Q LOSS WILD-TYPE   14   19
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D37V2, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  4
  11Q LOSS WILD-TYPE 20 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    4
  11Q LOSS WILD-TYPE   20   13
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D37V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  4
  11Q LOSS WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    4
  11Q LOSS WILD-TYPE   18   14
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        0      0      4
  11Q LOSS WILD-TYPE     13     10      9
D37V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                0                 10
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  3
  11Q LOSS WILD-TYPE 16  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    3
  11Q LOSS WILD-TYPE   16    7
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED        0      0      3      0      0      0      0
  11Q LOSS WILD-TYPE      4      4      2      5      2      4      2
D37V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  4
  CLUS_3                3                  2
  CLUS_4                0                  5
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  3
  11Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    3
  11Q LOSS WILD-TYPE   14    9
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q LOSS MUTATED        0      0      3      0      0      0
  11Q LOSS WILD-TYPE      3      4      4      6      2      4
D37V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                3                  4
  CLUS_4                0                  6
  CLUS_5                0                  2
  CLUS_6                0                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 13Q LOSS MUTATION ANALYSIS
D38V1, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   11  7
  13Q LOSS WILD-TYPE  5 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11    7
  13Q LOSS WILD-TYPE    5   14
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               11                  5
  CLUS_2                7                 14
[1] 2 2
[1] FALSE
D38V2, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    7 11
  13Q LOSS WILD-TYPE 13  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7   11
  13Q LOSS WILD-TYPE   13    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 13
  CLUS_2               11                  6
[1] 2 2
[1] FALSE
D38V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    7 11
  13Q LOSS WILD-TYPE 11  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7   11
  13Q LOSS WILD-TYPE   11    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2               11                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        6      4      8
  13Q LOSS WILD-TYPE      7      6      5
D38V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2                4                  6
  CLUS_3                8                  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"
D38V5, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   9 5
  13Q LOSS WILD-TYPE 7 5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    5
  13Q LOSS WILD-TYPE    7    5
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                  7
  CLUS_2                5                  5
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q LOSS MUTATED        2      4      3      2      1      1      1
  13Q LOSS WILD-TYPE      2      0      2      3      1      3      1
D38V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                4                  0
  CLUS_3                3                  2
  CLUS_4                2                  3
  CLUS_5                1                  1
  CLUS_6                1                  3
  CLUS_7                1                  1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   8 6
  13Q LOSS WILD-TYPE 6 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    6
  13Q LOSS WILD-TYPE    6    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                  6
  CLUS_2                6                  6
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q LOSS MUTATED        1      4      4      3      1      1
  13Q LOSS WILD-TYPE      2      0      3      3      1      3
D38V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                4                  0
  CLUS_3                4                  3
  CLUS_4                3                  3
  CLUS_5                1                  1
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 14Q LOSS MUTATION ANALYSIS
D39V1, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  5
  14Q LOSS WILD-TYPE  5 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    5
  14Q LOSS WILD-TYPE    5   16
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               11                  5
  CLUS_2                5                 16
[1] 2 2
[1] FALSE
D39V2, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    8  8
  14Q LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8    8
  14Q LOSS WILD-TYPE   12    9
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 12
  CLUS_2                8                  9
[1] 2 2
[1] FALSE
D39V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    8  8
  14Q LOSS WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8    8
  14Q LOSS WILD-TYPE   10   10
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED        4      7      5
  14Q LOSS WILD-TYPE      9      3      8
D39V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                7                  3
  CLUS_3                5                  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"
D39V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  3
  14Q LOSS WILD-TYPE  5  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    3
  14Q LOSS WILD-TYPE    5    7
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               11                  5
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  14Q LOSS MUTATED        1      3      2      5      1      2      0
  14Q LOSS WILD-TYPE      3      1      3      0      1      2      2
D39V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                3                  1
  CLUS_3                2                  3
  CLUS_4                5                  0
  CLUS_5                1                  1
  CLUS_6                2                  2
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                 0 1
  14Q LOSS MUTATED   9 5
  14Q LOSS WILD-TYPE 5 7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      9    5
  14Q LOSS WILD-TYPE    5    7
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                9                  5
  CLUS_2                5                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q LOSS MUTATED        0      3      2      6      1      2
  14Q LOSS WILD-TYPE      3      1      5      0      1      2
D39V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                3                  1
  CLUS_3                2                  5
  CLUS_4                6                  0
  CLUS_5                1                  1
  CLUS_6                2                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 15Q LOSS MUTATION ANALYSIS
D40V1, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  2
  15Q LOSS WILD-TYPE 12 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    2
  15Q LOSS WILD-TYPE   12   19
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D40V2, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  5
  15Q LOSS WILD-TYPE 19 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    5
  15Q LOSS WILD-TYPE   19   12
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                5                 12
[1] 2 2
[1] FALSE
D40V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  5
  15Q LOSS WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    5
  15Q LOSS WILD-TYPE   17   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        1      1      4
  15Q LOSS WILD-TYPE     12      9      9
D40V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  2
  15Q LOSS WILD-TYPE 14  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    2
  15Q LOSS WILD-TYPE   14    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED        1      0      2      1      0      0      0
  15Q LOSS WILD-TYPE      3      4      3      4      2      4      2
D40V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                2                  3
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  3
  15Q LOSS WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    3
  15Q LOSS WILD-TYPE   13    9
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q LOSS MUTATED        0      0      2      1      0      1
  15Q LOSS WILD-TYPE      3      4      5      5      2      3
D40V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                2                  5
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 16P LOSS MUTATION ANALYSIS
D41V1, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  1
  16P LOSS WILD-TYPE 14 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    1
  16P LOSS WILD-TYPE   14   20
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D41V2, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE   19   15
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D41V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE 17 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE   17   16
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED        1      0      2
  16P LOSS WILD-TYPE     12     10     11
D41V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                 10
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  1
  16P LOSS WILD-TYPE 15  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    1
  16P LOSS WILD-TYPE   15    9
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P LOSS MUTATED        1      0      1      0      0      0      0
  16P LOSS WILD-TYPE      3      4      4      5      2      4      2
D41V6, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-NQ-A57I         TCGA-NQ-A638         TCGA-SC-A6LM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D41V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    0  2
  16P LOSS WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    2
  16P LOSS WILD-TYPE   14   10
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P LOSS MUTATED        0      0      1      0      0      1
  16P LOSS WILD-TYPE      3      4      6      6      2      3
D41V8, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-NQ-A57I         TCGA-NQ-A638         TCGA-SC-A6LM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 

Clustering(42) Variable = 16Q LOSS MUTATION ANALYSIS
D42V1, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  1
  16Q LOSS WILD-TYPE 13 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    1
  16Q LOSS WILD-TYPE   13   20
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D42V2, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   18   15
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D42V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  1
  16Q LOSS WILD-TYPE 15 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    1
  16Q LOSS WILD-TYPE   15   17
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        1      1      2
  16Q LOSS WILD-TYPE     12      9     11
D42V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  1
  16Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    1
  16Q LOSS WILD-TYPE   14    9
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q LOSS MUTATED        1      0      1      1      0      0      0
  16Q LOSS WILD-TYPE      3      4      4      4      2      4      2
D42V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE 13 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE   13   10
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q LOSS MUTATED        0      0      1      1      0      1
  16Q LOSS WILD-TYPE      3      4      6      5      2      3
D42V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                1                  6
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 17P LOSS MUTATION ANALYSIS
D43V1, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4  5
  17P LOSS WILD-TYPE 12 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    5
  17P LOSS WILD-TYPE   12   16
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                5                 16
[1] 2 2
[1] FALSE
D43V2, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5  4
  17P LOSS WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    4
  17P LOSS WILD-TYPE   15   13
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                 15
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D43V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3  5
  17P LOSS WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    5
  17P LOSS WILD-TYPE   15   13
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        3      1      4
  17P LOSS WILD-TYPE     10      9      9
D43V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                1                  9
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    6  1
  17P LOSS WILD-TYPE 10  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    1
  17P LOSS WILD-TYPE   10    9
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P LOSS MUTATED        2      1      1      2      0      1      0
  17P LOSS WILD-TYPE      2      3      4      3      2      3      2
D43V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                2                  3
  CLUS_5                0                  2
  CLUS_6                1                  3
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5  2
  17P LOSS WILD-TYPE  9 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    2
  17P LOSS WILD-TYPE    9   10
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P LOSS MUTATED        1      1      1      3      0      1
  17P LOSS WILD-TYPE      2      3      6      3      2      3
D43V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                3                  3
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 17Q LOSS MUTATION ANALYSIS
D44V1, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE 15 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   15   19
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D44V2, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE 19 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   19   15
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 15
[1] 2 2
[1] FALSE
D44V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE 17 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   17   16
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        1      0      2
  17Q LOSS WILD-TYPE     12     10     11
D44V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                 10
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  1
  17Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    1
  17Q LOSS WILD-TYPE   14    9
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q LOSS MUTATED        1      0      1      1      0      0      0
  17Q LOSS WILD-TYPE      3      4      4      4      2      4      2
D44V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                0                  4
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE 13 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   13   10
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q LOSS MUTATED        0      0      1      1      0      1
  17Q LOSS WILD-TYPE      3      4      6      5      2      3
D44V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  4
  CLUS_3                1                  6
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 18P LOSS MUTATION ANALYSIS
D45V1, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 14 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   14   18
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                3                 18
[1] 2 2
[1] FALSE
D45V2, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   18   14
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                3                 14
[1] 2 2
[1] FALSE
D45V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 16 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   16   15
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      1      3
  18P LOSS WILD-TYPE     12      9     10
D45V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                  9
  CLUS_3                3                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  1
  18P LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   12    9
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED        1      1      1      1      0      1      0
  18P LOSS WILD-TYPE      3      3      4      4      2      3      2
D45V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   12    9
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P LOSS MUTATED        0      1      1      1      0      2
  18P LOSS WILD-TYPE      3      3      6      5      2      2
D45V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                1                  5
  CLUS_5                0                  2
  CLUS_6                2                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 18Q LOSS MUTATION ANALYSIS
D46V1, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  5
  18Q LOSS WILD-TYPE 12 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    5
  18Q LOSS WILD-TYPE   12   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                5                 16
[1] 2 2
[1] FALSE
D46V2, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  4
  18Q LOSS WILD-TYPE 15 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    4
  18Q LOSS WILD-TYPE   15   13
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 15
  CLUS_2                4                 13
[1] 2 2
[1] FALSE
D46V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  5
  18Q LOSS WILD-TYPE 14 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    5
  18Q LOSS WILD-TYPE   14   13
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        2      3      4
  18Q LOSS WILD-TYPE     11      7      9
D46V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                3                  7
  CLUS_3                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  2
  18Q LOSS WILD-TYPE 11  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    2
  18Q LOSS WILD-TYPE   11    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q LOSS MUTATED        1      1      1      2      0      2      0
  18Q LOSS WILD-TYPE      3      3      4      3      2      2      2
D46V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                2                  3
  CLUS_5                0                  2
  CLUS_6                2                  2
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  4
  18Q LOSS WILD-TYPE 11  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    4
  18Q LOSS WILD-TYPE   11    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                4                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q LOSS MUTATED        0      1      1      2      0      3
  18Q LOSS WILD-TYPE      3      3      6      4      2      1
D46V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                3                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 19Q LOSS MUTATION ANALYSIS
D47V1, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 15 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   15   19
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 19
[1] 2 2
[1] FALSE
D47V2, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 18 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   18   16
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 16
[1] 2 2
[1] FALSE
D47V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   16   17
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        2      0      1
  19Q LOSS WILD-TYPE     11     10     12
D47V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                0                 10
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  1
  19Q LOSS WILD-TYPE 15  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    1
  19Q LOSS WILD-TYPE   15    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q LOSS MUTATED        1      0      1      0      0      0      0
  19Q LOSS WILD-TYPE      3      4      4      5      2      4      2
D47V6, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-NQ-A638         TCGA-SC-A6LM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D47V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  2
  19Q LOSS WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    2
  19Q LOSS WILD-TYPE   14   10
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q LOSS MUTATED        0      0      1      0      0      1
  19Q LOSS WILD-TYPE      3      4      6      6      2      3
D47V8, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-NQ-A638         TCGA-SC-A6LM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 

Clustering(48) Variable = 20P LOSS MUTATION ANALYSIS
D48V1, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  1
  20P LOSS WILD-TYPE 10 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    1
  20P LOSS WILD-TYPE   10   20
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D48V2, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  1
  20P LOSS WILD-TYPE 14 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    1
  20P LOSS WILD-TYPE   14   16
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                 14
  CLUS_2                1                 16
[1] 2 2
[1] FALSE
D48V3, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    4  3
  20P LOSS WILD-TYPE 14 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    3
  20P LOSS WILD-TYPE   14   15
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        4      1      2
  20P LOSS WILD-TYPE      9      9     11
D48V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                1                  9
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    4  1
  20P LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    1
  20P LOSS WILD-TYPE   12    9
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P LOSS MUTATED        2      1      0      1      0      1      0
  20P LOSS WILD-TYPE      2      3      5      4      2      3      2
D48V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                  2
  CLUS_2                1                  3
  CLUS_3                0                  5
  CLUS_4                1                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  2
  20P LOSS WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    2
  20P LOSS WILD-TYPE   11   10
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P LOSS MUTATED        1      1      0      2      0      1
  20P LOSS WILD-TYPE      2      3      7      4      2      3
D48V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                  2
  CLUS_2                1                  3
  CLUS_3                0                  7
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 20Q LOSS MUTATION ANALYSIS
D49V1, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 13 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   13   21
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                0                 21
[1] 2 2
[1] FALSE
D49V2, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 18 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE   18   16
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 16
[1] 2 2
[1] FALSE
D49V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 16 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE   16   17
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        2      0      1
  20Q LOSS WILD-TYPE     11     10     12
D49V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                0                 10
  CLUS_3                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE 15  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE   15    9
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q LOSS MUTATED        1      1      0      0      0      0      0
  20Q LOSS WILD-TYPE      3      3      5      5      2      4      2
D49V6, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LK-A4O6         TCGA-LK-A4O7         TCGA-MQ-A4LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LJ         TCGA-MQ-A4LM         TCGA-MQ-A4LP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NQ-A57I         TCGA-NQ-A638         TCGA-SC-A6LM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D49V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  2
  20Q LOSS WILD-TYPE 14 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    2
  20Q LOSS WILD-TYPE   14   10
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q LOSS MUTATED        0      1      0      0      0      1
  20Q LOSS WILD-TYPE      3      3      7      6      2      3
D49V8, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-LK-A4NW         TCGA-LK-A4O2         TCGA-LK-A4O4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LK-A4O6         TCGA-LK-A4O7         TCGA-MQ-A4LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LJ         TCGA-MQ-A4LM         TCGA-MQ-A4LP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NQ-A57I         TCGA-NQ-A638         TCGA-SC-A6LM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LR         TCGA-SH-A7BC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-TS-A7OY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TS-A7P0         TCGA-TS-A7P8         TCGA-TS-A7PB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 

Clustering(50) Variable = 21Q LOSS MUTATION ANALYSIS
D50V1, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    5  1
  21Q LOSS WILD-TYPE 11 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    1
  21Q LOSS WILD-TYPE   11   20
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 20
[1] 2 2
[1] FALSE
D50V2, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  3
  21Q LOSS WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    3
  21Q LOSS WILD-TYPE   17   14
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                3                 14
[1] 2 2
[1] FALSE
D50V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    2  4
  21Q LOSS WILD-TYPE 16 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2    4
  21Q LOSS WILD-TYPE   16   14
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        2      2      2
  21Q LOSS WILD-TYPE     11      8     11
D50V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                2                  8
  CLUS_3                2                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4  1
  21Q LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    1
  21Q LOSS WILD-TYPE   12    9
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED        1      1      1      2      0      0      0
  21Q LOSS WILD-TYPE      3      3      4      3      2      4      2
D50V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  3
  CLUS_3                1                  4
  CLUS_4                2                  3
  CLUS_5                0                  2
  CLUS_6                0                  4
  CLUS_7                0                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  2
  21Q LOSS WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    2
  21Q LOSS WILD-TYPE   11   10
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q LOSS MUTATED        0      1      1      2      0      1
  21Q LOSS WILD-TYPE      3      3      6      4      2      3
D50V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                1                  3
  CLUS_3                1                  6
  CLUS_4                2                  4
  CLUS_5                0                  2
  CLUS_6                1                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 22Q LOSS MUTATION ANALYSIS
D51V1, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   15 14
  22Q LOSS WILD-TYPE  1  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   14
  22Q LOSS WILD-TYPE    1    7
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               15                  1
  CLUS_2               14                  7
[1] 2 2
[1] FALSE
D51V2, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   18 11
  22Q LOSS WILD-TYPE  2  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     18   11
  22Q LOSS WILD-TYPE    2    6
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               18                  2
  CLUS_2               11                  6
[1] 2 2
[1] FALSE
D51V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   15 13
  22Q LOSS WILD-TYPE  3  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   13
  22Q LOSS WILD-TYPE    3    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               15                  3
  CLUS_2               13                  5
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       10      8     10
  22Q LOSS WILD-TYPE      3      2      3
D51V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               10                  3
  CLUS_2                8                  2
  CLUS_3               10                  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"
D51V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 10
  22Q LOSS WILD-TYPE  6  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   10
  22Q LOSS WILD-TYPE    6    0
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               10                  6
  CLUS_2               10                  0
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  22Q LOSS MUTATED        1      3      5      4      1      4      2
  22Q LOSS WILD-TYPE      3      1      0      1      1      0      0
D51V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                3                  1
  CLUS_3                5                  0
  CLUS_4                4                  1
  CLUS_5                1                  1
  CLUS_6                4                  0
  CLUS_7                2                  0
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    8 12
  22Q LOSS WILD-TYPE  6  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8   12
  22Q LOSS WILD-TYPE    6    0
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                8                  6
  CLUS_2               12                  0
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q LOSS MUTATED        0      3      7      5      1      4
  22Q LOSS WILD-TYPE      3      1      0      1      1      0
D51V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                3                  1
  CLUS_3                7                  0
  CLUS_4                5                  1
  CLUS_5                1                  1
  CLUS_6                4                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = XQ LOSS MUTATION ANALYSIS
D52V1, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    6  1
  XQ LOSS WILD-TYPE 10 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6    1
  XQ LOSS WILD-TYPE   10   20
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               6                10
  CLUS_2               1                20
[1] 2 2
[1] FALSE
D52V2, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    7  0
  XQ LOSS WILD-TYPE 13 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      7    0
  XQ LOSS WILD-TYPE   13   17
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               7                13
  CLUS_2               0                17
[1] 2 2
[1] FALSE
D52V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    5  2
  XQ LOSS WILD-TYPE 13 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5    2
  XQ LOSS WILD-TYPE   13   16
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        2      3      2
  XQ LOSS WILD-TYPE     11      7     11
D52V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               3                 7
  CLUS_3               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  2
  XQ LOSS WILD-TYPE 12  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    2
  XQ LOSS WILD-TYPE   12    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ LOSS MUTATED        1      0      0      2      0      2      1
  XQ LOSS WILD-TYPE      3      4      5      3      2      2      1
D52V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                 3
  CLUS_2               0                 4
  CLUS_3               0                 5
  CLUS_4               2                 3
  CLUS_5               0                 2
  CLUS_6               2                 2
  CLUS_7               1                 1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  3
  XQ LOSS WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    3
  XQ LOSS WILD-TYPE   11    9
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               3                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ LOSS MUTATED        0      0      1      3      0      2
  XQ LOSS WILD-TYPE      3      4      6      3      2      2
D52V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               0                 4
  CLUS_3               1                 6
  CLUS_4               3                 3
  CLUS_5               0                 2
  CLUS_6               2                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
