[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"        "-oTTHCA-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/THCA-TP/10667977/THCA-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/10013832/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=494, common to both=494
[1] "Reduce the number of clustering variables from 80 to 57."
[1]  57 494
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               491 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               491 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               470 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               470 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               491 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               491 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               489 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               489 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               489 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               489 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               473 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               473 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               477 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               477 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               476 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               476 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               474 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               474 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               488 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               488 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               487 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               487 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               491 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               491 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               490 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               490 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                488 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                488 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                489 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                489 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                480 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                480 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                479 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                479 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                489 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                489 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                483 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                483 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                479 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                479 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                481 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                481 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                478 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                478 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                476 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                476 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                488 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                488 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                488 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                488 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                486 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                486 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                484 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                484 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                482 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                482 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                482 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                482 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                489 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                489 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               485 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               485 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               490 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               490 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               491 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               491 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               484 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               484 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               484 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               484 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               491 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               491 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               490 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               490 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               490 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               490 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               487 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               487 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               490 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               490 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               490 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               490 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               475 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               475 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               24               470 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               24               470 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                487 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                487 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                488 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                488 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                487 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                487 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                485 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                485 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                480 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                480 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                486 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                486 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                486 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                486 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                490 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                490 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                490 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                490 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                490 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                490 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                489 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                489 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                486 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                486 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                86                408 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                86                408 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               491 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               491 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 494 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 494 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        1      2      0
  1P GAIN WILD-TYPE     33    381     77
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                33
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        1      1      1
  1P GAIN WILD-TYPE    272    150     69
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               272
  CLUS_2               1               150
  CLUS_3               1                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        0      1      0
  1P GAIN WILD-TYPE     61     78     81
D1V3, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               220 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P GAIN MUTATED        0      0      0      0      0      1      0
  1P GAIN WILD-TYPE     46     28     33     29     49     26      9
D1V4, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               220 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        1      1      0      1
  1P GAIN WILD-TYPE    153     54    116    166
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               153
  CLUS_2               1                54
  CLUS_3               0               116
  CLUS_4               1               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P GAIN MUTATED        1      0      0      2      0
  1P GAIN WILD-TYPE    125    100     73    113     78
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               125
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               2               113
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        1      0      2
  1P GAIN WILD-TYPE    149    173    168
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               149
  CLUS_2               0               173
  CLUS_3               2               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        1      0      2
  1P GAIN WILD-TYPE    124    205    161
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               124
  CLUS_2               0               205
  CLUS_3               2               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        1      0      2
  1P GAIN WILD-TYPE    162    169    159
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               0               169
  CLUS_3               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        1      0      1      1
  1P GAIN WILD-TYPE    122    187    104     77
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               122
  CLUS_2               0               187
  CLUS_3               1               104
  CLUS_4               1                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        9     14      1
  1Q GAIN WILD-TYPE     25    369     76
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                25
  CLUS_2              14               369
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       17      2      5
  1Q GAIN WILD-TYPE    256    149     65
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              17               256
  CLUS_2               2               149
  CLUS_3               5                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        0      9      1
  1Q GAIN WILD-TYPE     61     70     80
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                61
  CLUS_2               9                70
  CLUS_3               1                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q GAIN MUTATED        0      1      3      0      2      4      0
  1Q GAIN WILD-TYPE     46     27     30     29     47     23      9
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               1                27
  CLUS_3               3                30
  CLUS_4               0                29
  CLUS_5               2                47
  CLUS_6               4                23
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        2      3      2     17
  1Q GAIN WILD-TYPE    152     52    114    150
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               152
  CLUS_2               3                52
  CLUS_3               2               114
  CLUS_4              17               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q GAIN MUTATED        2      0      2     16      4
  1Q GAIN WILD-TYPE    124    100     71     99     74
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               124
  CLUS_2               0               100
  CLUS_3               2                71
  CLUS_4              16                99
  CLUS_5               4                74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        5      6     13
  1Q GAIN WILD-TYPE    145    167    157
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5               145
  CLUS_2               6               167
  CLUS_3              13               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        3      8     13
  1Q GAIN WILD-TYPE    122    197    150
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3               122
  CLUS_2               8               197
  CLUS_3              13               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        5      6     13
  1Q GAIN WILD-TYPE    158    163    148
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5               158
  CLUS_2               6               163
  CLUS_3              13               148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        2      9      2     11
  1Q GAIN WILD-TYPE    121    178    103     67
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               121
  CLUS_2               9               178
  CLUS_3               2               103
  CLUS_4              11                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 3P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        3      0      0
  3P GAIN WILD-TYPE     31    383     77
D3V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                31
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        1      2      0
  3P GAIN WILD-TYPE    272    149     70
D3V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               272
  CLUS_2               2               149
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        0      1      1
  3P GAIN WILD-TYPE     61     78     80
D3V3, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3P GAIN MUTATED        0      0      0      0      1      1      0
  3P GAIN WILD-TYPE     46     28     33     29     48     26      9
D3V4, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        2      0      1      0
  3P GAIN WILD-TYPE    152     55    115    167
D3V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               152
  CLUS_2               0                55
  CLUS_3               1               115
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED        2      0      1      0      0
  3P GAIN WILD-TYPE    124    100     72    115     78
D3V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               124
  CLUS_2               0               100
  CLUS_3               1                72
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        2      0      1
  3P GAIN WILD-TYPE    148    173    169
D3V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               148
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        2      0      1
  3P GAIN WILD-TYPE    123    205    162
D3V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               123
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        2      0      1
  3P GAIN WILD-TYPE    161    169    160
D3V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        2      0      1      0
  3P GAIN WILD-TYPE    121    187    104     78
D3V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               121
  CLUS_2               0               187
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        5      0      0
  4P GAIN WILD-TYPE     29    383     77
D4V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5                29
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        0      5      0
  4P GAIN WILD-TYPE    273    146     70
D4V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               273
  CLUS_2               5               146
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        1      0      1
  4P GAIN WILD-TYPE     60     79     80
D4V3, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4P GAIN MUTATED        1      0      0      1      0      0      0
  4P GAIN WILD-TYPE     45     28     33     28     49     27      9
D4V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        5      0      0      0
  4P GAIN WILD-TYPE    149     55    116    167
D4V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               149
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED        5      0      0      0      0
  4P GAIN WILD-TYPE    121    100     73    115     78
D4V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               121
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        4      0      1
  4P GAIN WILD-TYPE    146    173    169
D4V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               146
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        4      0      1
  4P GAIN WILD-TYPE    121    205    162
D4V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               121
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        4      0      1
  4P GAIN WILD-TYPE    159    169    160
D4V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        4      0      1      0
  4P GAIN WILD-TYPE    119    187    104     78
D4V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0               187
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        5      0      0
  4Q GAIN WILD-TYPE     29    383     77
D5V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5                29
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        0      5      0
  4Q GAIN WILD-TYPE    273    146     70
D5V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               273
  CLUS_2               5               146
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        1      0      1
  4Q GAIN WILD-TYPE     60     79     80
D5V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4Q GAIN MUTATED        1      0      0      1      0      0      0
  4Q GAIN WILD-TYPE     45     28     33     28     49     27      9
D5V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        5      0      0      0
  4Q GAIN WILD-TYPE    149     55    116    167
D5V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5               149
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        5      0      0      0      0
  4Q GAIN WILD-TYPE    121    100     73    115     78
D5V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5               121
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      0      1
  4Q GAIN WILD-TYPE    146    173    169
D5V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               146
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      0      1
  4Q GAIN WILD-TYPE    121    205    162
D5V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               121
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      0      1
  4Q GAIN WILD-TYPE    159    169    160
D5V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        4      0      1      0
  4Q GAIN WILD-TYPE    119    187    104     78
D5V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0               187
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       19      2      0
  5P GAIN WILD-TYPE     15    381     77
D6V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              19                15
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        5     14      2
  5P GAIN WILD-TYPE    268    137     68
D6V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5               268
  CLUS_2              14               137
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        2      6      4
  5P GAIN WILD-TYPE     59     73     77
D6V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                59
  CLUS_2               6                73
  CLUS_3               4                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5P GAIN MUTATED        3      1      2      3      0      3      0
  5P GAIN WILD-TYPE     43     27     31     26     49     24      9
D6V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                43
  CLUS_2               1                27
  CLUS_3               2                31
  CLUS_4               3                26
  CLUS_5               0                49
  CLUS_6               3                24
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       14      1      1      5
  5P GAIN WILD-TYPE    140     54    115    162
D6V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              14               140
  CLUS_2               1                54
  CLUS_3               1               115
  CLUS_4               5               162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P GAIN MUTATED       13      1      1      6      0
  5P GAIN WILD-TYPE    113     99     72    109     78
D6V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               113
  CLUS_2               1                99
  CLUS_3               1                72
  CLUS_4               6               109
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       13      2      6
  5P GAIN WILD-TYPE    137    171    164
D6V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               137
  CLUS_2               2               171
  CLUS_3               6               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       13      1      7
  5P GAIN WILD-TYPE    112    204    156
D6V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               112
  CLUS_2               1               204
  CLUS_3               7               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       14      1      6
  5P GAIN WILD-TYPE    149    168    155
D6V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              14               149
  CLUS_2               1               168
  CLUS_3               6               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       13      1      2      5
  5P GAIN WILD-TYPE    110    186    103     73
D6V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               110
  CLUS_2               1               186
  CLUS_3               2               103
  CLUS_4               5                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       17      0      0
  5Q GAIN WILD-TYPE     17    383     77
D7V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              17                17
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        2     14      1
  5Q GAIN WILD-TYPE    271    137     69
D7V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2              14               137
  CLUS_3               1                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        2      4      4
  5Q GAIN WILD-TYPE     59     75     77
D7V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                59
  CLUS_2               4                75
  CLUS_3               4                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q GAIN MUTATED        3      1      0      3      0      3      0
  5Q GAIN WILD-TYPE     43     27     33     26     49     24      9
D7V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                43
  CLUS_2               1                27
  CLUS_3               0                33
  CLUS_4               3                26
  CLUS_5               0                49
  CLUS_6               3                24
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED       14      0      1      2
  5Q GAIN WILD-TYPE    140     55    115    165
D7V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              14               140
  CLUS_2               0                55
  CLUS_3               1               115
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED       13      1      1      2      0
  5Q GAIN WILD-TYPE    113     99     72    113     78
D7V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               113
  CLUS_2               1                99
  CLUS_3               1                72
  CLUS_4               2               113
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       13      2      2
  5Q GAIN WILD-TYPE    137    171    168
D7V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               137
  CLUS_2               2               171
  CLUS_3               2               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       13      1      3
  5Q GAIN WILD-TYPE    112    204    160
D7V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               112
  CLUS_2               1               204
  CLUS_3               3               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       14      1      2
  5Q GAIN WILD-TYPE    149    168    159
D7V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              14               149
  CLUS_2               1               168
  CLUS_3               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED       13      1      1      2
  5Q GAIN WILD-TYPE    110    186    104     76
D7V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               110
  CLUS_2               1               186
  CLUS_3               1               104
  CLUS_4               2                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       18      0      0
  7P GAIN WILD-TYPE     16    383     77
D8V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              18                16
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2     14      2
  7P GAIN WILD-TYPE    271    137     68
D8V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2              14               137
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2      5      3
  7P GAIN WILD-TYPE     59     74     78
D8V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                59
  CLUS_2               5                74
  CLUS_3               3                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P GAIN MUTATED        3      1      0      2      0      4      0
  7P GAIN WILD-TYPE     43     27     33     27     49     23      9
D8V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                43
  CLUS_2               1                27
  CLUS_3               0                33
  CLUS_4               2                27
  CLUS_5               0                49
  CLUS_6               4                23
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       14      1      1      2
  7P GAIN WILD-TYPE    140     54    115    165
D8V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14               140
  CLUS_2               1                54
  CLUS_3               1               115
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P GAIN MUTATED       13      2      1      2      0
  7P GAIN WILD-TYPE    113     98     72    113     78
D8V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13               113
  CLUS_2               2                98
  CLUS_3               1                72
  CLUS_4               2               113
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       13      2      3
  7P GAIN WILD-TYPE    137    171    167
D8V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13               137
  CLUS_2               2               171
  CLUS_3               3               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       13      1      4
  7P GAIN WILD-TYPE    112    204    159
D8V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13               112
  CLUS_2               1               204
  CLUS_3               4               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       14      1      3
  7P GAIN WILD-TYPE    149    168    158
D8V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14               149
  CLUS_2               1               168
  CLUS_3               3               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       13      1      2      2
  7P GAIN WILD-TYPE    110    186    103     76
D8V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13               110
  CLUS_2               1               186
  CLUS_3               2               103
  CLUS_4               2                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       19      0      1
  7Q GAIN WILD-TYPE     15    383     76
D9V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              19                15
  CLUS_2               0               383
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        2     16      2
  7Q GAIN WILD-TYPE    271    135     68
D9V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2              16               135
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        3      6      3
  7Q GAIN WILD-TYPE     58     73     78
D9V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                58
  CLUS_2               6                73
  CLUS_3               3                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7Q GAIN MUTATED        4      1      0      2      0      5      0
  7Q GAIN WILD-TYPE     42     27     33     27     49     22      9
D9V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                42
  CLUS_2               1                27
  CLUS_3               0                33
  CLUS_4               2                27
  CLUS_5               0                49
  CLUS_6               5                22
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       16      1      1      2
  7Q GAIN WILD-TYPE    138     54    115    165
D9V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16               138
  CLUS_2               1                54
  CLUS_3               1               115
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q GAIN MUTATED       15      2      1      2      0
  7Q GAIN WILD-TYPE    111     98     72    113     78
D9V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15               111
  CLUS_2               2                98
  CLUS_3               1                72
  CLUS_4               2               113
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       15      2      3
  7Q GAIN WILD-TYPE    135    171    167
D9V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15               135
  CLUS_2               2               171
  CLUS_3               3               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       14      2      4
  7Q GAIN WILD-TYPE    111    203    159
D9V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              14               111
  CLUS_2               2               203
  CLUS_3               4               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       16      1      3
  7Q GAIN WILD-TYPE    147    168    158
D9V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16               147
  CLUS_2               1               168
  CLUS_3               3               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       15      1      2      2
  7Q GAIN WILD-TYPE    108    186    103     76
D9V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15               108
  CLUS_2               1               186
  CLUS_3               2               103
  CLUS_4               2                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        4      2      0
  8P GAIN WILD-TYPE     30    381     77
D10V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                30
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        2      3      1
  8P GAIN WILD-TYPE    271    148     69
D10V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2               3               148
  CLUS_3               1                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        0      1      3
  8P GAIN WILD-TYPE     61     78     78
D10V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                61
  CLUS_2               1                78
  CLUS_3               3                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED        0      1      0      1      1      1      0
  8P GAIN WILD-TYPE     46     27     33     28     48     26      9
D10V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               1                27
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               1                48
  CLUS_6               1                26
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        3      0      2      1
  8P GAIN WILD-TYPE    151     55    114    166
D10V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               2               114
  CLUS_4               1               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P GAIN MUTATED        3      0      2      1      0
  8P GAIN WILD-TYPE    123    100     71    114     78
D10V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               2                71
  CLUS_4               1               114
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        3      2      1
  8P GAIN WILD-TYPE    147    171    169
D10V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3               147
  CLUS_2               2               171
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        3      2      1
  8P GAIN WILD-TYPE    122    203    162
D10V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3               122
  CLUS_2               2               203
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        4      1      1
  8P GAIN WILD-TYPE    159    168    160
D10V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               1               168
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        3      2      0      1
  8P GAIN WILD-TYPE    120    185    105     77
D10V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3               120
  CLUS_2               2               185
  CLUS_3               0               105
  CLUS_4               1                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        5      2      0
  8Q GAIN WILD-TYPE     29    381     77
D11V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5                29
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        2      3      2
  8Q GAIN WILD-TYPE    271    148     68
D11V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2               3               148
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        0      1      3
  8Q GAIN WILD-TYPE     61     78     78
D11V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                61
  CLUS_2               1                78
  CLUS_3               3                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q GAIN MUTATED        0      1      0      1      1      1      0
  8Q GAIN WILD-TYPE     46     27     33     28     48     26      9
D11V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               1                27
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               1                48
  CLUS_6               1                26
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        3      0      2      2
  8Q GAIN WILD-TYPE    151     55    114    165
D11V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               2               114
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED        3      0      2      2      0
  8Q GAIN WILD-TYPE    123    100     71    113     78
D11V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               2                71
  CLUS_4               2               113
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        3      2      2
  8Q GAIN WILD-TYPE    147    171    168
D11V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               147
  CLUS_2               2               171
  CLUS_3               2               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        3      2      2
  8Q GAIN WILD-TYPE    122    203    161
D11V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               122
  CLUS_2               2               203
  CLUS_3               2               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        4      1      2
  8Q GAIN WILD-TYPE    159    168    159
D11V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               1               168
  CLUS_3               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        3      2      0      2
  8Q GAIN WILD-TYPE    120    185    105     76
D11V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               120
  CLUS_2               2               185
  CLUS_3               0               105
  CLUS_4               2                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 9P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        2      0      1
  9P GAIN WILD-TYPE     32    383     76
D12V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                32
  CLUS_2               0               383
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      2      0
  9P GAIN WILD-TYPE    272    149     70
D12V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               272
  CLUS_2               2               149
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      0      0
  9P GAIN WILD-TYPE     60     79     81
D12V3, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1               220 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P GAIN MUTATED        1      0      0      0      0      0      0
  9P GAIN WILD-TYPE     45     28     33     29     49     27      9
D12V4, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1               220 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        2      0      1      0
  9P GAIN WILD-TYPE    152     55    115    167
D12V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               152
  CLUS_2               0                55
  CLUS_3               1               115
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        2      0      1      0      0
  9P GAIN WILD-TYPE    124    100     72    115     78
D12V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               124
  CLUS_2               0               100
  CLUS_3               1                72
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      1      1
  9P GAIN WILD-TYPE    149    172    169
D12V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               149
  CLUS_2               1               172
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      1      1
  9P GAIN WILD-TYPE    124    204    162
D12V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               124
  CLUS_2               1               204
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      1      1
  9P GAIN WILD-TYPE    162    168    160
D12V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               1               168
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        1      1      1      0
  9P GAIN WILD-TYPE    122    186    104     78
D12V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               122
  CLUS_2               1               186
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 9Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        2      1      1
  9Q GAIN WILD-TYPE     32    382     76
D13V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                32
  CLUS_2               1               382
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        2      2      0
  9Q GAIN WILD-TYPE    271    149     70
D13V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               271
  CLUS_2               2               149
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      0      1
  9Q GAIN WILD-TYPE     60     79     80
D13V3, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q GAIN MUTATED        1      0      0      0      1      0      0
  9Q GAIN WILD-TYPE     45     28     33     29     48     27      9
D13V4, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        2      0      1      1
  9Q GAIN WILD-TYPE    152     55    115    166
D13V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               152
  CLUS_2               0                55
  CLUS_3               1               115
  CLUS_4               1               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        2      0      2      0      0
  9Q GAIN WILD-TYPE    124    100     71    115     78
D13V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               124
  CLUS_2               0               100
  CLUS_3               2                71
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      2      1
  9Q GAIN WILD-TYPE    149    171    169
D13V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               149
  CLUS_2               2               171
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      2      1
  9Q GAIN WILD-TYPE    124    203    162
D13V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               124
  CLUS_2               2               203
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      2      1
  9Q GAIN WILD-TYPE    162    167    160
D13V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               2               167
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        1      2      1      0
  9Q GAIN WILD-TYPE    122    185    104     78
D13V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               122
  CLUS_2               2               185
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        4      1      1
  11P GAIN WILD-TYPE     30    382     76
D14V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 30
  CLUS_2                1                382
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        1      5      0
  11P GAIN WILD-TYPE    272    146     70
D14V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2                5                146
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        0      1      2
  11P GAIN WILD-TYPE     61     78     79
D14V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 61
  CLUS_2                1                 78
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P GAIN MUTATED        0      1      0      1      0      1      0
  11P GAIN WILD-TYPE     46     27     33     28     49     26      9
D14V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        5      0      1      0
  11P GAIN WILD-TYPE    149     55    115    167
D14V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                149
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED        5      0      1      0      0
  11P GAIN WILD-TYPE    121    100     72    115     78
D14V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                121
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        5      1      0
  11P GAIN WILD-TYPE    145    172    170
D14V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                145
  CLUS_2                1                172
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        5      1      0
  11P GAIN WILD-TYPE    120    204    163
D14V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                120
  CLUS_2                1                204
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        6      0      0
  11P GAIN WILD-TYPE    157    169    161
D14V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                157
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        5      1      0      0
  11P GAIN WILD-TYPE    118    186    105     78
D14V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                118
  CLUS_2                1                186
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        4      0      1
  11Q GAIN WILD-TYPE     30    383     76
D15V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 30
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        1      4      0
  11Q GAIN WILD-TYPE    272    147     70
D15V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2                4                147
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        0      1      2
  11Q GAIN WILD-TYPE     61     78     79
D15V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 61
  CLUS_2                1                 78
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q GAIN MUTATED        0      1      0      1      0      1      0
  11Q GAIN WILD-TYPE     46     27     33     28     49     26      9
D15V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        4      0      1      0
  11Q GAIN WILD-TYPE    150     55    115    167
D15V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                150
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        4      0      1      0      0
  11Q GAIN WILD-TYPE    122    100     72    115     78
D15V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                122
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        4      1      0
  11Q GAIN WILD-TYPE    146    172    170
D15V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                146
  CLUS_2                1                172
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        4      1      0
  11Q GAIN WILD-TYPE    121    204    163
D15V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                121
  CLUS_2                1                204
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        5      0      0
  11Q GAIN WILD-TYPE    158    169    161
D15V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        4      1      0      0
  11Q GAIN WILD-TYPE    119    186    105     78
D15V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                119
  CLUS_2                1                186
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       13      0      1
  12P GAIN WILD-TYPE     21    383     76
D16V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               13                 21
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        1     13      0
  12P GAIN WILD-TYPE    272    138     70
D16V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               13                138
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        2      4      4
  12P GAIN WILD-TYPE     59     75     77
D16V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 59
  CLUS_2                4                 75
  CLUS_3                4                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12P GAIN MUTATED        3      1      0      3      0      3      0
  12P GAIN WILD-TYPE     43     27     33     26     49     24      9
D16V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 43
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                3                 26
  CLUS_5                0                 49
  CLUS_6                3                 24
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       13      0      1      0
  12P GAIN WILD-TYPE    141     55    115    167
D16V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               13                141
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED       12      1      1      0      0
  12P GAIN WILD-TYPE    114     99     72    115     78
D16V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                114
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       12      1      1
  12P GAIN WILD-TYPE    138    172    169
D16V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                138
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       12      1      1
  12P GAIN WILD-TYPE    113    204    162
D16V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                113
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       13      0      1
  12P GAIN WILD-TYPE    150    169    160
D16V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               13                150
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       12      1      1      0
  12P GAIN WILD-TYPE    111    186    104     78
D16V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                111
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       13      0      2
  12Q GAIN WILD-TYPE     21    383     75
D17V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                 21
  CLUS_2                0                383
  CLUS_3                2                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        1     14      0
  12Q GAIN WILD-TYPE    272    137     70
D17V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               14                137
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        2      4      4
  12Q GAIN WILD-TYPE     59     75     77
D17V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 59
  CLUS_2                4                 75
  CLUS_3                4                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q GAIN MUTATED        3      1      0      3      0      3      0
  12Q GAIN WILD-TYPE     43     27     33     26     49     24      9
D17V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 43
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                3                 26
  CLUS_5                0                 49
  CLUS_6                3                 24
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED       14      0      1      0
  12Q GAIN WILD-TYPE    140     55    115    167
D17V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               14                140
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q GAIN MUTATED       13      1      1      0      0
  12Q GAIN WILD-TYPE    113     99     72    115     78
D17V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                113
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       13      1      1
  12Q GAIN WILD-TYPE    137    172    169
D17V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                137
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       13      1      1
  12Q GAIN WILD-TYPE    112    204    162
D17V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                112
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       14      0      1
  12Q GAIN WILD-TYPE    149    169    160
D17V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               14                149
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED       13      1      1      0
  12Q GAIN WILD-TYPE    110    186    104     78
D17V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                110
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        5      0      0
  13Q GAIN WILD-TYPE     29    383     77
D18V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                 29
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        0      4      1
  13Q GAIN WILD-TYPE    273    147     69
D18V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                273
  CLUS_2                4                147
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        1      2      0
  13Q GAIN WILD-TYPE     60     77     81
D18V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                2                 77
  CLUS_3                0                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q GAIN MUTATED        1      0      0      0      0      2      0
  13Q GAIN WILD-TYPE     45     28     33     29     49     25      9
D18V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                0                 29
  CLUS_5                0                 49
  CLUS_6                2                 25
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        4      1      0      0
  13Q GAIN WILD-TYPE    150     54    116    167
D18V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                150
  CLUS_2                1                 54
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q GAIN MUTATED        4      1      0      0      0
  13Q GAIN WILD-TYPE    122     99     73    115     78
D18V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                122
  CLUS_2                1                 99
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3      0      2
  13Q GAIN WILD-TYPE    147    173    168
D18V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                147
  CLUS_2                0                173
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3      0      2
  13Q GAIN WILD-TYPE    122    205    161
D18V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                122
  CLUS_2                0                205
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3      0      2
  13Q GAIN WILD-TYPE    160    169    159
D18V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                160
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        3      0      2      0
  13Q GAIN WILD-TYPE    120    187    103     78
D18V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                120
  CLUS_2                0                187
  CLUS_3                2                103
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 14Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        9      1      1
  14Q GAIN WILD-TYPE     25    382     76
D19V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                 25
  CLUS_2                1                382
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1     10      0
  14Q GAIN WILD-TYPE    272    141     70
D19V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               10                141
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      2      2
  14Q GAIN WILD-TYPE     60     77     79
D19V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                2                 77
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  14Q GAIN MUTATED        1      0      0      2      0      2      0
  14Q GAIN WILD-TYPE     45     28     33     27     49     25      9
D19V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                2                 27
  CLUS_5                0                 49
  CLUS_6                2                 25
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED       10      0      0      1
  14Q GAIN WILD-TYPE    144     55    116    166
D19V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                144
  CLUS_2                0                 55
  CLUS_3                0                116
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q GAIN MUTATED       10      0      0      0      1
  14Q GAIN WILD-TYPE    116    100     73    115     77
D19V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                116
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                1                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        9      0      2
  14Q GAIN WILD-TYPE    141    173    168
D19V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                141
  CLUS_2                0                173
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        9      0      2
  14Q GAIN WILD-TYPE    116    205    161
D19V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                116
  CLUS_2                0                205
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        9      0      2
  14Q GAIN WILD-TYPE    154    169    159
D19V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                154
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        9      0      1      1
  14Q GAIN WILD-TYPE    114    187    104     77
D19V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                114
  CLUS_2                0                187
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       14      0      1
  16P GAIN WILD-TYPE     20    383     76
D20V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                 20
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        1     13      1
  16P GAIN WILD-TYPE    272    138     69
D20V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               13                138
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        1      4      4
  16P GAIN WILD-TYPE     60     75     77
D20V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                4                 75
  CLUS_3                4                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P GAIN MUTATED        2      1      0      3      0      3      0
  16P GAIN WILD-TYPE     44     27     33     26     49     24      9
D20V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                3                 26
  CLUS_5                0                 49
  CLUS_6                3                 24
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED       13      0      1      1
  16P GAIN WILD-TYPE    141     55    115    166
D20V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               13                141
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED       12      1      1      1      0
  16P GAIN WILD-TYPE    114     99     72    114     78
D20V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               12                114
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       12      1      2
  16P GAIN WILD-TYPE    138    172    168
D20V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               12                138
  CLUS_2                1                172
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       11      2      2
  16P GAIN WILD-TYPE    114    203    161
D20V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               11                114
  CLUS_2                2                203
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       13      0      2
  16P GAIN WILD-TYPE    150    169    159
D20V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               13                150
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED       12      1      1      1
  16P GAIN WILD-TYPE    111    186    104     77
D20V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               12                111
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       13      0      0
  16Q GAIN WILD-TYPE     21    383     77
D21V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               13                 21
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        1     11      1
  16Q GAIN WILD-TYPE    272    140     69
D21V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               11                140
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        1      3      3
  16Q GAIN WILD-TYPE     60     76     78
D21V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                3                 76
  CLUS_3                3                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        2      1      0      2      0      2      0
  16Q GAIN WILD-TYPE     44     27     33     27     49     25      9
D21V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                2                 27
  CLUS_5                0                 49
  CLUS_6                2                 25
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED       11      0      1      1
  16Q GAIN WILD-TYPE    143     55    115    166
D21V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               11                143
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED       10      1      1      1      0
  16Q GAIN WILD-TYPE    116     99     72    114     78
D21V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                116
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       10      1      2
  16Q GAIN WILD-TYPE    140    172    168
D21V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                140
  CLUS_2                1                172
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       10      1      2
  16Q GAIN WILD-TYPE    115    204    161
D21V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                115
  CLUS_2                1                204
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       11      0      2
  16Q GAIN WILD-TYPE    152    169    159
D21V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               11                152
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED       10      1      1      1
  16Q GAIN WILD-TYPE    113    186    104     77
D21V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                113
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 17P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       12      2      2
  17P GAIN WILD-TYPE     22    381     75
D22V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               12                 22
  CLUS_2                2                381
  CLUS_3                2                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        1     15      0
  17P GAIN WILD-TYPE    272    136     70
D22V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               15                136
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        1      4      3
  17P GAIN WILD-TYPE     60     75     78
D22V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                4                 75
  CLUS_3                3                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P GAIN MUTATED        1      1      0      2      0      4      0
  17P GAIN WILD-TYPE     45     27     33     27     49     23      9
D22V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                2                 27
  CLUS_5                0                 49
  CLUS_6                4                 23
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED       15      0      1      0
  17P GAIN WILD-TYPE    139     55    115    167
D22V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               15                139
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P GAIN MUTATED       15      0      1      0      0
  17P GAIN WILD-TYPE    111    100     72    115     78
D22V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               15                111
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       14      1      1
  17P GAIN WILD-TYPE    136    172    169
D22V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               14                136
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       14      1      1
  17P GAIN WILD-TYPE    111    204    162
D22V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               14                111
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       15      0      1
  17P GAIN WILD-TYPE    148    169    160
D22V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               15                148
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED       14      1      1      0
  17P GAIN WILD-TYPE    109    186    104     78
D22V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               14                109
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       13      2      3
  17Q GAIN WILD-TYPE     21    381     74
D23V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               13                 21
  CLUS_2                2                381
  CLUS_3                3                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        2     16      0
  17Q GAIN WILD-TYPE    271    135     70
D23V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                271
  CLUS_2               16                135
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      4      4
  17Q GAIN WILD-TYPE     60     75     77
D23V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                4                 75
  CLUS_3                4                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q GAIN MUTATED        1      1      0      3      0      4      0
  17Q GAIN WILD-TYPE     45     27     33     26     49     23      9
D23V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                3                 26
  CLUS_5                0                 49
  CLUS_6                4                 23
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED       16      0      1      1
  17Q GAIN WILD-TYPE    138     55    115    166
D23V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                138
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED       16      0      1      1      0
  17Q GAIN WILD-TYPE    110    100     72    114     78
D23V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                110
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       15      2      1
  17Q GAIN WILD-TYPE    135    171    169
D23V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               15                135
  CLUS_2                2                171
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       15      1      2
  17Q GAIN WILD-TYPE    110    204    161
D23V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               15                110
  CLUS_2                1                204
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       16      1      1
  17Q GAIN WILD-TYPE    147    168    160
D23V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                147
  CLUS_2                1                168
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED       15      1      1      1
  17Q GAIN WILD-TYPE    108    186    104     77
D23V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               15                108
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        5      0      1
  18P GAIN WILD-TYPE     29    383     76
D24V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 29
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        1      4      1
  18P GAIN WILD-TYPE    272    147     69
D24V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2                4                147
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        0      0      2
  18P GAIN WILD-TYPE     61     79     79
D24V3, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P GAIN MUTATED        0      1      0      1      0      0      0
  18P GAIN WILD-TYPE     46     27     33     28     49     27      9
D24V4, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        4      1      1      0
  18P GAIN WILD-TYPE    150     54    115    167
D24V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                150
  CLUS_2                1                 54
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P GAIN MUTATED        4      1      1      0      0
  18P GAIN WILD-TYPE    122     99     72    115     78
D24V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                122
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        4      1      1
  18P GAIN WILD-TYPE    146    172    169
D24V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                146
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        4      1      1
  18P GAIN WILD-TYPE    121    204    162
D24V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                121
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        5      0      1
  18P GAIN WILD-TYPE    158    169    160
D24V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        4      1      1      0
  18P GAIN WILD-TYPE    119    186    104     78
D24V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                119
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        5      0      1
  18Q GAIN WILD-TYPE     29    383     76
D25V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                 29
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        1      4      1
  18Q GAIN WILD-TYPE    272    147     69
D25V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2                4                147
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        0      0      2
  18Q GAIN WILD-TYPE     61     79     79
D25V3, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q GAIN MUTATED        0      1      0      1      0      0      0
  18Q GAIN WILD-TYPE     46     27     33     28     49     27      9
D25V4, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        4      1      1      0
  18Q GAIN WILD-TYPE    150     54    115    167
D25V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                150
  CLUS_2                1                 54
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q GAIN MUTATED        4      1      1      0      0
  18Q GAIN WILD-TYPE    122     99     72    115     78
D25V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                122
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        4      1      1
  18Q GAIN WILD-TYPE    146    172    169
D25V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                146
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        4      1      1
  18Q GAIN WILD-TYPE    121    204    162
D25V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                121
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        5      0      1
  18Q GAIN WILD-TYPE    158    169    160
D25V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        4      1      1      0
  18Q GAIN WILD-TYPE    119    186    104     78
D25V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                119
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        8      0      0
  19P GAIN WILD-TYPE     26    383     77
D26V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 26
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      8      0
  19P GAIN WILD-TYPE    273    143     70
D26V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                273
  CLUS_2                8                143
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      2      0
  19P GAIN WILD-TYPE     61     77     81
D26V3, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YD         TCGA-EM-A1YE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CS         TCGA-EM-A2CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A2P1         TCGA-EM-A3AI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39L         TCGA-ET-A39M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39P         TCGA-ET-A39R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P GAIN MUTATED        0      0      0      0      0      2      0
  19P GAIN WILD-TYPE     46     28     33     29     49     25      9
D26V4, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YD         TCGA-EM-A1YE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CS         TCGA-EM-A2CU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A2P1         TCGA-EM-A3AI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39L         TCGA-ET-A39M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39P         TCGA-ET-A39R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        8      0      0      0
  19P GAIN WILD-TYPE    146     55    116    167
D26V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                146
  CLUS_2                0                 55
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED        8      0      0      0      0
  19P GAIN WILD-TYPE    118    100     73    115     78
D26V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                118
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        8      0      0
  19P GAIN WILD-TYPE    142    173    170
D26V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                142
  CLUS_2                0                173
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        8      0      0
  19P GAIN WILD-TYPE    117    205    163
D26V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                117
  CLUS_2                0                205
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        8      0      0
  19P GAIN WILD-TYPE    155    169    161
D26V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                155
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        8      0      0      0
  19P GAIN WILD-TYPE    115    187    105     78
D26V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                115
  CLUS_2                0                187
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        9      0      1
  19Q GAIN WILD-TYPE     25    383     76
D27V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                9                 25
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0     10      0
  19Q GAIN WILD-TYPE    273    141     70
D27V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                273
  CLUS_2               10                141
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      2      1
  19Q GAIN WILD-TYPE     61     77     80
D27V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 61
  CLUS_2                2                 77
  CLUS_3                1                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q GAIN MUTATED        0      0      0      1      0      2      0
  19Q GAIN WILD-TYPE     46     28     33     28     49     25      9
D27V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                0                 49
  CLUS_6                2                 25
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       10      0      0      0
  19Q GAIN WILD-TYPE    144     55    116    167
D27V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                144
  CLUS_2                0                 55
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED       10      0      0      0      0
  19Q GAIN WILD-TYPE    116    100     73    115     78
D27V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                116
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       10      0      0
  19Q GAIN WILD-TYPE    140    173    170
D27V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                140
  CLUS_2                0                173
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       10      0      0
  19Q GAIN WILD-TYPE    115    205    163
D27V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                115
  CLUS_2                0                205
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       10      0      0
  19Q GAIN WILD-TYPE    153    169    161
D27V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                153
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       10      0      0      0
  19Q GAIN WILD-TYPE    113    187    105     78
D27V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                113
  CLUS_2                0                187
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 20P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       12      0      0
  20P GAIN WILD-TYPE     22    383     77
D28V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               12                 22
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        1     10      1
  20P GAIN WILD-TYPE    272    141     69
D28V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               10                141
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        1      3      3
  20P GAIN WILD-TYPE     60     76     78
D28V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                3                 76
  CLUS_3                3                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P GAIN MUTATED        1      1      0      2      0      3      0
  20P GAIN WILD-TYPE     45     27     33     27     49     24      9
D28V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                2                 27
  CLUS_5                0                 49
  CLUS_6                3                 24
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       10      0      1      1
  20P GAIN WILD-TYPE    144     55    115    166
D28V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                144
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P GAIN MUTATED       10      0      1      1      0
  20P GAIN WILD-TYPE    116    100     72    114     78
D28V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                116
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        9      1      2
  20P GAIN WILD-TYPE    141    172    168
D28V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                141
  CLUS_2                1                172
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        9      1      2
  20P GAIN WILD-TYPE    116    204    161
D28V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                116
  CLUS_2                1                204
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       10      0      2
  20P GAIN WILD-TYPE    153    169    159
D28V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                153
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        9      1      1      1
  20P GAIN WILD-TYPE    114    186    104     77
D28V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                114
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 20Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       12      0      0
  20Q GAIN WILD-TYPE     22    383     77
D29V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               12                 22
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        1     10      1
  20Q GAIN WILD-TYPE    272    141     69
D29V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2               10                141
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        1      3      3
  20Q GAIN WILD-TYPE     60     76     78
D29V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                3                 76
  CLUS_3                3                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q GAIN MUTATED        1      1      0      2      0      3      0
  20Q GAIN WILD-TYPE     45     27     33     27     49     24      9
D29V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                1                 27
  CLUS_3                0                 33
  CLUS_4                2                 27
  CLUS_5                0                 49
  CLUS_6                3                 24
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       10      0      1      1
  20Q GAIN WILD-TYPE    144     55    115    166
D29V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                144
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q GAIN MUTATED       10      0      1      1      0
  20Q GAIN WILD-TYPE    116    100     72    114     78
D29V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                116
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        9      1      2
  20Q GAIN WILD-TYPE    141    172    168
D29V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                141
  CLUS_2                1                172
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        9      1      2
  20Q GAIN WILD-TYPE    116    204    161
D29V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                116
  CLUS_2                1                204
  CLUS_3                2                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       10      0      2
  20Q GAIN WILD-TYPE    153    169    159
D29V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                153
  CLUS_2                0                169
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        9      1      1      1
  20Q GAIN WILD-TYPE    114    186    104     77
D29V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                114
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                1                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        4      0      1
  21Q GAIN WILD-TYPE     30    383     76
D30V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                 30
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        1      3      1
  21Q GAIN WILD-TYPE    272    148     69
D30V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                272
  CLUS_2                3                148
  CLUS_3                1                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        0      0      2
  21Q GAIN WILD-TYPE     61     79     79
D30V3, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q GAIN MUTATED        0      1      0      1      0      0      0
  21Q GAIN WILD-TYPE     46     27     33     28     49     27      9
D30V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28Z         TCGA-BJ-A290 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N7         TCGA-BJ-A2N9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-CE-A13K         TCGA-CE-A27D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-DE-A0Y2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DJ-A13M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QI         TCGA-DJ-A1QL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QN         TCGA-DJ-A1QO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A2QC         TCGA-DO-A1JZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CL         TCGA-EL-A3CM         TCGA-EL-A3CN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CP         TCGA-EL-A3CR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3GR         TCGA-EL-A3GS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3GY         TCGA-EL-A3GZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H1         TCGA-EL-A3H2         TCGA-EL-A3H3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3N3         TCGA-EM-A1CT         TCGA-EM-A1CU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YB         TCGA-EM-A1YC         TCGA-EM-A1YD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22L         TCGA-EM-A22M         TCGA-EM-A22O 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CJ         TCGA-EM-A2CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CL         TCGA-EM-A2CN         TCGA-EM-A2CO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2N0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        3      1      1      0
  21Q GAIN WILD-TYPE    151     54    115    167
D30V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                151
  CLUS_2                1                 54
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        3      1      1      0      0
  21Q GAIN WILD-TYPE    123     99     72    115     78
D30V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                123
  CLUS_2                1                 99
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        3      1      1
  21Q GAIN WILD-TYPE    147    172    169
D30V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                147
  CLUS_2                1                172
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        3      1      1
  21Q GAIN WILD-TYPE    122    204    162
D30V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                122
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        4      0      1
  21Q GAIN WILD-TYPE    159    169    160
D30V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                159
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        3      1      1      0
  21Q GAIN WILD-TYPE    120    186    104     78
D30V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                120
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        7      2      0
  XQ GAIN WILD-TYPE     27    381     77
D31V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               7                27
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1      6      2
  XQ GAIN WILD-TYPE    272    145     68
D31V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               272
  CLUS_2               6               145
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1      2      1
  XQ GAIN WILD-TYPE     60     77     80
D31V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                60
  CLUS_2               2                77
  CLUS_3               1                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ GAIN MUTATED        2      0      0      1      0      1      0
  XQ GAIN WILD-TYPE     44     28     33     28     49     26      9
D31V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               0                49
  CLUS_6               1                26
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        6      1      0      2
  XQ GAIN WILD-TYPE    148     54    116    165
D31V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               6               148
  CLUS_2               1                54
  CLUS_3               0               116
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED        5      2      0      1      1
  XQ GAIN WILD-TYPE    121     98     73    114     77
D31V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               121
  CLUS_2               2                98
  CLUS_3               0                73
  CLUS_4               1               114
  CLUS_5               1                77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        5      2      2
  XQ GAIN WILD-TYPE    145    171    168
D31V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               145
  CLUS_2               2               171
  CLUS_3               2               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        5      2      2
  XQ GAIN WILD-TYPE    120    203    161
D31V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               120
  CLUS_2               2               203
  CLUS_3               2               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        5      2      2
  XQ GAIN WILD-TYPE    158    167    159
D31V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               158
  CLUS_2               2               167
  CLUS_3               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        5      2      1      1
  XQ GAIN WILD-TYPE    118    185    104     77
D31V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               118
  CLUS_2               2               185
  CLUS_3               1               104
  CLUS_4               1                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        4      0      0
  1P LOSS WILD-TYPE     30    383     77
D32V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                30
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      3      0
  1P LOSS WILD-TYPE    272    148     70
D32V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               272
  CLUS_2               3               148
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        0      0      2
  1P LOSS WILD-TYPE     61     79     79
D32V3, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P LOSS MUTATED        1      0      0      1      0      0      0
  1P LOSS WILD-TYPE     45     28     33     28     49     27      9
D32V4, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        3      0      1      0
  1P LOSS WILD-TYPE    151     55    115    167
D32V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               1               115
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED        3      1      0      0      0
  1P LOSS WILD-TYPE    123     99     73    115     78
D32V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               123
  CLUS_2               1                99
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        3      0      1
  1P LOSS WILD-TYPE    147    173    169
D32V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               147
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        3      0      1
  1P LOSS WILD-TYPE    122    205    162
D32V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               122
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        3      0      1
  1P LOSS WILD-TYPE    160    169    160
D32V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        3      0      1      0
  1P LOSS WILD-TYPE    120    187    104     78
D32V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               120
  CLUS_2               0               187
  CLUS_3               1               104
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        3      0      0
  1Q LOSS WILD-TYPE     31    383     77
D33V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                31
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        0      3      0
  1Q LOSS WILD-TYPE    273    148     70
D33V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               3               148
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        0      0      2
  1Q LOSS WILD-TYPE     61     79     79
D33V3, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q LOSS MUTATED        1      0      0      1      0      0      0
  1Q LOSS WILD-TYPE     45     28     33     28     49     27      9
D33V4, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        3      0      0      0
  1Q LOSS WILD-TYPE    151     55    116    167
D33V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q LOSS MUTATED        3      0      0      0      0
  1Q LOSS WILD-TYPE    123    100     73    115     78
D33V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        3      0      0
  1Q LOSS WILD-TYPE    147    173    170
D33V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               147
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        3      0      0
  1Q LOSS WILD-TYPE    122    205    163
D33V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               122
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        3      0      0
  1Q LOSS WILD-TYPE    160    169    161
D33V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        3      0      0      0
  1Q LOSS WILD-TYPE    120    187    105     78
D33V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               120
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        9      0      1
  2P LOSS WILD-TYPE     25    383     76
D34V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9                25
  CLUS_2               0               383
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        0     10      0
  2P LOSS WILD-TYPE    273    141     70
D34V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2              10               141
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        1      3      2
  2P LOSS WILD-TYPE     60     76     79
D34V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                60
  CLUS_2               3                76
  CLUS_3               2                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2P LOSS MUTATED        2      0      0      1      0      3      0
  2P LOSS WILD-TYPE     44     28     33     28     49     24      9
D34V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               0                49
  CLUS_6               3                24
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED       10      0      0      0
  2P LOSS WILD-TYPE    144     55    116    167
D34V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               144
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P LOSS MUTATED       10      0      0      0      0
  2P LOSS WILD-TYPE    116    100     73    115     78
D34V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               116
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       10      0      0
  2P LOSS WILD-TYPE    140    173    170
D34V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               140
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       10      0      0
  2P LOSS WILD-TYPE    115    205    163
D34V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               115
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       10      0      0
  2P LOSS WILD-TYPE    153    169    161
D34V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               153
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED       10      0      0      0
  2P LOSS WILD-TYPE    113    187    105     78
D34V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               113
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      0      0
  2Q LOSS WILD-TYPE     24    383     77
D35V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10                24
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        0     10      0
  2Q LOSS WILD-TYPE    273    141     70
D35V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2              10               141
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        1      3      2
  2Q LOSS WILD-TYPE     60     76     79
D35V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                60
  CLUS_2               3                76
  CLUS_3               2                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2Q LOSS MUTATED        2      0      0      1      0      3      0
  2Q LOSS WILD-TYPE     44     28     33     28     49     24      9
D35V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               0                49
  CLUS_6               3                24
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED       10      0      0      0
  2Q LOSS WILD-TYPE    144     55    116    167
D35V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               144
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q LOSS MUTATED       10      0      0      0      0
  2Q LOSS WILD-TYPE    116    100     73    115     78
D35V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               116
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      0      0
  2Q LOSS WILD-TYPE    140    173    170
D35V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               140
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      0      0
  2Q LOSS WILD-TYPE    115    205    163
D35V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               115
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      0      0
  2Q LOSS WILD-TYPE    153    169    161
D35V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               153
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED       10      0      0      0
  2Q LOSS WILD-TYPE    113    187    105     78
D35V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               113
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        3      0      0
  3P LOSS WILD-TYPE     31    383     77
D36V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                31
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        0      3      0
  3P LOSS WILD-TYPE    273    148     70
D36V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               3               148
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        1      0      1
  3P LOSS WILD-TYPE     60     79     80
D36V3, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3P LOSS MUTATED        1      0      0      1      0      0      0
  3P LOSS WILD-TYPE     45     28     33     28     49     27      9
D36V4, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        3      0      0      0
  3P LOSS WILD-TYPE    151     55    116    167
D36V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P LOSS MUTATED        3      0      0      0      0
  3P LOSS WILD-TYPE    123    100     73    115     78
D36V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        3      0      0
  3P LOSS WILD-TYPE    147    173    170
D36V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               147
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        3      0      0
  3P LOSS WILD-TYPE    122    205    163
D36V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               122
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        3      0      0
  3P LOSS WILD-TYPE    160    169    161
D36V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        3      0      0      0
  3P LOSS WILD-TYPE    120    187    105     78
D36V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3               120
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        4      0      0
  3Q LOSS WILD-TYPE     30    383     77
D37V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4                30
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        0      4      0
  3Q LOSS WILD-TYPE    273    147     70
D37V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               4               147
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        1      0      2
  3Q LOSS WILD-TYPE     60     79     79
D37V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                60
  CLUS_2               0                79
  CLUS_3               2                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3Q LOSS MUTATED        2      0      0      1      0      0      0
  3Q LOSS WILD-TYPE     44     28     33     28     49     27      9
D37V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               0                49
  CLUS_6               0                27
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        4      0      0      0
  3Q LOSS WILD-TYPE    150     55    116    167
D37V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               150
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q LOSS MUTATED        4      0      0      0      0
  3Q LOSS WILD-TYPE    122    100     73    115     78
D37V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               122
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        4      0      0
  3Q LOSS WILD-TYPE    146    173    170
D37V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               146
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        4      0      0
  3Q LOSS WILD-TYPE    121    205    163
D37V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               121
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        4      0      0
  3Q LOSS WILD-TYPE    159    169    161
D37V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               159
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        4      0      0      0
  3Q LOSS WILD-TYPE    119    187    105     78
D37V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        3      1      0
  6P LOSS WILD-TYPE     31    382     77
D38V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                31
  CLUS_2               1               382
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        0      3      1
  6P LOSS WILD-TYPE    273    148     69
D38V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               3               148
  CLUS_3               1                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        0      0      2
  6P LOSS WILD-TYPE     61     79     79
D38V3, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6P LOSS MUTATED        0      0      0      1      1      0      0
  6P LOSS WILD-TYPE     46     28     33     28     48     27      9
D38V4, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-E3-A3DY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-EL-A3CL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P        TCGA-ET-A39R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        3      0      0      1
  6P LOSS WILD-TYPE    151     55    116    166
D38V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               1               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P LOSS MUTATED        3      0      0      1      0
  6P LOSS WILD-TYPE    123    100     73    114     78
D38V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               1               114
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        3      0      1
  6P LOSS WILD-TYPE    147    173    169
D38V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               147
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        3      0      1
  6P LOSS WILD-TYPE    122    205    162
D38V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               122
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        3      0      1
  6P LOSS WILD-TYPE    160    169    160
D38V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        3      0      0      1
  6P LOSS WILD-TYPE    120    187    105     77
D38V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               120
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               1                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        5      2      0
  6Q LOSS WILD-TYPE     29    381     77
D39V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                29
  CLUS_2               2               381
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        0      6      1
  6Q LOSS WILD-TYPE    273    145     69
D39V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               6               145
  CLUS_3               1                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        0      0      5
  6Q LOSS WILD-TYPE     61     79     76
D39V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                61
  CLUS_2               0                79
  CLUS_3               5                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED        2      0      0      2      1      0      0
  6Q LOSS WILD-TYPE     44     28     33     27     48     27      9
D39V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               2                27
  CLUS_5               1                48
  CLUS_6               0                27
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        6      0      0      1
  6Q LOSS WILD-TYPE    148     55    116    166
D39V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               148
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               1               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6Q LOSS MUTATED        6      0      0      1      0
  6Q LOSS WILD-TYPE    120    100     73    114     78
D39V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               120
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               1               114
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        6      0      1
  6Q LOSS WILD-TYPE    144    173    169
D39V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               144
  CLUS_2               0               173
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        6      0      1
  6Q LOSS WILD-TYPE    119    205    162
D39V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               119
  CLUS_2               0               205
  CLUS_3               1               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        6      0      1
  6Q LOSS WILD-TYPE    157    169    160
D39V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               157
  CLUS_2               0               169
  CLUS_3               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        6      0      0      1
  6Q LOSS WILD-TYPE    117    187    105     77
D39V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6               117
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               1                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        4      0      0
  8P LOSS WILD-TYPE     30    383     77
D40V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                30
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      4      0
  8P LOSS WILD-TYPE    273    147     70
D40V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               4               147
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        1      1      0
  8P LOSS WILD-TYPE     60     78     81
D40V3, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC        TCGA-DO-A1JZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A2EA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P LOSS MUTATED        1      0      0      0      0      1      0
  8P LOSS WILD-TYPE     45     28     33     29     49     26      9
D40V4, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC        TCGA-DO-A1JZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A2EA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        4      0      0      0
  8P LOSS WILD-TYPE    150     55    116    167
D40V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               150
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P LOSS MUTATED        4      0      0      0      0
  8P LOSS WILD-TYPE    122    100     73    115     78
D40V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               122
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        4      0      0
  8P LOSS WILD-TYPE    146    173    170
D40V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               146
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        4      0      0
  8P LOSS WILD-TYPE    121    205    163
D40V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               121
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        4      0      0
  8P LOSS WILD-TYPE    159    169    161
D40V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               159
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        4      0      0      0
  8P LOSS WILD-TYPE    119    187    105     78
D40V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        4      0      0
  8Q LOSS WILD-TYPE     30    383     77
D41V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                30
  CLUS_2               0               383
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      4      0
  8Q LOSS WILD-TYPE    273    147     70
D41V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               4               147
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        1      1      0
  8Q LOSS WILD-TYPE     60     78     81
D41V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC        TCGA-DO-A1JZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A2EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q LOSS MUTATED        1      0      0      0      0      1      0
  8Q LOSS WILD-TYPE     45     28     33     29     49     26      9
D41V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               219 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z0        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-CE-A13K        TCGA-CE-A27D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-DE-A0Y2        TCGA-DE-A2OL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A2QC        TCGA-DO-A1JZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A2EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3NZ        TCGA-J8-A3O0        TCGA-J8-A3O1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        4      0      0      0
  8Q LOSS WILD-TYPE    150     55    116    167
D41V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               150
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED        4      0      0      0      0
  8Q LOSS WILD-TYPE    122    100     73    115     78
D41V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               122
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        4      0      0
  8Q LOSS WILD-TYPE    146    173    170
D41V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               146
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        4      0      0
  8Q LOSS WILD-TYPE    121    205    163
D41V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               121
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        4      0      0
  8Q LOSS WILD-TYPE    159    169    161
D41V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               159
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        4      0      0      0
  8Q LOSS WILD-TYPE    119    187    105     78
D41V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       13      5      1
  9P LOSS WILD-TYPE     21    378     76
D42V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              13                21
  CLUS_2               5               378
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        6     11      2
  9P LOSS WILD-TYPE    267    140     68
D42V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               6               267
  CLUS_2              11               140
  CLUS_3               2                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        0      2      4
  9P LOSS WILD-TYPE     61     77     77
D42V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                61
  CLUS_2               2                77
  CLUS_3               4                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P LOSS MUTATED        1      0      0      1      2      2      0
  9P LOSS WILD-TYPE     45     28     33     28     47     25      9
D42V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                45
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               2                47
  CLUS_6               2                25
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       11      3      3      2
  9P LOSS WILD-TYPE    143     52    113    165
D42V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               143
  CLUS_2               3                52
  CLUS_3               3               113
  CLUS_4               2               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P LOSS MUTATED       11      2      1      4      1
  9P LOSS WILD-TYPE    115     98     72    111     77
D42V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               115
  CLUS_2               2                98
  CLUS_3               1                72
  CLUS_4               4               111
  CLUS_5               1                77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       10      1      8
  9P LOSS WILD-TYPE    140    172    162
D42V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              10               140
  CLUS_2               1               172
  CLUS_3               8               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       10      2      7
  9P LOSS WILD-TYPE    115    203    156
D42V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              10               115
  CLUS_2               2               203
  CLUS_3               7               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       10      1      8
  9P LOSS WILD-TYPE    153    168    153
D42V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              10               153
  CLUS_2               1               168
  CLUS_3               8               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       11      1      5      2
  9P LOSS WILD-TYPE    112    186    100     76
D42V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               112
  CLUS_2               1               186
  CLUS_3               5               100
  CLUS_4               2                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       16      7      1
  9Q LOSS WILD-TYPE     18    376     76
D43V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              16                18
  CLUS_2               7               376
  CLUS_3               1                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        8     12      4
  9Q LOSS WILD-TYPE    265    139     66
D43V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               8               265
  CLUS_2              12               139
  CLUS_3               4                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        0      4      4
  9Q LOSS WILD-TYPE     61     75     77
D43V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                61
  CLUS_2               4                75
  CLUS_3               4                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q LOSS MUTATED        1      0      0      1      2      4      0
  9Q LOSS WILD-TYPE     45     28     33     28     47     23      9
D43V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                45
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               2                47
  CLUS_6               4                23
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       12      4      3      5
  9Q LOSS WILD-TYPE    142     51    113    162
D43V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              12               142
  CLUS_2               4                51
  CLUS_3               3               113
  CLUS_4               5               162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q LOSS MUTATED       12      2      1      7      2
  9Q LOSS WILD-TYPE    114     98     72    108     76
D43V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              12               114
  CLUS_2               2                98
  CLUS_3               1                72
  CLUS_4               7               108
  CLUS_5               2                76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       11      2     11
  9Q LOSS WILD-TYPE    139    171    159
D43V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               139
  CLUS_2               2               171
  CLUS_3              11               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       11      3     10
  9Q LOSS WILD-TYPE    114    202    153
D43V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               114
  CLUS_2               3               202
  CLUS_3              10               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       11      2     11
  9Q LOSS WILD-TYPE    152    167    150
D43V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               152
  CLUS_2               2               167
  CLUS_3              11               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       12      2      5      5
  9Q LOSS WILD-TYPE    111    185    100     73
D43V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              12               111
  CLUS_2               2               185
  CLUS_3               5               100
  CLUS_4               5                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        7      0      0
  10P LOSS WILD-TYPE     27    383     77
D44V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                 27
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        1      6      0
  10P LOSS WILD-TYPE    272    145     70
D44V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                272
  CLUS_2                6                145
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        1      0      2
  10P LOSS WILD-TYPE     60     79     79
D44V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                0                 79
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10P LOSS MUTATED        2      0      0      1      0      0      0
  10P LOSS WILD-TYPE     44     28     33     28     49     27      9
D44V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                0                 49
  CLUS_6                0                 27
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        6      0      1      0
  10P LOSS WILD-TYPE    148     55    115    167
D44V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                148
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P LOSS MUTATED        6      1      0      0      0
  10P LOSS WILD-TYPE    120     99     73    115     78
D44V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                120
  CLUS_2                1                 99
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        6      0      1
  10P LOSS WILD-TYPE    144    173    169
D44V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                144
  CLUS_2                0                173
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        6      0      1
  10P LOSS WILD-TYPE    119    205    162
D44V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                119
  CLUS_2                0                205
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        6      0      1
  10P LOSS WILD-TYPE    157    169    160
D44V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        6      0      1      0
  10P LOSS WILD-TYPE    117    187    104     78
D44V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                117
  CLUS_2                0                187
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        6      0      0
  10Q LOSS WILD-TYPE     28    383     77
D45V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 28
  CLUS_2                0                383
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        1      5      0
  10Q LOSS WILD-TYPE    272    146     70
D45V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                272
  CLUS_2                5                146
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        1      0      1
  10Q LOSS WILD-TYPE     60     79     80
D45V3, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A191 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-CE-A27D         TCGA-CE-A3MD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CE-A3ME         TCGA-DE-A0Y2         TCGA-DE-A2OL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DJ-A13M         TCGA-DJ-A13O 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13V 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A13W         TCGA-DJ-A13X         TCGA-DJ-A1QD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QI         TCGA-DJ-A1QL         TCGA-DJ-A1QM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QN         TCGA-DJ-A1QO         TCGA-DJ-A2PN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PP         TCGA-DJ-A2PQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PS         TCGA-DJ-A2PU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q4         TCGA-DJ-A2Q5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q6         TCGA-DJ-A2Q7         TCGA-DJ-A2Q8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2QC         TCGA-DO-A1JZ         TCGA-DO-A1K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E3         TCGA-E3-A3E5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A2JQ         TCGA-EL-A3CL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CS         TCGA-EM-A2CU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A2OY         TCGA-EM-A2P1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-EM-A3AJ         TCGA-EM-A3AL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FL         TCGA-EM-A3FN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-ET-A25G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25O 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10Q LOSS MUTATED        1      0      0      1      0      0      0
  10Q LOSS WILD-TYPE     45     28     33     28     49     27      9
D45V4, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                219 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z0         TCGA-BJ-A0Z2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A191 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-CE-A27D         TCGA-CE-A3MD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CE-A3ME         TCGA-DE-A0Y2         TCGA-DE-A2OL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DJ-A13M         TCGA-DJ-A13O 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13V 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A13W         TCGA-DJ-A13X         TCGA-DJ-A1QD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QI         TCGA-DJ-A1QL         TCGA-DJ-A1QM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QN         TCGA-DJ-A1QO         TCGA-DJ-A2PN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PP         TCGA-DJ-A2PQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PS         TCGA-DJ-A2PU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q4         TCGA-DJ-A2Q5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q6         TCGA-DJ-A2Q7         TCGA-DJ-A2Q8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DJ-A2QC         TCGA-DO-A1JZ         TCGA-DO-A1K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E3         TCGA-E3-A3E5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A2JQ         TCGA-EL-A3CL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CS         TCGA-EM-A2CU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A2OY         TCGA-EM-A2P1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-EM-A3AJ         TCGA-EM-A3AL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FL         TCGA-EM-A3FN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-ET-A25G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25O 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39P         TCGA-ET-A39R 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3BX 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DV         TCGA-ET-A3DW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FY-A2QD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3ON         TCGA-GE-A2C6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-IM-A3EB         TCGA-IM-A3ED 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        5      0      1      0
  10Q LOSS WILD-TYPE    149     55    115    167
D45V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                149
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q LOSS MUTATED        5      1      0      0      0
  10Q LOSS WILD-TYPE    121     99     73    115     78
D45V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                121
  CLUS_2                1                 99
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        5      0      1
  10Q LOSS WILD-TYPE    145    173    169
D45V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                145
  CLUS_2                0                173
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        5      0      1
  10Q LOSS WILD-TYPE    120    205    162
D45V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                120
  CLUS_2                0                205
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        5      0      1
  10Q LOSS WILD-TYPE    158    169    160
D45V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                158
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        5      0      1      0
  10Q LOSS WILD-TYPE    118    187    104     78
D45V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                118
  CLUS_2                0                187
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        6      0      1
  11P LOSS WILD-TYPE     28    383     76
D46V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 28
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        1      6      0
  11P LOSS WILD-TYPE    272    145     70
D46V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                272
  CLUS_2                6                145
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        1      0      2
  11P LOSS WILD-TYPE     60     79     79
D46V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                0                 79
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED        1      0      0      1      1      0      0
  11P LOSS WILD-TYPE     45     28     33     28     48     27      9
D46V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                1                 48
  CLUS_6                0                 27
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        6      1      0      0
  11P LOSS WILD-TYPE    148     54    116    167
D46V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                148
  CLUS_2                1                 54
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P LOSS MUTATED        6      0      0      1      0
  11P LOSS WILD-TYPE    120    100     73    114     78
D46V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                120
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                1                114
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        6      0      1
  11P LOSS WILD-TYPE    144    173    169
D46V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                144
  CLUS_2                0                173
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        6      0      1
  11P LOSS WILD-TYPE    119    205    162
D46V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                119
  CLUS_2                0                205
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        6      0      1
  11P LOSS WILD-TYPE    157    169    160
D46V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        6      0      1      0
  11P LOSS WILD-TYPE    117    187    104     78
D46V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                117
  CLUS_2                0                187
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        6      2      1
  11Q LOSS WILD-TYPE     28    381     76
D47V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                 28
  CLUS_2                2                381
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        2      7      0
  11Q LOSS WILD-TYPE    271    144     70
D47V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                271
  CLUS_2                7                144
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        2      0      2
  11Q LOSS WILD-TYPE     59     79     79
D47V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 59
  CLUS_2                0                 79
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED        2      0      0      1      1      0      0
  11Q LOSS WILD-TYPE     44     28     33     28     48     27      9
D47V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                1                 48
  CLUS_6                0                 27
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        7      1      0      1
  11Q LOSS WILD-TYPE    147     54    116    166
D47V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                147
  CLUS_2                1                 54
  CLUS_3                0                116
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q LOSS MUTATED        7      0      0      1      1
  11Q LOSS WILD-TYPE    119    100     73    114     77
D47V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                119
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                1                114
  CLUS_5                1                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        8      0      1
  11Q LOSS WILD-TYPE    142    173    169
D47V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                142
  CLUS_2                0                173
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        7      1      1
  11Q LOSS WILD-TYPE    118    204    162
D47V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                118
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        8      0      1
  11Q LOSS WILD-TYPE    155    169    160
D47V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                155
  CLUS_2                0                169
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        7      1      1      0
  11Q LOSS WILD-TYPE    116    186    104     78
D47V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                116
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        4      7      3
  13Q LOSS WILD-TYPE     30    376     74
D48V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 30
  CLUS_2                7                376
  CLUS_3                3                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        3      9      2
  13Q LOSS WILD-TYPE    270    142     68
D48V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                270
  CLUS_2                9                142
  CLUS_3                2                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        1      1      7
  13Q LOSS WILD-TYPE     60     78     74
D48V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                1                 78
  CLUS_3                7                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q LOSS MUTATED        1      0      0      4      3      1      0
  13Q LOSS WILD-TYPE     45     28     33     25     46     26      9
D48V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                4                 25
  CLUS_5                3                 46
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        9      2      3      0
  13Q LOSS WILD-TYPE    145     53    113    167
D48V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                145
  CLUS_2                2                 53
  CLUS_3                3                113
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q LOSS MUTATED        9      3      2      0      0
  13Q LOSS WILD-TYPE    117     97     71    115     78
D48V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                117
  CLUS_2                3                 97
  CLUS_3                2                 71
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        9      5      0
  13Q LOSS WILD-TYPE    141    168    170
D48V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                141
  CLUS_2                5                168
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        9      5      0
  13Q LOSS WILD-TYPE    116    200    163
D48V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                116
  CLUS_2                5                200
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       10      4      0
  13Q LOSS WILD-TYPE    153    165    161
D48V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               10                153
  CLUS_2                4                165
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        9      4      1      0
  13Q LOSS WILD-TYPE    114    183    104     78
D48V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                114
  CLUS_2                4                183
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        5      2      1
  15Q LOSS WILD-TYPE     29    381     76
D49V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                 29
  CLUS_2                2                381
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        0      8      0
  15Q LOSS WILD-TYPE    273    143     70
D49V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                273
  CLUS_2                8                143
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        0      1      4
  15Q LOSS WILD-TYPE     61     78     77
D49V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 61
  CLUS_2                1                 78
  CLUS_3                4                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED        1      0      0      3      0      1      0
  15Q LOSS WILD-TYPE     45     28     33     26     49     26      9
D49V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                3                 26
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        8      0      0      0
  15Q LOSS WILD-TYPE    146     55    116    167
D49V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                146
  CLUS_2                0                 55
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q LOSS MUTATED        8      0      0      0      0
  15Q LOSS WILD-TYPE    118    100     73    115     78
D49V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                118
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        8      0      0
  15Q LOSS WILD-TYPE    142    173    170
D49V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                142
  CLUS_2                0                173
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        8      0      0
  15Q LOSS WILD-TYPE    117    205    163
D49V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                117
  CLUS_2                0                205
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        8      0      0
  15Q LOSS WILD-TYPE    155    169    161
D49V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                155
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        8      0      0      0
  15Q LOSS WILD-TYPE    115    187    105     78
D49V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                115
  CLUS_2                0                187
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      4      0
  17P LOSS WILD-TYPE     30    379     77
D50V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 30
  CLUS_2                4                379
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      4      0
  17P LOSS WILD-TYPE    269    147     70
D50V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                269
  CLUS_2                4                147
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        1      1      1
  17P LOSS WILD-TYPE     60     78     80
D50V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                1                 78
  CLUS_3                1                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P LOSS MUTATED        2      0      0      0      0      1      0
  17P LOSS WILD-TYPE     44     28     33     29     49     26      9
D50V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                0                 29
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        4      0      1      3
  17P LOSS WILD-TYPE    150     55    115    164
D50V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                150
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                3                164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P LOSS MUTATED        4      1      0      2      1
  17P LOSS WILD-TYPE    122     99     73    113     77
D50V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                122
  CLUS_2                1                 99
  CLUS_3                0                 73
  CLUS_4                2                113
  CLUS_5                1                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      1      3
  17P LOSS WILD-TYPE    146    172    167
D50V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                146
  CLUS_2                1                172
  CLUS_3                3                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      1      3
  17P LOSS WILD-TYPE    121    204    160
D50V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                121
  CLUS_2                1                204
  CLUS_3                3                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      2      2
  17P LOSS WILD-TYPE    159    167    159
D50V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                159
  CLUS_2                2                167
  CLUS_3                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        4      1      1      2
  17P LOSS WILD-TYPE    119    186    104     76
D50V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                119
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                2                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        2      2      0
  17Q LOSS WILD-TYPE     32    381     77
D51V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 32
  CLUS_2                2                381
  CLUS_3                0                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        2      2      0
  17Q LOSS WILD-TYPE    271    149     70
D51V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                271
  CLUS_2                2                149
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        0      0      0
  17Q LOSS WILD-TYPE     61     79     81
D51V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q LOSS MUTATED        0      0      0      0      0      0      0
  17Q LOSS WILD-TYPE     46     28     33     29     49     27      9
D51V4, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        2      0      1      1
  17Q LOSS WILD-TYPE    152     55    115    166
D51V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                152
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                1                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        2      1      0      0      1
  17Q LOSS WILD-TYPE    124     99     73    115     77
D51V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                124
  CLUS_2                1                 99
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                1                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        2      0      2
  17Q LOSS WILD-TYPE    148    173    168
D51V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                148
  CLUS_2                0                173
  CLUS_3                2                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        2      1      1
  17Q LOSS WILD-TYPE    123    204    162
D51V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                123
  CLUS_2                1                204
  CLUS_3                1                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        2      1      1
  17Q LOSS WILD-TYPE    161    168    160
D51V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                161
  CLUS_2                1                168
  CLUS_3                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        2      1      1      0
  17Q LOSS WILD-TYPE    121    186    104     78
D51V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                121
  CLUS_2                1                186
  CLUS_3                1                104
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        3      0      1
  18P LOSS WILD-TYPE     31    383     76
D52V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 31
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      3      0
  18P LOSS WILD-TYPE    272    148     70
D52V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                272
  CLUS_2                3                148
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      1      1
  18P LOSS WILD-TYPE     60     78     80
D52V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                1                 78
  CLUS_3                1                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED        2      0      0      0      0      1      0
  18P LOSS WILD-TYPE     44     28     33     29     49     26      9
D52V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                0                 29
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        3      0      1      0
  18P LOSS WILD-TYPE    151     55    115    167
D52V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                151
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED        3      0      1      0      0
  18P LOSS WILD-TYPE    123    100     72    115     78
D52V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                123
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        3      1      0
  18P LOSS WILD-TYPE    147    172    170
D52V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                147
  CLUS_2                1                172
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        3      1      0
  18P LOSS WILD-TYPE    122    204    163
D52V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                122
  CLUS_2                1                204
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        4      0      0
  18P LOSS WILD-TYPE    159    169    161
D52V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                159
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        3      1      0      0
  18P LOSS WILD-TYPE    120    186    105     78
D52V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                120
  CLUS_2                1                186
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        3      0      1
  18Q LOSS WILD-TYPE     31    383     76
D53V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 31
  CLUS_2                0                383
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      3      0
  18Q LOSS WILD-TYPE    272    148     70
D53V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                272
  CLUS_2                3                148
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      1      1
  18Q LOSS WILD-TYPE     60     78     80
D53V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                1                 78
  CLUS_3                1                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q LOSS MUTATED        2      0      0      0      0      1      0
  18Q LOSS WILD-TYPE     44     28     33     29     49     26      9
D53V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 44
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                0                 29
  CLUS_5                0                 49
  CLUS_6                1                 26
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        3      0      1      0
  18Q LOSS WILD-TYPE    151     55    115    167
D53V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                151
  CLUS_2                0                 55
  CLUS_3                1                115
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q LOSS MUTATED        3      0      1      0      0
  18Q LOSS WILD-TYPE    123    100     72    115     78
D53V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                123
  CLUS_2                0                100
  CLUS_3                1                 72
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        3      1      0
  18Q LOSS WILD-TYPE    147    172    170
D53V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                147
  CLUS_2                1                172
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        3      1      0
  18Q LOSS WILD-TYPE    122    204    163
D53V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                122
  CLUS_2                1                204
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        4      0      0
  18Q LOSS WILD-TYPE    159    169    161
D53V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                159
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        3      1      0      0
  18Q LOSS WILD-TYPE    120    186    105     78
D53V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                120
  CLUS_2                1                186
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        2      2      1
  19P LOSS WILD-TYPE     32    381     76
D54V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 32
  CLUS_2                2                381
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        0      5      0
  19P LOSS WILD-TYPE    273    146     70
D54V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                273
  CLUS_2                5                146
  CLUS_3                0                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        2      0      2
  19P LOSS WILD-TYPE     59     79     79
D54V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 59
  CLUS_2                0                 79
  CLUS_3                2                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P LOSS MUTATED        3      0      0      1      0      0      0
  19P LOSS WILD-TYPE     43     28     33     28     49     27      9
D54V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 43
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                1                 28
  CLUS_5                0                 49
  CLUS_6                0                 27
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        5      0      0      0
  19P LOSS WILD-TYPE    149     55    116    167
D54V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                149
  CLUS_2                0                 55
  CLUS_3                0                116
  CLUS_4                0                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED        5      0      0      0      0
  19P LOSS WILD-TYPE    121    100     73    115     78
D54V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                121
  CLUS_2                0                100
  CLUS_3                0                 73
  CLUS_4                0                115
  CLUS_5                0                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        5      0      0
  19P LOSS WILD-TYPE    145    173    170
D54V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                145
  CLUS_2                0                173
  CLUS_3                0                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        5      0      0
  19P LOSS WILD-TYPE    120    205    163
D54V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                120
  CLUS_2                0                205
  CLUS_3                0                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        5      0      0
  19P LOSS WILD-TYPE    158    169    161
D54V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                158
  CLUS_2                0                169
  CLUS_3                0                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        5      0      0      0
  19P LOSS WILD-TYPE    118    187    105     78
D54V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                118
  CLUS_2                0                187
  CLUS_3                0                105
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        5      2      1
  21Q LOSS WILD-TYPE     29    381     76
D55V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 29
  CLUS_2                2                381
  CLUS_3                1                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        2      4      2
  21Q LOSS WILD-TYPE    271    147     68
D55V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                271
  CLUS_2                4                147
  CLUS_3                2                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        1      2      0
  21Q LOSS WILD-TYPE     60     77     81
D55V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 60
  CLUS_2                2                 77
  CLUS_3                0                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED        1      0      0      0      0      2      0
  21Q LOSS WILD-TYPE     45     28     33     29     49     25      9
D55V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                0                 28
  CLUS_3                0                 33
  CLUS_4                0                 29
  CLUS_5                0                 49
  CLUS_6                2                 25
  CLUS_7                0                  9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        4      1      1      2
  21Q LOSS WILD-TYPE    150     54    115    165
D55V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                150
  CLUS_2                1                 54
  CLUS_3                1                115
  CLUS_4                2                165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q LOSS MUTATED        4      2      0      1      1
  21Q LOSS WILD-TYPE    122     98     73    114     77
D55V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                122
  CLUS_2                2                 98
  CLUS_3                0                 73
  CLUS_4                1                114
  CLUS_5                1                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        4      0      4
  21Q LOSS WILD-TYPE    146    173    166
D55V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                146
  CLUS_2                0                173
  CLUS_3                4                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        4      1      3
  21Q LOSS WILD-TYPE    121    204    160
D55V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                121
  CLUS_2                1                204
  CLUS_3                3                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        4      0      4
  21Q LOSS WILD-TYPE    159    169    157
D55V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                159
  CLUS_2                0                169
  CLUS_3                4                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        4      0      4      0
  21Q LOSS WILD-TYPE    119    187    101     78
D55V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                119
  CLUS_2                0                187
  CLUS_3                4                101
  CLUS_4                0                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        9      0     77
  22Q LOSS WILD-TYPE     25    383      0
D56V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                9                 25
  CLUS_2                0                383
  CLUS_3               77                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       35     45      6
  22Q LOSS WILD-TYPE    238    106     64
D56V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               35                238
  CLUS_2               45                106
  CLUS_3                6                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       15      9     14
  22Q LOSS WILD-TYPE     46     70     67
D56V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               15                 46
  CLUS_2                9                 70
  CLUS_3               14                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  22Q LOSS MUTATED       11      5      2      5      8      6      1
  22Q LOSS WILD-TYPE     35     23     31     24     41     21      8
D56V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                 35
  CLUS_2                5                 23
  CLUS_3                2                 31
  CLUS_4                5                 24
  CLUS_5                8                 41
  CLUS_6                6                 21
  CLUS_7                1                  8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       45      8     26      7
  22Q LOSS WILD-TYPE    109     47     90    160
D56V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               45                109
  CLUS_2                8                 47
  CLUS_3               26                 90
  CLUS_4                7                160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q LOSS MUTATED       40     13     22      9      2
  22Q LOSS WILD-TYPE     86     87     51    106     76
D56V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               40                 86
  CLUS_2               13                 87
  CLUS_3               22                 51
  CLUS_4                9                106
  CLUS_5                2                 76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       41     24     21
  22Q LOSS WILD-TYPE    109    149    149
D56V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               41                109
  CLUS_2               24                149
  CLUS_3               21                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       38     28     20
  22Q LOSS WILD-TYPE     87    177    143
D56V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               38                 87
  CLUS_2               28                177
  CLUS_3               20                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       49     18     19
  22Q LOSS WILD-TYPE    114    151    142
D56V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               49                114
  CLUS_2               18                151
  CLUS_3               19                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       38     26     18      4
  22Q LOSS WILD-TYPE     85    161     87     74
D56V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               38                 85
  CLUS_2               26                161
  CLUS_3               18                 87
  CLUS_4                4                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        2      1      0
  XQ LOSS WILD-TYPE     32    382     77
D57V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                32
  CLUS_2               1               382
  CLUS_3               0                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        0      3      0
  XQ LOSS WILD-TYPE    273    148     70
D57V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               273
  CLUS_2               3               148
  CLUS_3               0                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        2      0      1
  XQ LOSS WILD-TYPE     59     79     80
D57V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                59
  CLUS_2               0                79
  CLUS_3               1                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ LOSS MUTATED        3      0      0      0      0      0      0
  XQ LOSS WILD-TYPE     43     28     33     29     49     27      9
D57V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                43
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               0                29
  CLUS_5               0                49
  CLUS_6               0                27
  CLUS_7               0                 9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        3      0      0      0
  XQ LOSS WILD-TYPE    151     55    116    167
D57V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               151
  CLUS_2               0                55
  CLUS_3               0               116
  CLUS_4               0               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED        3      0      0      0      0
  XQ LOSS WILD-TYPE    123    100     73    115     78
D57V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               123
  CLUS_2               0               100
  CLUS_3               0                73
  CLUS_4               0               115
  CLUS_5               0                78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        3      0      0
  XQ LOSS WILD-TYPE    147    173    170
D57V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               147
  CLUS_2               0               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        3      0      0
  XQ LOSS WILD-TYPE    122    205    163
D57V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               122
  CLUS_2               0               205
  CLUS_3               0               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        3      0      0
  XQ LOSS WILD-TYPE    160    169    161
D57V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               0               169
  CLUS_3               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        3      0      0      0
  XQ LOSS WILD-TYPE    120    187    105     78
D57V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               120
  CLUS_2               0               187
  CLUS_3               0               105
  CLUS_4               0                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
