[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/22542946/THCA-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511440/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=499, common to both=499
[1] "Reduce the number of clustering variables from 82 to 59."
[1]  59 499
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               495 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               495 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               473 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               473 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               496 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               496 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               494 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               494 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               494 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               494 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               478 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               478 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               482 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               482 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               481 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               481 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               479 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               479 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               493 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               493 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               492 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               492 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               496 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               496 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               495 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               495 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                493 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                493 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                494 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                494 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                484 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                484 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                484 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                484 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                494 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                494 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                488 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                488 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                484 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                484 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                486 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                486 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                483 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                483 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                481 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                481 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                493 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                493 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                493 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                493 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                491 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                491 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                489 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                489 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                487 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                487 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                487 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                487 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                494 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                494 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               491 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               491 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               492 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               492 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               495 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               495 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               496 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               496 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               489 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               489 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               489 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               489 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               496 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               496 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               495 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               495 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               495 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               495 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               492 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               492 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               495 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               495 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               495 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               495 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               480 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               480 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25               474 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25               474 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                492 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                492 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                493 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                493 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                492 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                492 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                490 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                490 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                485 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                485 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                491 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                491 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                491 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                491 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                495 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                495 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                495 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                495 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                495 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                495 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                494 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                494 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                491 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                491 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                89                410 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                89                410 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               495 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               495 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               494 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               494 
[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 499 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=4,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 499 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, 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=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        2      1      1
  1P GAIN WILD-TYPE    130    137    228
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               1               137
  CLUS_3               1               228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      1      0      1
  1P GAIN WILD-TYPE     45    146     83     42    179
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                45
  CLUS_2               1               146
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  1P GAIN MUTATED        0      1      0      0
  1P GAIN WILD-TYPE     64     63     42     49
D1V3, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               218 
       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-EL-A3CL        TCGA-EL-A3CM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1 
"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     47     26      9
D1V4, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               218 
       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-EL-A3CL        TCGA-EL-A3CM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BN        TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        2      1      1      0
  1P GAIN WILD-TYPE    156    166     57    114
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2               1               166
  CLUS_3               1                57
  CLUS_4               0               114
[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        2      1      1      0      0
  1P GAIN WILD-TYPE    102    133     85     95     78
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               1               133
  CLUS_3               1                85
  CLUS_4               0                95
  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 CLUS_4
  1P GAIN MUTATED        3      1      0      0
  1P GAIN WILD-TYPE    162    144    119     69
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               162
  CLUS_2               1               144
  CLUS_3               0               119
  CLUS_4               0                69
[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
  1P GAIN MUTATED        3      1      0
  1P GAIN WILD-TYPE    175    127    192
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               175
  CLUS_2               1               127
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      1      0      0
  1P GAIN WILD-TYPE    129    124    108    104
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               129
  CLUS_2               1               124
  CLUS_3               0               108
  CLUS_4               0               104
[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
  1P GAIN MUTATED        2      1      0
  1P GAIN WILD-TYPE    161    119    185
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               1               119
  CLUS_3               0               185
[1] 3 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       11      6      9
  1Q GAIN WILD-TYPE    121    132    220
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11               121
  CLUS_2               6               132
  CLUS_3               9               220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      2      7      1      5
  1Q GAIN WILD-TYPE     35    145     77     41    175
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11                35
  CLUS_2               2               145
  CLUS_3               7                77
  CLUS_4               1                41
  CLUS_5               5               175
[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 CLUS_4
  1Q GAIN MUTATED        0      5      1      4
  1Q GAIN WILD-TYPE     64     59     41     45
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               5                59
  CLUS_3               1                41
  CLUS_4               4                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q GAIN MUTATED        0      1      3      0      2      4      0
  1Q GAIN WILD-TYPE     46     27     30     29     45     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                45
  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       17      2      5      2
  1Q GAIN WILD-TYPE    141    165     53    112
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              17               141
  CLUS_2               2               165
  CLUS_3               5                53
  CLUS_4               2               112
[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       17      2      1      2      4
  1Q GAIN WILD-TYPE     87    132     85     93     74
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              17                87
  CLUS_2               2               132
  CLUS_3               1                85
  CLUS_4               2                93
  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 CLUS_4
  1Q GAIN MUTATED       15      3      3      5
  1Q GAIN WILD-TYPE    150    142    116     64
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15               150
  CLUS_2               3               142
  CLUS_3               3               116
  CLUS_4               5                64
[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
  1Q GAIN MUTATED       15      3      8
  1Q GAIN WILD-TYPE    163    125    184
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15               163
  CLUS_2               3               125
  CLUS_3               8               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12      2      4      4
  1Q GAIN WILD-TYPE    119    123    104    100
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              12               119
  CLUS_2               2               123
  CLUS_3               4               104
  CLUS_4               4               100
[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
  1Q GAIN MUTATED       14      2      6
  1Q GAIN WILD-TYPE    149    118    179
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              14               149
  CLUS_2               2               118
  CLUS_3               6               179
[1] 3 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        1      0      2
  3P GAIN WILD-TYPE    131    138    227
D3V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               2               227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      2      0      0      1
  3P GAIN WILD-TYPE     46    145     84     42    179
D3V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               2               145
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  3P GAIN MUTATED        0      1      0      1
  3P GAIN WILD-TYPE     64     63     42     48
D3V3, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"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     46     26      9
D3V4, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        0      2      0      1
  3P GAIN WILD-TYPE    158    165     58    113
D3V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0               158
  CLUS_2               2               165
  CLUS_3               0                58
  CLUS_4               1               113
[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        0      2      0      1      0
  3P GAIN WILD-TYPE    104    132     86     94     78
D3V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               2               132
  CLUS_3               0                86
  CLUS_4               1                94
  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 CLUS_4
  3P GAIN MUTATED        1      2      0      0
  3P GAIN WILD-TYPE    164    143    119     69
D3V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               164
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               0                69
[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
  3P GAIN MUTATED        1      2      0
  3P GAIN WILD-TYPE    177    126    192
D3V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               2               126
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      2      0      0
  3P GAIN WILD-TYPE    130    123    108    104
D3V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               2               123
  CLUS_3               0               108
  CLUS_4               0               104
[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
  3P GAIN MUTATED        1      2      0
  3P GAIN WILD-TYPE    162    118    185
D3V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               2               118
  CLUS_3               0               185
[1] 3 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        0      0      5
  4P GAIN WILD-TYPE    132    138    224
D4V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               5               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      5      0      0      0
  4P GAIN WILD-TYPE     46    142     84     42    180
D4V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               5               142
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  4P GAIN MUTATED        1      0      1      0
  4P GAIN WILD-TYPE     63     64     41     49
D4V3, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A23A        TCGA-FY-A2QD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     27      9
D4V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A23A        TCGA-FY-A2QD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        0      5      0      0
  4P GAIN WILD-TYPE    158    162     58    114
D4V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               158
  CLUS_2               5               162
  CLUS_3               0                58
  CLUS_4               0               114
[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        0      5      0      0      0
  4P GAIN WILD-TYPE    104    129     86     95     78
D4V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               5               129
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  4P GAIN MUTATED        2      3      0      0
  4P GAIN WILD-TYPE    163    142    119     69
D4V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               3               142
  CLUS_3               0               119
  CLUS_4               0                69
[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
  4P GAIN MUTATED        1      4      0
  4P GAIN WILD-TYPE    177    124    192
D4V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               4               124
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      4      0      0
  4P GAIN WILD-TYPE    130    121    108    104
D4V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               4               121
  CLUS_3               0               108
  CLUS_4               0               104
[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
  4P GAIN MUTATED        1      4      0
  4P GAIN WILD-TYPE    162    116    185
D4V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               4               116
  CLUS_3               0               185
[1] 3 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        0      0      5
  4Q GAIN WILD-TYPE    132    138    224
D5V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               5               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      5      0      0      0
  4Q GAIN WILD-TYPE     46    142     84     42    180
D5V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               5               142
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  4Q GAIN MUTATED        1      0      1      0
  4Q GAIN WILD-TYPE     63     64     41     49
D5V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A23A        TCGA-FY-A2QD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     27      9
D5V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A23A        TCGA-FY-A2QD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        0      5      0      0
  4Q GAIN WILD-TYPE    158    162     58    114
D5V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               158
  CLUS_2               5               162
  CLUS_3               0                58
  CLUS_4               0               114
[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        0      5      0      0      0
  4Q GAIN WILD-TYPE    104    129     86     95     78
D5V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               5               129
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  4Q GAIN MUTATED        2      3      0      0
  4Q GAIN WILD-TYPE    163    142    119     69
D5V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               3               142
  CLUS_3               0               119
  CLUS_4               0                69
[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
  4Q GAIN MUTATED        1      4      0
  4Q GAIN WILD-TYPE    177    124    192
D5V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               4               124
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      4      0      0
  4Q GAIN WILD-TYPE    130    121    108    104
D5V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               4               121
  CLUS_3               0               108
  CLUS_4               0               104
[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
  4Q GAIN MUTATED        1      4      0
  4Q GAIN WILD-TYPE    162    116    185
D5V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               4               116
  CLUS_3               0               185
[1] 3 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        4      1     16
  5P GAIN WILD-TYPE    128    137    213
D6V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               128
  CLUS_2               1               137
  CLUS_3              16               213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2     14      2      0      3
  5P GAIN WILD-TYPE     44    133     82     42    177
D6V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                44
  CLUS_2              14               133
  CLUS_3               2                82
  CLUS_4               0                42
  CLUS_5               3               177
[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 CLUS_4
  5P GAIN MUTATED        3      6      3      0
  5P GAIN WILD-TYPE     61     58     39     49
D6V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               6                58
  CLUS_3               3                39
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5P GAIN MUTATED        3      1      2      3      0      3      0
  5P GAIN WILD-TYPE     43     27     31     26     47     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                47
  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        5     14      1      1
  5P GAIN WILD-TYPE    153    153     57    113
D6V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5               153
  CLUS_2              14               153
  CLUS_3               1                57
  CLUS_4               1               113
[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        6     14      0      1      0
  5P GAIN WILD-TYPE     98    120     86     94     78
D6V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6                98
  CLUS_2              14               120
  CLUS_3               0                86
  CLUS_4               1                94
  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 CLUS_4
  5P GAIN MUTATED        8     12      0      1
  5P GAIN WILD-TYPE    157    133    119     68
D6V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8               157
  CLUS_2              12               133
  CLUS_3               0               119
  CLUS_4               1                68
[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
  5P GAIN MUTATED        7     13      1
  5P GAIN WILD-TYPE    171    115    191
D6V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7               171
  CLUS_2              13               115
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6     10      2      0
  5P GAIN WILD-TYPE    125    115    106    104
D6V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6               125
  CLUS_2              10               115
  CLUS_3               2               106
  CLUS_4               0               104
[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
  5P GAIN MUTATED        7     10      1
  5P GAIN WILD-TYPE    156    110    184
D6V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7               156
  CLUS_2              10               110
  CLUS_3               1               184
[1] 3 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        2      0     15
  5Q GAIN WILD-TYPE    130    138    214
D7V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               0               138
  CLUS_3              15               214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     14      1      0      1
  5Q GAIN WILD-TYPE     45    133     83     42    179
D7V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                45
  CLUS_2              14               133
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  5Q GAIN MUTATED        3      4      3      0
  5Q GAIN WILD-TYPE     61     60     39     49
D7V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               4                60
  CLUS_3               3                39
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q GAIN MUTATED        3      1      0      3      0      3      0
  5Q GAIN WILD-TYPE     43     27     33     26     47     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                47
  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        2     14      0      1
  5Q GAIN WILD-TYPE    156    153     58    113
D7V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2              14               153
  CLUS_3               0                58
  CLUS_4               1               113
[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        2     14      0      1      0
  5Q GAIN WILD-TYPE    102    120     86     94     78
D7V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2              14               120
  CLUS_3               0                86
  CLUS_4               1                94
  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 CLUS_4
  5Q GAIN MUTATED        4     12      0      1
  5Q GAIN WILD-TYPE    161    133    119     68
D7V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4               161
  CLUS_2              12               133
  CLUS_3               0               119
  CLUS_4               1                68
[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
  5Q GAIN MUTATED        3     13      1
  5Q GAIN WILD-TYPE    175    115    191
D7V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3               175
  CLUS_2              13               115
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3     10      1      0
  5Q GAIN WILD-TYPE    128    115    107    104
D7V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3               128
  CLUS_2              10               115
  CLUS_3               1               107
  CLUS_4               0               104
[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
  5Q GAIN MUTATED        3     10      1
  5Q GAIN WILD-TYPE    160    110    184
D7V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3               160
  CLUS_2              10               110
  CLUS_3               1               184
[1] 3 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        2      1     15
  7P GAIN WILD-TYPE    130    137    214
D8V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               1               137
  CLUS_3              15               214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     13      3      0      1
  7P GAIN WILD-TYPE     45    134     81     42    179
D8V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                45
  CLUS_2              13               134
  CLUS_3               3                81
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  7P GAIN MUTATED        3      5      2      0
  7P GAIN WILD-TYPE     61     59     40     49
D8V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               5                59
  CLUS_3               2                40
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P GAIN MUTATED        3      1      0      2      0      4      0
  7P GAIN WILD-TYPE     43     27     33     27     47     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                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
  7P GAIN MUTATED        2     14      1      1
  7P GAIN WILD-TYPE    156    153     57    113
D8V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2              14               153
  CLUS_3               1                57
  CLUS_4               1               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P GAIN MUTATED        2     14      1      1      0
  7P GAIN WILD-TYPE    102    120     85     94     78
D8V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2              14               120
  CLUS_3               1                85
  CLUS_4               1                94
  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 CLUS_4
  7P GAIN MUTATED        5     10      0      3
  7P GAIN WILD-TYPE    160    135    119     66
D8V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5               160
  CLUS_2              10               135
  CLUS_3               0               119
  CLUS_4               3                66
[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
  7P GAIN MUTATED        4     13      1
  7P GAIN WILD-TYPE    174    115    191
D8V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4               174
  CLUS_2              13               115
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        4     10      1      0
  7P GAIN WILD-TYPE    127    115    107    104
D8V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4               127
  CLUS_2              10               115
  CLUS_3               1               107
  CLUS_4               0               104
[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
  7P GAIN MUTATED        4     10      1
  7P GAIN WILD-TYPE    159    110    184
D8V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2              10               110
  CLUS_3               1               184
[1] 3 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        3      1     16
  7Q GAIN WILD-TYPE    129    137    213
D9V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3               129
  CLUS_2               1               137
  CLUS_3              16               213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     15      3      0      1
  7Q GAIN WILD-TYPE     45    132     81     42    179
D9V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                45
  CLUS_2              15               132
  CLUS_3               3                81
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  7Q GAIN MUTATED        4      6      2      0
  7Q GAIN WILD-TYPE     60     58     40     49
D9V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                60
  CLUS_2               6                58
  CLUS_3               2                40
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7Q GAIN MUTATED        4      1      0      2      0      5      0
  7Q GAIN WILD-TYPE     42     27     33     27     47     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                47
  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        2     16      1      1
  7Q GAIN WILD-TYPE    156    151     57    113
D9V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2              16               151
  CLUS_3               1                57
  CLUS_4               1               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q GAIN MUTATED        2     16      1      1      0
  7Q GAIN WILD-TYPE    102    118     85     94     78
D9V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2              16               118
  CLUS_3               1                85
  CLUS_4               1                94
  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 CLUS_4
  7Q GAIN MUTATED        5     12      0      3
  7Q GAIN WILD-TYPE    160    133    119     66
D9V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5               160
  CLUS_2              12               133
  CLUS_3               0               119
  CLUS_4               3                66
[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
  7Q GAIN MUTATED        4     15      1
  7Q GAIN WILD-TYPE    174    113    191
D9V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4               174
  CLUS_2              15               113
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4     12      1      0
  7Q GAIN WILD-TYPE    127    113    107    104
D9V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4               127
  CLUS_2              12               113
  CLUS_3               1               107
  CLUS_4               0               104
[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
  7Q GAIN MUTATED        4     12      1
  7Q GAIN WILD-TYPE    159    108    184
D9V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2              12               108
  CLUS_3               1               184
[1] 3 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        0      0      6
  8P GAIN WILD-TYPE    132    138    223
D10V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               6               223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P GAIN MUTATED        0      3      1      0      2
  8P GAIN WILD-TYPE     46    144     83     42    178
D10V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               2               178
[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 CLUS_4
  8P GAIN MUTATED        1      1      1      1
  8P GAIN WILD-TYPE     63     63     41     48
D10V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1                63
  CLUS_3               1                41
  CLUS_4               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED        0      1      0      1      1      1      0
  8P GAIN WILD-TYPE     46     27     33     28     46     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                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
  8P GAIN MUTATED        1      3      0      2
  8P GAIN WILD-TYPE    157    164     58    112
D10V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1               157
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               2               112
[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        1      3      0      2      0
  8P GAIN WILD-TYPE    103    131     86     93     78
D10V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1               103
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               2                93
  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 CLUS_4
  8P GAIN MUTATED        2      3      1      0
  8P GAIN WILD-TYPE    163    142    118     69
D10V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               3               142
  CLUS_3               1               118
  CLUS_4               0                69
[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
  8P GAIN MUTATED        1      3      2
  8P GAIN WILD-TYPE    177    125    190
D10V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               3               125
  CLUS_3               2               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      2      1      1
  8P GAIN WILD-TYPE    129    123    107    103
D10V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2               129
  CLUS_2               2               123
  CLUS_3               1               107
  CLUS_4               1               103
[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
  8P GAIN MUTATED        1      3      2
  8P GAIN WILD-TYPE    162    117    183
D10V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               3               117
  CLUS_3               2               183
[1] 3 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        1      0      6
  8Q GAIN WILD-TYPE    131    138    223
D11V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               6               223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED        0      3      2      0      2
  8Q GAIN WILD-TYPE     46    144     82     42    178
D11V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               2                82
  CLUS_4               0                42
  CLUS_5               2               178
[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 CLUS_4
  8Q GAIN MUTATED        1      1      1      1
  8Q GAIN WILD-TYPE     63     63     41     48
D11V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1                63
  CLUS_3               1                41
  CLUS_4               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q GAIN MUTATED        0      1      0      1      1      1      0
  8Q GAIN WILD-TYPE     46     27     33     28     46     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                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
  8Q GAIN MUTATED        2      3      0      2
  8Q GAIN WILD-TYPE    156    164     58    112
D11V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               2               112
[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        2      3      0      2      0
  8Q GAIN WILD-TYPE    102    131     86     93     78
D11V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               2                93
  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 CLUS_4
  8Q GAIN MUTATED        3      3      1      0
  8Q GAIN WILD-TYPE    162    142    118     69
D11V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               162
  CLUS_2               3               142
  CLUS_3               1               118
  CLUS_4               0                69
[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
  8Q GAIN MUTATED        2      3      2
  8Q GAIN WILD-TYPE    176    125    190
D11V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2               176
  CLUS_2               3               125
  CLUS_3               2               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      1
  8Q GAIN WILD-TYPE    128    123    107    103
D11V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3               128
  CLUS_2               2               123
  CLUS_3               1               107
  CLUS_4               1               103
[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
  8Q GAIN MUTATED        2      3      2
  8Q GAIN WILD-TYPE    161    117    183
D11V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               3               117
  CLUS_3               2               183
[1] 3 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        1      0      2
  9P GAIN WILD-TYPE    131    138    227
D12V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               2               227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        0      2      0      0      1
  9P GAIN WILD-TYPE     46    145     84     42    179
D12V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               2               145
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  9P GAIN MUTATED        1      0      0      0
  9P GAIN WILD-TYPE     63     64     42     49
D12V3, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1               218 
       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-EL-A3CL        TCGA-EL-A3CM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1 
"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     47     27      9
D12V4, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1               218 
       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-EL-A3CL        TCGA-EL-A3CM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DW        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        0      2      0      1
  9P GAIN WILD-TYPE    158    165     58    113
D12V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0               158
  CLUS_2               2               165
  CLUS_3               0                58
  CLUS_4               1               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        0      2      0      1      0
  9P GAIN WILD-TYPE    104    132     86     94     78
D12V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               2               132
  CLUS_3               0                86
  CLUS_4               1                94
  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 CLUS_4
  9P GAIN MUTATED        2      0      1      0
  9P GAIN WILD-TYPE    163    145    118     69
D12V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               0               145
  CLUS_3               1               118
  CLUS_4               0                69
[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
  9P GAIN MUTATED        1      1      1
  9P GAIN WILD-TYPE    177    127    191
D12V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               1               127
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      1
  9P GAIN WILD-TYPE    130    124    108    103
D12V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               1               124
  CLUS_3               0               108
  CLUS_4               1               103
[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
  9P GAIN MUTATED        1      1      1
  9P GAIN WILD-TYPE    162    119    184
D12V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               1               119
  CLUS_3               1               184
[1] 3 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        1      0      3
  9Q GAIN WILD-TYPE    131    138    226
D13V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               3               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        0      2      0      0      2
  9Q GAIN WILD-TYPE     46    145     84     42    178
D13V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               2               145
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               2               178
[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 CLUS_4
  9Q GAIN MUTATED        1      0      0      1
  9Q GAIN WILD-TYPE     63     64     42     48
D13V3, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"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     46     27      9
D13V4, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-J8-A3O1 
"9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        0      2      0      2
  9Q GAIN WILD-TYPE    158    165     58    112
D13V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0               158
  CLUS_2               2               165
  CLUS_3               0                58
  CLUS_4               2               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        0      2      0      2      0
  9Q GAIN WILD-TYPE    104    132     86     93     78
D13V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               2               132
  CLUS_3               0                86
  CLUS_4               2                93
  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 CLUS_4
  9Q GAIN MUTATED        2      0      2      0
  9Q GAIN WILD-TYPE    163    145    117     69
D13V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               0               145
  CLUS_3               2               117
  CLUS_4               0                69
[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
  9Q GAIN MUTATED        1      1      2
  9Q GAIN WILD-TYPE    177    127    190
D13V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               177
  CLUS_2               1               127
  CLUS_3               2               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      0      2
  9Q GAIN WILD-TYPE    130    124    108    102
D13V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               1               124
  CLUS_3               0               108
  CLUS_4               2               102
[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
  9Q GAIN MUTATED        1      1      2
  9Q GAIN WILD-TYPE    162    119    183
D13V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               1               119
  CLUS_3               2               183
[1] 3 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        0      0      6
  11P GAIN WILD-TYPE    132    138    223
D14V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                0                138
  CLUS_3                6                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED        0      5      0      0      1
  11P GAIN WILD-TYPE     46    142     84     42    179
D14V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                5                142
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  11P GAIN MUTATED        1      1      1      0
  11P GAIN WILD-TYPE     63     63     41     49
D14V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 63
  CLUS_3                1                 41
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P GAIN MUTATED        0      1      0      1      0      1      0
  11P GAIN WILD-TYPE     46     27     33     28     47     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                 47
  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        0      5      0      1
  11P GAIN WILD-TYPE    158    162     58    113
D14V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                5                162
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED        0      5      0      1      0
  11P GAIN WILD-TYPE    104    129     86     94     78
D14V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                5                129
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  11P GAIN MUTATED        0      6      0      0
  11P GAIN WILD-TYPE    165    139    119     69
D14V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                165
  CLUS_2                6                139
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  11P GAIN MUTATED        0      5      1
  11P GAIN WILD-TYPE    178    123    191
D14V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                178
  CLUS_2                5                123
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      1      0
  11P GAIN WILD-TYPE    131    122    107    104
D14V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                131
  CLUS_2                3                122
  CLUS_3                1                107
  CLUS_4                0                104
[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
  11P GAIN MUTATED        0      3      1
  11P GAIN WILD-TYPE    163    117    184
D14V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                3                117
  CLUS_3                1                184
[1] 3 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        0      0      5
  11Q GAIN WILD-TYPE    132    138    224
D15V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                0                138
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        0      4      0      0      1
  11Q GAIN WILD-TYPE     46    143     84     42    179
D15V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  11Q GAIN MUTATED        1      1      1      0
  11Q GAIN WILD-TYPE     63     63     41     49
D15V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 63
  CLUS_3                1                 41
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q GAIN MUTATED        0      1      0      1      0      1      0
  11Q GAIN WILD-TYPE     46     27     33     28     47     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                 47
  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        0      4      0      1
  11Q GAIN WILD-TYPE    158    163     58    113
D15V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                4                163
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        0      4      0      1      0
  11Q GAIN WILD-TYPE    104    130     86     94     78
D15V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                4                130
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  11Q GAIN MUTATED        0      5      0      0
  11Q GAIN WILD-TYPE    165    140    119     69
D15V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                165
  CLUS_2                5                140
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  11Q GAIN MUTATED        0      4      1
  11Q GAIN WILD-TYPE    178    124    191
D15V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                178
  CLUS_2                4                124
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      2      1      0
  11Q GAIN WILD-TYPE    131    123    107    104
D15V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                131
  CLUS_2                2                123
  CLUS_3                1                107
  CLUS_4                0                104
[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
  11Q GAIN MUTATED        0      2      1
  11Q GAIN WILD-TYPE    163    118    184
D15V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                2                118
  CLUS_3                1                184
[1] 3 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        1      0     14
  12P GAIN WILD-TYPE    131    138    215
D16V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               14                215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED        0     14      0      0      1
  12P GAIN WILD-TYPE     46    133     84     42    179
D16V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2               14                133
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  12P GAIN MUTATED        3      4      2      1
  12P GAIN WILD-TYPE     61     60     40     48
D16V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                4                 60
  CLUS_3                2                 40
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12P GAIN MUTATED        3      1      0      3      0      3      0
  12P GAIN WILD-TYPE     43     27     33     26     47     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                 47
  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        0     14      0      1
  12P GAIN WILD-TYPE    158    153     58    113
D16V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2               14                153
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED        0     14      0      1      0
  12P GAIN WILD-TYPE    104    120     86     94     78
D16V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2               14                120
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  12P GAIN MUTATED        2     12      0      1
  12P GAIN WILD-TYPE    163    133    119     68
D16V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2               12                133
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  12P GAIN MUTATED        1     13      1
  12P GAIN WILD-TYPE    177    115    191
D16V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2               13                115
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     10      1      0
  12P GAIN WILD-TYPE    130    115    107    104
D16V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2               10                115
  CLUS_3                1                107
  CLUS_4                0                104
[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
  12P GAIN MUTATED        1     10      1
  12P GAIN WILD-TYPE    162    110    184
D16V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2               10                110
  CLUS_3                1                184
[1] 3 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        1      0     14
  12Q GAIN WILD-TYPE    131    138    215
D17V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               14                215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q GAIN MUTATED        0     14      0      0      1
  12Q GAIN WILD-TYPE     46    133     84     42    179
D17V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2               14                133
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  12Q GAIN MUTATED        3      4      2      1
  12Q GAIN WILD-TYPE     61     60     40     48
D17V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                4                 60
  CLUS_3                2                 40
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q GAIN MUTATED        3      1      0      3      0      3      0
  12Q GAIN WILD-TYPE     43     27     33     26     47     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                 47
  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        0     14      0      1
  12Q GAIN WILD-TYPE    158    153     58    113
D17V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2               14                153
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q GAIN MUTATED        0     14      0      1      0
  12Q GAIN WILD-TYPE    104    120     86     94     78
D17V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2               14                120
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  12Q GAIN MUTATED        2     12      0      1
  12Q GAIN WILD-TYPE    163    133    119     68
D17V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2               12                133
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  12Q GAIN MUTATED        1     13      1
  12Q GAIN WILD-TYPE    177    115    191
D17V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2               13                115
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     10      1      0
  12Q GAIN WILD-TYPE    130    115    107    104
D17V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2               10                115
  CLUS_3                1                107
  CLUS_4                0                104
[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
  12Q GAIN MUTATED        1     10      1
  12Q GAIN WILD-TYPE    162    110    184
D17V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2               10                110
  CLUS_3                1                184
[1] 3 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        0      1      4
  13Q GAIN WILD-TYPE    132    137    225
D18V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                137
  CLUS_3                4                225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      1      0      0
  13Q GAIN WILD-TYPE     46    143     83     42    180
D18V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  13Q GAIN MUTATED        1      2      0      0
  13Q GAIN WILD-TYPE     63     62     42     49
D18V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 62
  CLUS_3                0                 42
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q GAIN MUTATED        1      0      0      0      0      2      0
  13Q GAIN WILD-TYPE     45     28     33     29     47     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                 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
  13Q GAIN MUTATED        0      4      1      0
  13Q GAIN WILD-TYPE    158    163     57    114
D18V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                4                163
  CLUS_3                1                 57
  CLUS_4                0                114
[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        0      4      1      0      0
  13Q GAIN WILD-TYPE    104    130     85     95     78
D18V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                4                130
  CLUS_3                1                 85
  CLUS_4                0                 95
  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 CLUS_4
  13Q GAIN MUTATED        2      2      0      1
  13Q GAIN WILD-TYPE    163    143    119     68
D18V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2                2                143
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  13Q GAIN MUTATED        2      3      0
  13Q GAIN WILD-TYPE    176    125    192
D18V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2                3                125
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      3      0      0
  13Q GAIN WILD-TYPE    130    122    108    104
D18V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2                3                122
  CLUS_3                0                108
  CLUS_4                0                104
[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
  13Q GAIN MUTATED        2      2      0
  13Q GAIN WILD-TYPE    161    118    185
D18V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                2                118
  CLUS_3                0                185
[1] 3 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        0      0     11
  14Q GAIN WILD-TYPE    132    138    218
D19V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                0                138
  CLUS_3               11                218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     10      0      0      0
  14Q GAIN WILD-TYPE     45    137     84     42    180
D19V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2               10                137
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  14Q GAIN MUTATED        1      2      2      0
  14Q GAIN WILD-TYPE     63     62     40     49
D19V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 62
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  14Q GAIN MUTATED        1      0      0      2      0      2      0
  14Q GAIN WILD-TYPE     45     28     33     27     47     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                 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
  14Q GAIN MUTATED        1     10      0      0
  14Q GAIN WILD-TYPE    157    157     58    114
D19V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               10                157
  CLUS_3                0                 58
  CLUS_4                0                114
[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        0     10      0      0      1
  14Q GAIN WILD-TYPE    104    124     86     95     77
D19V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2               10                124
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  14Q GAIN MUTATED        3      7      0      1
  14Q GAIN WILD-TYPE    162    138    119     68
D19V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2                7                138
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  14Q GAIN MUTATED        2      9      0
  14Q GAIN WILD-TYPE    176    119    192
D19V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2                9                119
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      8      0      0
  14Q GAIN WILD-TYPE    129    117    108    104
D19V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                8                117
  CLUS_3                0                108
  CLUS_4                0                104
[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
  14Q GAIN MUTATED        2      8      0
  14Q GAIN WILD-TYPE    161    112    185
D19V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                8                112
  CLUS_3                0                185
[1] 3 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        1      0     14
  16P GAIN WILD-TYPE    131    138    215
D20V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               14                215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0     12      2      0      1
  16P GAIN WILD-TYPE     46    135     82     42    179
D20V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2               12                135
  CLUS_3                2                 82
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  16P GAIN MUTATED        2      4      2      1
  16P GAIN WILD-TYPE     62     60     40     48
D20V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                4                 60
  CLUS_3                2                 40
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P GAIN MUTATED        2      1      0      3      0      3      0
  16P GAIN WILD-TYPE     44     27     33     26     47     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                 47
  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        1     13      0      1
  16P GAIN WILD-TYPE    157    154     58    113
D20V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               13                154
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED        1     13      0      1      0
  16P GAIN WILD-TYPE    103    121     86     94     78
D20V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2               13                121
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  16P GAIN MUTATED        3     10      0      2
  16P GAIN WILD-TYPE    162    135    119     67
D20V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2               10                135
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        2     12      1
  16P GAIN WILD-TYPE    176    116    191
D20V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2               12                116
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2     11      1      0
  16P GAIN WILD-TYPE    129    114    107    104
D20V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2               11                114
  CLUS_3                1                107
  CLUS_4                0                104
[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
  16P GAIN MUTATED        2     11      1
  16P GAIN WILD-TYPE    161    109    184
D20V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2               11                109
  CLUS_3                1                184
[1] 3 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        1      0     12
  16Q GAIN WILD-TYPE    131    138    217
D21V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               12                217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        0     10      2      0      1
  16Q GAIN WILD-TYPE     46    137     82     42    179
D21V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2               10                137
  CLUS_3                2                 82
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  16Q GAIN MUTATED        2      3      2      0
  16Q GAIN WILD-TYPE     62     61     40     49
D21V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                3                 61
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        2      1      0      2      0      2      0
  16Q GAIN WILD-TYPE     44     27     33     27     47     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                 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
  16Q GAIN MUTATED        1     11      0      1
  16Q GAIN WILD-TYPE    157    156     58    113
D21V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               11                156
  CLUS_3                0                 58
  CLUS_4                1                113
[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        1     11      0      1      0
  16Q GAIN WILD-TYPE    103    123     86     94     78
D21V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2               11                123
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  16Q GAIN MUTATED        3      8      0      2
  16Q GAIN WILD-TYPE    162    137    119     67
D21V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2                8                137
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        2     10      1
  16Q GAIN WILD-TYPE    176    118    191
D21V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2               10                118
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      9      1      0
  16Q GAIN WILD-TYPE    129    116    107    104
D21V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                9                116
  CLUS_3                1                107
  CLUS_4                0                104
[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
  16Q GAIN MUTATED        2      9      1
  16Q GAIN WILD-TYPE    161    111    184
D21V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                9                111
  CLUS_3                1                184
[1] 3 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        1      0     15
  17P GAIN WILD-TYPE    131    138    214
D22V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               15                214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0     15      0      0      1
  17P GAIN WILD-TYPE     46    132     84     42    179
D22V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2               15                132
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  17P GAIN MUTATED        2      4      2      0
  17P GAIN WILD-TYPE     62     60     40     49
D22V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                4                 60
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P GAIN MUTATED        1      1      0      2      0      4      0
  17P GAIN WILD-TYPE     45     27     33     27     47     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                 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
  17P GAIN MUTATED        0     15      0      1
  17P GAIN WILD-TYPE    158    152     58    113
D22V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2               15                152
  CLUS_3                0                 58
  CLUS_4                1                113
[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        0     15      0      1      0
  17P GAIN WILD-TYPE    104    119     86     94     78
D22V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2               15                119
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  17P GAIN MUTATED        2     12      0      2
  17P GAIN WILD-TYPE    163    133    119     67
D22V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2               12                133
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        1     14      1
  17P GAIN WILD-TYPE    177    114    191
D22V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2               14                114
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     11      1      0
  17P GAIN WILD-TYPE    130    114    107    104
D22V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2               11                114
  CLUS_3                1                107
  CLUS_4                0                104
[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
  17P GAIN MUTATED        1     11      1
  17P GAIN WILD-TYPE    162    109    184
D22V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2               11                109
  CLUS_3                1                184
[1] 3 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        2      0     16
  17Q GAIN WILD-TYPE    130    138    213
D23V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                138
  CLUS_3               16                213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1     16      0      0      1
  17Q GAIN WILD-TYPE     45    131     84     42    179
D23V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 45
  CLUS_2               16                131
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  17Q GAIN MUTATED        2      4      2      1
  17Q GAIN WILD-TYPE     62     60     40     48
D23V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                4                 60
  CLUS_3                2                 40
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q GAIN MUTATED        1      1      0      3      0      4      0
  17Q GAIN WILD-TYPE     45     27     33     26     47     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                 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
  17Q GAIN MUTATED        1     16      0      1
  17Q GAIN WILD-TYPE    157    151     58    113
D23V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               16                151
  CLUS_3                0                 58
  CLUS_4                1                113
[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        1     16      0      1      0
  17Q GAIN WILD-TYPE    103    118     86     94     78
D23V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2               16                118
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  17Q GAIN MUTATED        3     13      0      2
  17Q GAIN WILD-TYPE    162    132    119     67
D23V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2               13                132
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        2     15      1
  17Q GAIN WILD-TYPE    176    113    191
D23V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2               15                113
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2     12      1      0
  17Q GAIN WILD-TYPE    129    113    107    104
D23V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2               12                113
  CLUS_3                1                107
  CLUS_4                0                104
[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
  17Q GAIN MUTATED        2     12      1
  17Q GAIN WILD-TYPE    161    108    184
D23V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2               12                108
  CLUS_3                1                184
[1] 3 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        0      1      5
  18P GAIN WILD-TYPE    132    137    224
D24V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                137
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      1      0      1
  18P GAIN WILD-TYPE     46    143     83     42    179
D24V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  18P GAIN MUTATED        1      0      1      0
  18P GAIN WILD-TYPE     63     64     41     49
D24V3, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"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     47     27      9
D24V4, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"18P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        0      4      1      1
  18P GAIN WILD-TYPE    158    163     57    113
D24V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                4                163
  CLUS_3                1                 57
  CLUS_4                1                113
[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        0      4      1      1      0
  18P GAIN WILD-TYPE    104    130     85     94     78
D24V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                4                130
  CLUS_3                1                 85
  CLUS_4                1                 94
  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 CLUS_4
  18P GAIN MUTATED        2      4      0      0
  18P GAIN WILD-TYPE    163    141    119     69
D24V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2                4                141
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  18P GAIN MUTATED        1      4      1
  18P GAIN WILD-TYPE    177    124    191
D24V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2                4                124
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      3      1      0
  18P GAIN WILD-TYPE    129    122    107    104
D24V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                3                122
  CLUS_3                1                107
  CLUS_4                0                104
[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
  18P GAIN MUTATED        1      4      1
  18P GAIN WILD-TYPE    162    116    184
D24V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2                4                116
  CLUS_3                1                184
[1] 3 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        0      1      5
  18Q GAIN WILD-TYPE    132    137    224
D25V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                137
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      1      0      1
  18Q GAIN WILD-TYPE     46    143     83     42    179
D25V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  18Q GAIN MUTATED        1      0      1      0
  18Q GAIN WILD-TYPE     63     64     41     49
D25V3, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"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     47     27      9
D25V4, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"18Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        0      4      1      1
  18Q GAIN WILD-TYPE    158    163     57    113
D25V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                4                163
  CLUS_3                1                 57
  CLUS_4                1                113
[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        0      4      1      1      0
  18Q GAIN WILD-TYPE    104    130     85     94     78
D25V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                4                130
  CLUS_3                1                 85
  CLUS_4                1                 94
  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 CLUS_4
  18Q GAIN MUTATED        2      4      0      0
  18Q GAIN WILD-TYPE    163    141    119     69
D25V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2                4                141
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  18Q GAIN MUTATED        1      4      1
  18Q GAIN WILD-TYPE    177    124    191
D25V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2                4                124
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      3      1      0
  18Q GAIN WILD-TYPE    129    122    107    104
D25V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                3                122
  CLUS_3                1                107
  CLUS_4                0                104
[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
  18Q GAIN MUTATED        1      4      1
  18Q GAIN WILD-TYPE    162    116    184
D25V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2                4                116
  CLUS_3                1                184
[1] 3 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        0      0      8
  19P GAIN WILD-TYPE    132    138    221
D26V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                0                138
  CLUS_3                8                221
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED        0      7      1      0      0
  19P GAIN WILD-TYPE     46    140     83     42    180
D26V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                7                140
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  19P GAIN MUTATED        0      2      0      0
  19P GAIN WILD-TYPE     64     62     42     49
D26V3, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22L         TCGA-EM-A22M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A22Q         TCGA-EM-A2CJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CK         TCGA-EM-A2CL         TCGA-EM-A2CN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CO         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2P1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-EM-A3AJ         TCGA-EM-A3AL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FL         TCGA-EM-A3FN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-ET-A25G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25O 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"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     47     25      9
D26V4, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22L         TCGA-EM-A22M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A22Q         TCGA-EM-A2CJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CK         TCGA-EM-A2CL         TCGA-EM-A2CN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CO         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2P1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-EM-A3AJ         TCGA-EM-A3AL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FL         TCGA-EM-A3FN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-ET-A25G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25O 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A2N5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"19P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      8      0      0
  19P GAIN WILD-TYPE    158    159     58    114
D26V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                8                159
  CLUS_3                0                 58
  CLUS_4                0                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED        0      8      0      0      0
  19P GAIN WILD-TYPE    104    126     86     95     78
D26V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                8                126
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  19P GAIN MUTATED        1      5      0      2
  19P GAIN WILD-TYPE    164    140    119     67
D26V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                164
  CLUS_2                5                140
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      8      0
  19P GAIN WILD-TYPE    178    120    192
D26V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                178
  CLUS_2                8                120
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      4      0      0
  19P GAIN WILD-TYPE    130    121    108    104
D26V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2                4                121
  CLUS_3                0                108
  CLUS_4                0                104
[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
  19P GAIN MUTATED        0      5      0
  19P GAIN WILD-TYPE    163    115    185
D26V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                5                115
  CLUS_3                0                185
[1] 3 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        1      0      9
  19Q GAIN WILD-TYPE    131    138    220
D27V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                9                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED        0      9      1      0      0
  19Q GAIN WILD-TYPE     46    138     83     42    180
D27V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                9                138
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  19Q GAIN MUTATED        0      2      1      0
  19Q GAIN WILD-TYPE     64     62     41     49
D27V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                2                 62
  CLUS_3                1                 41
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q GAIN MUTATED        0      0      0      1      0      2      0
  19Q GAIN WILD-TYPE     46     28     33     28     47     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                 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
  19Q GAIN MUTATED        0     10      0      0
  19Q GAIN WILD-TYPE    158    157     58    114
D27V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2               10                157
  CLUS_3                0                 58
  CLUS_4                0                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED        0     10      0      0      0
  19Q GAIN WILD-TYPE    104    124     86     95     78
D27V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2               10                124
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  19Q GAIN MUTATED        1      7      0      2
  19Q GAIN WILD-TYPE    164    138    119     67
D27V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                164
  CLUS_2                7                138
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0     10      0
  19Q GAIN WILD-TYPE    178    118    192
D27V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                178
  CLUS_2               10                118
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      6      0      0
  19Q GAIN WILD-TYPE    130    119    108    104
D27V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2                6                119
  CLUS_3                0                108
  CLUS_4                0                104
[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
  19Q GAIN MUTATED        0      7      0
  19Q GAIN WILD-TYPE    163    113    185
D27V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                7                113
  CLUS_3                0                185
[1] 3 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        1      0     11
  20P GAIN WILD-TYPE    131    138    218
D28V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               11                218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P GAIN MUTATED        0      9      2      0      1
  20P GAIN WILD-TYPE     46    138     82     42    179
D28V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                9                138
  CLUS_3                2                 82
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  20P GAIN MUTATED        2      3      2      0
  20P GAIN WILD-TYPE     62     61     40     49
D28V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                3                 61
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P GAIN MUTATED        1      1      0      2      0      3      0
  20P GAIN WILD-TYPE     45     27     33     27     47     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                 47
  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        1     10      0      1
  20P GAIN WILD-TYPE    157    157     58    113
D28V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               10                157
  CLUS_3                0                 58
  CLUS_4                1                113
[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        1     10      0      1      0
  20P GAIN WILD-TYPE    103    124     86     94     78
D28V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2               10                124
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  20P GAIN MUTATED        3      7      0      2
  20P GAIN WILD-TYPE    162    138    119     67
D28V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2                7                138
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        2      9      1
  20P GAIN WILD-TYPE    176    119    191
D28V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2                9                119
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      6      1      0
  20P GAIN WILD-TYPE    129    119    107    104
D28V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                6                119
  CLUS_3                1                107
  CLUS_4                0                104
[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
  20P GAIN MUTATED        2      6      1
  20P GAIN WILD-TYPE    161    114    184
D28V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                6                114
  CLUS_3                1                184
[1] 3 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        1      0     11
  20Q GAIN WILD-TYPE    131    138    218
D29V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3               11                218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q GAIN MUTATED        0      9      2      0      1
  20Q GAIN WILD-TYPE     46    138     82     42    179
D29V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                9                138
  CLUS_3                2                 82
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  20Q GAIN MUTATED        2      3      2      0
  20Q GAIN WILD-TYPE     62     61     40     49
D29V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                3                 61
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q GAIN MUTATED        1      1      0      2      0      3      0
  20Q GAIN WILD-TYPE     45     27     33     27     47     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                 47
  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        1     10      0      1
  20Q GAIN WILD-TYPE    157    157     58    113
D29V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2               10                157
  CLUS_3                0                 58
  CLUS_4                1                113
[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        1     10      0      1      0
  20Q GAIN WILD-TYPE    103    124     86     94     78
D29V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2               10                124
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  20Q GAIN MUTATED        3      7      0      2
  20Q GAIN WILD-TYPE    162    138    119     67
D29V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2                7                138
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        2      9      1
  20Q GAIN WILD-TYPE    176    119    191
D29V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                176
  CLUS_2                9                119
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      6      1      0
  20Q GAIN WILD-TYPE    129    119    107    104
D29V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                129
  CLUS_2                6                119
  CLUS_3                1                107
  CLUS_4                0                104
[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
  20Q GAIN MUTATED        2      6      1
  20Q GAIN WILD-TYPE    161    114    184
D29V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                6                114
  CLUS_3                1                184
[1] 3 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        0      1      4
  21Q GAIN WILD-TYPE    132    137    225
D30V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                137
  CLUS_3                4                225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        0      3      1      0      1
  21Q GAIN WILD-TYPE     46    144     83     42    179
D30V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                3                144
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  21Q GAIN MUTATED        1      0      1      0
  21Q GAIN WILD-TYPE     63     64     41     49
D30V3, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"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     47     27      9
D30V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                217 
        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-EL-A3CL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CR         TCGA-EL-A3CS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YA         TCGA-EM-A1YB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YC         TCGA-EM-A1YD         TCGA-EM-A1YE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22I         TCGA-EM-A22J         TCGA-EM-A22L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A22Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CJ         TCGA-EM-A2CK         TCGA-EM-A2CL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CO         TCGA-EM-A2CP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CQ         TCGA-EM-A2CU         TCGA-EM-A2OV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2P1         TCGA-EM-A3AI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AL         TCGA-EM-A3AN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AO         TCGA-EM-A3AP         TCGA-EM-A3FJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FN         TCGA-EM-A3FO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FP         TCGA-ET-A25G         TCGA-ET-A25L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25O         TCGA-ET-A2MY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3O1 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        0      3      1      1
  21Q GAIN WILD-TYPE    158    164     57    113
D30V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                158
  CLUS_2                3                164
  CLUS_3                1                 57
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        0      3      1      1      0
  21Q GAIN WILD-TYPE    104    131     85     94     78
D30V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                3                131
  CLUS_3                1                 85
  CLUS_4                1                 94
  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 CLUS_4
  21Q GAIN MUTATED        1      4      0      0
  21Q GAIN WILD-TYPE    164    141    119     69
D30V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                164
  CLUS_2                4                141
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  21Q GAIN MUTATED        1      3      1
  21Q GAIN WILD-TYPE    177    125    191
D30V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                177
  CLUS_2                3                125
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        1      2      1      0
  21Q GAIN WILD-TYPE    130    123    107    104
D30V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                130
  CLUS_2                2                123
  CLUS_3                1                107
  CLUS_4                0                104
[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
  21Q GAIN MUTATED        1      2      1
  21Q GAIN WILD-TYPE    162    118    184
D30V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2                2                118
  CLUS_3                1                184
[1] 3 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 = XP GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED        1      0      7
  XP GAIN WILD-TYPE    131    138    222
D31V1, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               7               222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP GAIN MUTATED        0      6      2      0      0
  XP GAIN WILD-TYPE     46    141     82     42    180
D31V2, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               6               141
  CLUS_3               2                82
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  XP GAIN MUTATED        1      2      1      0
  XP GAIN WILD-TYPE     63     62     41     49
D31V3, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               2                62
  CLUS_3               1                41
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XP GAIN MUTATED        2      0      0      1      0      1      0
  XP GAIN WILD-TYPE     44     28     33     28     47     26      9
D31V4, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2                44
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               1                28
  CLUS_5               0                47
  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
  XP GAIN MUTATED        1      6      1      0
  XP GAIN WILD-TYPE    157    161     57    114
D31V5, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1               157
  CLUS_2               6               161
  CLUS_3               1                57
  CLUS_4               0               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP GAIN MUTATED        1      6      1      0      0
  XP GAIN WILD-TYPE    103    128     85     95     78
D31V6, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1               103
  CLUS_2               6               128
  CLUS_3               1                85
  CLUS_4               0                95
  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 CLUS_4
  XP GAIN MUTATED        2      5      1      0
  XP GAIN WILD-TYPE    163    140    118     69
D31V7, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               5               140
  CLUS_3               1               118
  CLUS_4               0                69
[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
  XP GAIN MUTATED        2      5      1
  XP GAIN WILD-TYPE    176    123    191
D31V8, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2               176
  CLUS_2               5               123
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        1      5      1      0
  XP GAIN WILD-TYPE    130    120    107    104
D31V9, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               5               120
  CLUS_3               1               107
  CLUS_4               0               104
[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
  XP GAIN MUTATED        2      4      1
  XP GAIN WILD-TYPE    161    116    184
D31V10, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               4               116
  CLUS_3               1               184
[1] 3 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 = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1      0      6
  XQ GAIN WILD-TYPE    131    138    223
D32V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               6               223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED        0      6      1      0      0
  XQ GAIN WILD-TYPE     46    141     83     42    180
D32V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                46
  CLUS_2               6               141
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  XQ GAIN MUTATED        1      2      1      0
  XQ GAIN WILD-TYPE     63     62     41     49
D32V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               2                62
  CLUS_3               1                41
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ GAIN MUTATED        2      0      0      1      0      1      0
  XQ GAIN WILD-TYPE     44     28     33     28     47     26      9
D32V4, 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                47
  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        1      6      0      0
  XQ GAIN WILD-TYPE    157    161     58    114
D32V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               157
  CLUS_2               6               161
  CLUS_3               0                58
  CLUS_4               0               114
[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        1      6      0      0      0
  XQ GAIN WILD-TYPE    103    128     86     95     78
D32V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               103
  CLUS_2               6               128
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  XQ GAIN MUTATED        2      5      0      0
  XQ GAIN WILD-TYPE    163    140    119     69
D32V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               5               140
  CLUS_3               0               119
  CLUS_4               0                69
[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
  XQ GAIN MUTATED        2      5      0
  XQ GAIN WILD-TYPE    176    123    192
D32V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2               176
  CLUS_2               5               123
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      5      0      0
  XQ GAIN WILD-TYPE    130    120    108    104
D32V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               130
  CLUS_2               5               120
  CLUS_3               0               108
  CLUS_4               0               104
[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
  XQ GAIN MUTATED        2      4      0
  XQ GAIN WILD-TYPE    161    116    185
D32V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               4               116
  CLUS_3               0               185
[1] 3 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 = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      0      3
  1P LOSS WILD-TYPE    131    138    226
D33V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               3               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0      1
  1P LOSS WILD-TYPE     46    144     84     42    179
D33V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  1P LOSS MUTATED        1      0      1      0
  1P LOSS WILD-TYPE     63     64     41     49
D33V3, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     27      9
D33V4, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        0      3      0      1
  1P LOSS WILD-TYPE    158    164     58    113
D33V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               1               113
[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        0      3      0      1      0
  1P LOSS WILD-TYPE    104    131     86     94     78
D33V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               1                94
  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 CLUS_4
  1P LOSS MUTATED        2      2      0      0
  1P LOSS WILD-TYPE    163    143    119     69
D33V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2               163
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               0                69
[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
  1P LOSS MUTATED        1      3      0
  1P LOSS WILD-TYPE    177    125    192
D33V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               177
  CLUS_2               3               125
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      2      0      0
  1P LOSS WILD-TYPE    129    123    108    104
D33V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2               129
  CLUS_2               2               123
  CLUS_3               0               108
  CLUS_4               0               104
[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
  1P LOSS MUTATED        1      3      0
  1P LOSS WILD-TYPE    162    117    185
D33V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 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 = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        0      0      3
  1Q LOSS WILD-TYPE    132    138    226
D34V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               3               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0      0
  1Q LOSS WILD-TYPE     46    144     84     42    180
D34V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  1Q LOSS MUTATED        1      0      1      0
  1Q LOSS WILD-TYPE     63     64     41     49
D34V3, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     27      9
D34V4, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        0      3      0      0
  1Q LOSS WILD-TYPE    158    164     58    114
D34V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               0               114
[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        0      3      0      0      0
  1Q LOSS WILD-TYPE    104    131     86     95     78
D34V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  1Q LOSS MUTATED        1      2      0      0
  1Q LOSS WILD-TYPE    164    143    119     69
D34V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               0                69
[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
  1Q LOSS MUTATED        0      3      0
  1Q LOSS WILD-TYPE    178    125    192
D34V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               3               125
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      2      0      0
  1Q LOSS WILD-TYPE    130    123    108    104
D34V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               130
  CLUS_2               2               123
  CLUS_3               0               108
  CLUS_4               0               104
[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
  1Q LOSS MUTATED        0      3      0
  1Q LOSS WILD-TYPE    163    117    185
D34V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 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 = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        0      0     10
  2P LOSS WILD-TYPE    132    138    219
D35V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3              10               219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      9      1      0      0
  2P LOSS WILD-TYPE     46    138     83     42    180
D35V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               9               138
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  2P LOSS MUTATED        2      3      0      1
  2P LOSS WILD-TYPE     62     61     42     48
D35V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               3                61
  CLUS_3               0                42
  CLUS_4               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2P LOSS MUTATED        2      0      0      1      0      3      0
  2P LOSS WILD-TYPE     44     28     33     28     47     24      9
D35V4, 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                47
  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        0     10      0      0
  2P LOSS WILD-TYPE    158    157     58    114
D35V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2              10               157
  CLUS_3               0                58
  CLUS_4               0               114
[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        0     10      0      0      0
  2P LOSS WILD-TYPE    104    124     86     95     78
D35V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2              10               124
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  2P LOSS MUTATED        1      6      0      3
  2P LOSS WILD-TYPE    164    139    119     66
D35V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               6               139
  CLUS_3               0               119
  CLUS_4               3                66
[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
  2P LOSS MUTATED        0     10      0
  2P LOSS WILD-TYPE    178    118    192
D35V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2              10               118
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      7      0      0
  2P LOSS WILD-TYPE    130    118    108    104
D35V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               130
  CLUS_2               7               118
  CLUS_3               0               108
  CLUS_4               0               104
[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
  2P LOSS MUTATED        0      8      0
  2P LOSS WILD-TYPE    163    112    185
D35V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               8               112
  CLUS_3               0               185
[1] 3 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 = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        0      0     10
  2Q LOSS WILD-TYPE    132    138    219
D36V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3              10               219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      9      1      0      0
  2Q LOSS WILD-TYPE     46    138     83     42    180
D36V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               9               138
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  2Q LOSS MUTATED        2      3      1      0
  2Q LOSS WILD-TYPE     62     61     41     49
D36V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               3                61
  CLUS_3               1                41
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2Q LOSS MUTATED        2      0      0      1      0      3      0
  2Q LOSS WILD-TYPE     44     28     33     28     47     24      9
D36V4, 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                47
  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        0     10      0      0
  2Q LOSS WILD-TYPE    158    157     58    114
D36V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2              10               157
  CLUS_3               0                58
  CLUS_4               0               114
[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        0     10      0      0      0
  2Q LOSS WILD-TYPE    104    124     86     95     78
D36V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2              10               124
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  2Q LOSS MUTATED        1      6      0      3
  2Q LOSS WILD-TYPE    164    139    119     66
D36V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               6               139
  CLUS_3               0               119
  CLUS_4               3                66
[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
  2Q LOSS MUTATED        0     10      0
  2Q LOSS WILD-TYPE    178    118    192
D36V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2              10               118
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      7      0      0
  2Q LOSS WILD-TYPE    130    118    108    104
D36V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               130
  CLUS_2               7               118
  CLUS_3               0               108
  CLUS_4               0               104
[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
  2Q LOSS MUTATED        0      8      0
  2Q LOSS WILD-TYPE    163    112    185
D36V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               8               112
  CLUS_3               0               185
[1] 3 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 = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        0      0      3
  3P LOSS WILD-TYPE    132    138    226
D37V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               3               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0      0
  3P LOSS WILD-TYPE     46    144     84     42    180
D37V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  3P LOSS MUTATED        1      0      1      0
  3P LOSS WILD-TYPE     63     64     41     49
D37V3, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     27      9
D37V4, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      3      0      0
  3P LOSS WILD-TYPE    158    164     58    114
D37V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               0               114
[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        0      3      0      0      0
  3P LOSS WILD-TYPE    104    131     86     95     78
D37V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  3P LOSS MUTATED        1      2      0      0
  3P LOSS WILD-TYPE    164    143    119     69
D37V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               0                69
[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
  3P LOSS MUTATED        0      3      0
  3P LOSS WILD-TYPE    178    125    192
D37V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               3               125
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      2      0      0
  3P LOSS WILD-TYPE    130    123    108    104
D37V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1               130
  CLUS_2               2               123
  CLUS_3               0               108
  CLUS_4               0               104
[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
  3P LOSS MUTATED        0      3      0
  3P LOSS WILD-TYPE    163    117    185
D37V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 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 = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        0      0      4
  3Q LOSS WILD-TYPE    132    138    225
D38V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               4               225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      0      0      0
  3Q LOSS WILD-TYPE     46    143     84     42    180
D38V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               4               143
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  3Q LOSS MUTATED        2      0      1      0
  3Q LOSS WILD-TYPE     62     64     41     49
D38V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                64
  CLUS_3               1                41
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3Q LOSS MUTATED        2      0      0      1      0      0      0
  3Q LOSS WILD-TYPE     44     28     33     28     47     27      9
D38V4, 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                47
  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        0      4      0      0
  3Q LOSS WILD-TYPE    158    163     58    114
D38V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               4               163
  CLUS_3               0                58
  CLUS_4               0               114
[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        0      4      0      0      0
  3Q LOSS WILD-TYPE    104    130     86     95     78
D38V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               4               130
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  3Q LOSS MUTATED        1      3      0      0
  3Q LOSS WILD-TYPE    164    142    119     69
D38V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               3               142
  CLUS_3               0               119
  CLUS_4               0                69
[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
  3Q LOSS MUTATED        0      4      0
  3Q LOSS WILD-TYPE    178    124    192
D38V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               4               124
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      3      0      0
  3Q LOSS WILD-TYPE    130    122    108    104
D38V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1               130
  CLUS_2               3               122
  CLUS_3               0               108
  CLUS_4               0               104
[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
  3Q LOSS MUTATED        0      4      0
  3Q LOSS WILD-TYPE    163    116    185
D38V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               4               116
  CLUS_3               0               185
[1] 3 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 = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        0      0      4
  6P LOSS WILD-TYPE    132    138    225
D39V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               4               225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      1      0      0
  6P LOSS WILD-TYPE     46    144     83     42    180
D39V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  6P LOSS MUTATED        0      0      1      1
  6P LOSS WILD-TYPE     64     64     41     48
D39V3, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     46     27      9
D39V4, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22Q 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OY        TCGA-EM-A2P1        TCGA-EM-A3AI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AP        TCGA-EM-A3FJ        TCGA-EM-A3FL        TCGA-EM-A3FN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-ET-A25G        TCGA-ET-A25L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25O        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A2N5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39L        TCGA-ET-A39M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"6P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        1      3      0      0
  6P LOSS WILD-TYPE    157    164     58    114
D39V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1               157
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               0               114
[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        1      3      0      0      0
  6P LOSS WILD-TYPE    103    131     86     95     78
D39V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1               103
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  6P LOSS MUTATED        2      2      0      0
  6P LOSS WILD-TYPE    163    143    119     69
D39V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2               163
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               0                69
[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
  6P LOSS MUTATED        1      3      0
  6P LOSS WILD-TYPE    177    125    192
D39V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1               177
  CLUS_2               3               125
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      2      0      0
  6P LOSS WILD-TYPE    129    123    108    104
D39V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2               129
  CLUS_2               2               123
  CLUS_3               0               108
  CLUS_4               0               104
[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
  6P LOSS MUTATED        1      3      0
  6P LOSS WILD-TYPE    162    117    185
D39V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        0      0      7
  6Q LOSS WILD-TYPE    132    138    222
D40V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               7               222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      6      1      0      0
  6Q LOSS WILD-TYPE     46    141     83     42    180
D40V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               6               141
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  6Q LOSS MUTATED        1      0      3      1
  6Q LOSS WILD-TYPE     63     64     39     48
D40V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0                64
  CLUS_3               3                39
  CLUS_4               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED        2      0      0      2      1      0      0
  6Q LOSS WILD-TYPE     44     28     33     27     46     27      9
D40V4, 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                46
  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        1      6      0      0
  6Q LOSS WILD-TYPE    157    161     58    114
D40V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1               157
  CLUS_2               6               161
  CLUS_3               0                58
  CLUS_4               0               114
[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        1      6      0      0      0
  6Q LOSS WILD-TYPE    103    128     86     95     78
D40V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1               103
  CLUS_2               6               128
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  6Q LOSS MUTATED        2      4      0      1
  6Q LOSS WILD-TYPE    163    141    119     68
D40V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2               163
  CLUS_2               4               141
  CLUS_3               0               119
  CLUS_4               1                68
[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
  6Q LOSS MUTATED        1      6      0
  6Q LOSS WILD-TYPE    177    122    192
D40V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1               177
  CLUS_2               6               122
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      5      0      0
  6Q LOSS WILD-TYPE    129    120    108    104
D40V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2               129
  CLUS_2               5               120
  CLUS_3               0               108
  CLUS_4               0               104
[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
  6Q LOSS MUTATED        1      6      0
  6Q LOSS WILD-TYPE    162    114    185
D40V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               6               114
  CLUS_3               0               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      0      4
  8P LOSS WILD-TYPE    132    138    225
D41V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               4               225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P LOSS MUTATED        0      3      1      0      0
  8P LOSS WILD-TYPE     46    144     83     42    180
D41V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  8P LOSS MUTATED        1      1      0      0
  8P LOSS WILD-TYPE     63     63     42     49
D41V3, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     26      9
D41V4, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"8P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        0      4      0      0
  8P LOSS WILD-TYPE    158    163     58    114
D41V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               4               163
  CLUS_3               0                58
  CLUS_4               0               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P LOSS MUTATED        0      4      0      0      0
  8P LOSS WILD-TYPE    104    130     86     95     78
D41V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               4               130
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  8P LOSS MUTATED        0      2      0      2
  8P LOSS WILD-TYPE    165    143    119     67
D41V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               2                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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      4      0
  8P LOSS WILD-TYPE    178    124    192
D41V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               4               124
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0
  8P LOSS WILD-TYPE    131    122    108    104
D41V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               131
  CLUS_2               3               122
  CLUS_3               0               108
  CLUS_4               0               104
[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
  8P LOSS MUTATED        0      3      0
  8P LOSS WILD-TYPE    163    117    185
D41V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      0      4
  8Q LOSS WILD-TYPE    132    138    225
D42V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               138
  CLUS_3               4               225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED        0      3      1      0      0
  8Q LOSS WILD-TYPE     46    144     83     42    180
D42V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               0               180
[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 CLUS_4
  8Q LOSS MUTATED        1      1      0      0
  8Q LOSS WILD-TYPE     63     63     42     49
D42V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"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     47     26      9
D42V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               217 
       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-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EM-A1CT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22L        TCGA-EM-A22M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22Q        TCGA-EM-A2CJ        TCGA-EM-A2CK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO        TCGA-EM-A2CP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3FJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DV        TCGA-ET-A3DW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FY-A2QD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3BL        TCGA-FY-A3ON        TCGA-GE-A2C6        TCGA-H2-A2K9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1 
"8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        0      4      0      0
  8Q LOSS WILD-TYPE    158    163     58    114
D42V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               158
  CLUS_2               4               163
  CLUS_3               0                58
  CLUS_4               0               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED        0      4      0      0      0
  8Q LOSS WILD-TYPE    104    130     86     95     78
D42V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               4               130
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  8Q LOSS MUTATED        0      2      0      2
  8Q LOSS WILD-TYPE    165    143    119     67
D42V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               2               143
  CLUS_3               0               119
  CLUS_4               2                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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      4      0
  8Q LOSS WILD-TYPE    178    124    192
D42V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               4               124
  CLUS_3               0               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0
  8Q LOSS WILD-TYPE    131    122    108    104
D42V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               131
  CLUS_2               3               122
  CLUS_3               0               108
  CLUS_4               0               104
[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
  8Q LOSS MUTATED        0      3      0
  8Q LOSS WILD-TYPE    163    117    185
D42V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               0               185
[1] 3 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 = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        9      1      9
  9P LOSS WILD-TYPE    123    137    220
D43V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9               123
  CLUS_2               1               137
  CLUS_3               9               220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2     10      4      0      3
  9P LOSS WILD-TYPE     44    137     80     42    177
D43V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                44
  CLUS_2              10               137
  CLUS_3               4                80
  CLUS_4               0                42
  CLUS_5               3               177
[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 CLUS_4
  9P LOSS MUTATED        1      2      1      2
  9P LOSS WILD-TYPE     63     62     41     47
D43V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               2                62
  CLUS_3               1                41
  CLUS_4               2                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P LOSS MUTATED        1      0      0      1      2      2      0
  9P LOSS WILD-TYPE     45     28     33     28     45     25      9
D43V4, 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                45
  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        2     11      3      3
  9P LOSS WILD-TYPE    156    156     55    111
D43V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2               156
  CLUS_2              11               156
  CLUS_3               3                55
  CLUS_4               3               111
[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        3     11      1      3      1
  9P LOSS WILD-TYPE    101    123     85     92     77
D43V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3               101
  CLUS_2              11               123
  CLUS_3               1                85
  CLUS_4               3                92
  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 CLUS_4
  9P LOSS MUTATED        8      7      1      3
  9P LOSS WILD-TYPE    157    138    118     66
D43V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8               157
  CLUS_2               7               138
  CLUS_3               1               118
  CLUS_4               3                66
[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
  9P LOSS MUTATED        7     10      2
  9P LOSS WILD-TYPE    171    118    190
D43V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7               171
  CLUS_2              10               118
  CLUS_3               2               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      8      0      2
  9P LOSS WILD-TYPE    124    117    108    102
D43V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7               124
  CLUS_2               8               117
  CLUS_3               0               108
  CLUS_4               2               102
[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
  9P LOSS MUTATED        7      8      2
  9P LOSS WILD-TYPE    156    112    183
D43V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7               156
  CLUS_2               8               112
  CLUS_3               2               183
[1] 3 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 = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       14      1     10
  9Q LOSS WILD-TYPE    118    137    219
D44V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              14               118
  CLUS_2               1               137
  CLUS_3              10               219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4     11      6      0      4
  9Q LOSS WILD-TYPE     42    136     78     42    176
D44V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                42
  CLUS_2              11               136
  CLUS_3               6                78
  CLUS_4               0                42
  CLUS_5               4               176
[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 CLUS_4
  9Q LOSS MUTATED        1      4      1      2
  9Q LOSS WILD-TYPE     63     60     41     47
D44V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               4                60
  CLUS_3               1                41
  CLUS_4               2                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q LOSS MUTATED        1      0      0      1      2      4      0
  9Q LOSS WILD-TYPE     45     28     33     28     45     23      9
D44V4, 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                45
  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        6     12      4      3
  9Q LOSS WILD-TYPE    152    155     54    111
D44V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               6               152
  CLUS_2              12               155
  CLUS_3               4                54
  CLUS_4               3               111
[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        7     12      1      3      2
  9Q LOSS WILD-TYPE     97    122     85     92     76
D44V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                97
  CLUS_2              12               122
  CLUS_3               1                85
  CLUS_4               3                92
  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 CLUS_4
  9Q LOSS MUTATED       12      8      1      4
  9Q LOSS WILD-TYPE    153    137    118     65
D44V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              12               153
  CLUS_2               8               137
  CLUS_3               1               118
  CLUS_4               4                65
[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
  9Q LOSS MUTATED       11     11      3
  9Q LOSS WILD-TYPE    167    117    189
D44V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               167
  CLUS_2              11               117
  CLUS_3               3               189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      9      1      2
  9Q LOSS WILD-TYPE    120    116    107    102
D44V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               120
  CLUS_2               9               116
  CLUS_3               1               107
  CLUS_4               2               102
[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
  9Q LOSS MUTATED       11      9      3
  9Q LOSS WILD-TYPE    152    111    182
D44V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               152
  CLUS_2               9               111
  CLUS_3               3               182
[1] 3 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 = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        1      0      6
  10P LOSS WILD-TYPE    131    138    223
D45V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                6                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      5      1      0      1
  10P LOSS WILD-TYPE     46    142     83     42    179
D45V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                5                142
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  10P LOSS MUTATED        2      0      1      0
  10P LOSS WILD-TYPE     62     64     41     49
D45V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                0                 64
  CLUS_3                1                 41
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10P LOSS MUTATED        2      0      0      1      0      0      0
  10P LOSS WILD-TYPE     44     28     33     28     47     27      9
D45V4, 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                 47
  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        0      6      0      1
  10P LOSS WILD-TYPE    158    161     58    113
D45V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                6                161
  CLUS_3                0                 58
  CLUS_4                1                113
[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        0      6      0      1      0
  10P LOSS WILD-TYPE    104    128     86     94     78
D45V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                6                128
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  10P LOSS MUTATED        2      4      0      1
  10P LOSS WILD-TYPE    163    141    119     68
D45V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                4                141
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  10P LOSS MUTATED        1      6      0
  10P LOSS WILD-TYPE    177    122    192
D45V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                177
  CLUS_2                6                122
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      5      0      0
  10P LOSS WILD-TYPE    129    120    108    104
D45V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                129
  CLUS_2                5                120
  CLUS_3                0                108
  CLUS_4                0                104
[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
  10P LOSS MUTATED        1      6      0
  10P LOSS WILD-TYPE    162    114    185
D45V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                6                114
  CLUS_3                0                185
[1] 3 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 = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        1      0      5
  10Q LOSS WILD-TYPE    131    138    224
D46V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      1      0      1
  10Q LOSS WILD-TYPE     46    143     83     42    179
D46V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                1                179
[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 CLUS_4
  10Q LOSS MUTATED        1      0      1      0
  10Q LOSS WILD-TYPE     63     64     41     49
D46V3, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                217 
        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-EL-A3CL         TCGA-EL-A3CM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EM-A1CT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CU         TCGA-EM-A1CV         TCGA-EM-A1CW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YA         TCGA-EM-A1YB         TCGA-EM-A1YC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22L         TCGA-EM-A22M 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A22Q         TCGA-EM-A2CJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CK         TCGA-EM-A2CL         TCGA-EM-A2CN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CO         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-J8-A3O1 
"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     47     27      9
D46V4, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                217 
        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-EL-A3CL         TCGA-EL-A3CM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EM-A1CT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1CU         TCGA-EM-A1CV         TCGA-EM-A1CW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YA         TCGA-EM-A1YB         TCGA-EM-A1YC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22L         TCGA-EM-A22M 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A22Q         TCGA-EM-A2CJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CK         TCGA-EM-A2CL         TCGA-EM-A2CN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CO         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2CU         TCGA-EM-A2OV         TCGA-EM-A2OY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A3AI         TCGA-EM-A3AJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AL         TCGA-EM-A3AN         TCGA-EM-A3AO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3AP         TCGA-EM-A3FJ         TCGA-EM-A3FL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25L         TCGA-ET-A25M 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39M         TCGA-ET-A39P 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39T         TCGA-ET-A3BN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BS         TCGA-ET-A3BT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DO         TCGA-ET-A3DP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-FE-A22Z         TCGA-FE-A230 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3ON 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A2K9         TCGA-IM-A3EB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-J8-A3NZ         TCGA-J8-A3O0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-J8-A3O1 
"10Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        0      5      0      1
  10Q LOSS WILD-TYPE    158    162     58    113
D46V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                5                162
  CLUS_3                0                 58
  CLUS_4                1                113
[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        0      5      0      1      0
  10Q LOSS WILD-TYPE    104    129     86     94     78
D46V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                5                129
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  10Q LOSS MUTATED        2      3      0      1
  10Q LOSS WILD-TYPE    163    142    119     68
D46V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                3                142
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  10Q LOSS MUTATED        1      5      0
  10Q LOSS WILD-TYPE    177    123    192
D46V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                177
  CLUS_2                5                123
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      4      0      0
  10Q LOSS WILD-TYPE    129    121    108    104
D46V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                129
  CLUS_2                4                121
  CLUS_3                0                108
  CLUS_4                0                104
[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
  10Q LOSS MUTATED        1      5      0
  10Q LOSS WILD-TYPE    162    115    185
D46V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                5                115
  CLUS_3                0                185
[1] 3 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 = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        2      0      5
  11P LOSS WILD-TYPE    130    138    224
D47V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                138
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      6      1      0      0
  11P LOSS WILD-TYPE     46    141     83     42    180
D47V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                6                141
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  11P LOSS MUTATED        1      0      1      1
  11P LOSS WILD-TYPE     63     64     41     48
D47V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 64
  CLUS_3                1                 41
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED        1      0      0      1      1      0      0
  11P LOSS WILD-TYPE     45     28     33     28     46     27      9
D47V4, 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                 46
  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        0      6      1      0
  11P LOSS WILD-TYPE    158    161     57    114
D47V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                6                161
  CLUS_3                1                 57
  CLUS_4                0                114
[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        1      6      0      0      0
  11P LOSS WILD-TYPE    103    128     86     95     78
D47V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                6                128
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  11P LOSS MUTATED        2      5      0      0
  11P LOSS WILD-TYPE    163    140    119     69
D47V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                5                140
  CLUS_3                0                119
  CLUS_4                0                 69
[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
  11P LOSS MUTATED        1      6      0
  11P LOSS WILD-TYPE    177    122    192
D47V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                177
  CLUS_2                6                122
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      5      0      0
  11P LOSS WILD-TYPE    129    120    108    104
D47V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                129
  CLUS_2                5                120
  CLUS_3                0                108
  CLUS_4                0                104
[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
  11P LOSS MUTATED        1      6      0
  11P LOSS WILD-TYPE    162    114    185
D47V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                6                114
  CLUS_3                0                185
[1] 3 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 = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        2      1      6
  11Q LOSS WILD-TYPE    130    137    223
D48V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                1                137
  CLUS_3                6                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      7      1      0      0
  11Q LOSS WILD-TYPE     45    140     83     42    180
D48V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                7                140
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  11Q LOSS MUTATED        2      0      1      1
  11Q LOSS WILD-TYPE     62     64     41     48
D48V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                0                 64
  CLUS_3                1                 41
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED        2      0      0      1      1      0      0
  11Q LOSS WILD-TYPE     44     28     33     28     46     27      9
D48V4, 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                 46
  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        1      7      1      0
  11Q LOSS WILD-TYPE    157    160     57    114
D48V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                157
  CLUS_2                7                160
  CLUS_3                1                 57
  CLUS_4                0                114
[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        1      7      0      0      1
  11Q LOSS WILD-TYPE    103    127     86     95     77
D48V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                7                127
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  11Q LOSS MUTATED        2      6      0      1
  11Q LOSS WILD-TYPE    163    139    119     68
D48V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                6                139
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  11Q LOSS MUTATED        1      7      1
  11Q LOSS WILD-TYPE    177    121    191
D48V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                177
  CLUS_2                7                121
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      6      0      0
  11Q LOSS WILD-TYPE    129    119    108    104
D48V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                129
  CLUS_2                6                119
  CLUS_3                0                108
  CLUS_4                0                104
[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
  11Q LOSS MUTATED        1      7      0
  11Q LOSS WILD-TYPE    162    113    185
D48V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                7                113
  CLUS_3                0                185
[1] 3 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 = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        3      0     11
  13Q LOSS WILD-TYPE    129    138    218
D49V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                129
  CLUS_2                0                138
  CLUS_3               11                218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      9      2      1      2
  13Q LOSS WILD-TYPE     46    138     82     41    178
D49V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                9                138
  CLUS_3                2                 82
  CLUS_4                1                 41
  CLUS_5                2                178
[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 CLUS_4
  13Q LOSS MUTATED        1      1      6      1
  13Q LOSS WILD-TYPE     63     63     36     48
D49V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 63
  CLUS_3                6                 36
  CLUS_4                1                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q LOSS MUTATED        1      0      0      4      3      1      0
  13Q LOSS WILD-TYPE     45     28     33     25     44     26      9
D49V4, 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                 44
  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        0      9      2      3
  13Q LOSS WILD-TYPE    158    158     56    111
D49V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                9                158
  CLUS_3                2                 56
  CLUS_4                3                111
[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        0      9      2      3      0
  13Q LOSS WILD-TYPE    104    125     84     92     78
D49V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                9                125
  CLUS_3                2                 84
  CLUS_4                3                 92
  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 CLUS_4
  13Q LOSS MUTATED        1      6      5      2
  13Q LOSS WILD-TYPE    164    139    114     67
D49V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                164
  CLUS_2                6                139
  CLUS_3                5                114
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        0      9      5
  13Q LOSS WILD-TYPE    178    119    187
D49V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                178
  CLUS_2                9                119
  CLUS_3                5                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      9      2      1
  13Q LOSS WILD-TYPE    130    116    106    103
D49V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                130
  CLUS_2                9                116
  CLUS_3                2                106
  CLUS_4                1                103
[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
  13Q LOSS MUTATED        0      9      4
  13Q LOSS WILD-TYPE    163    111    181
D49V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                9                111
  CLUS_3                4                181
[1] 3 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 = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        2      0      6
  15Q LOSS WILD-TYPE    130    138    223
D50V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                138
  CLUS_3                6                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      7      1      0      0
  15Q LOSS WILD-TYPE     46    140     83     42    180
D50V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                7                140
  CLUS_3                1                 83
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  15Q LOSS MUTATED        1      1      3      0
  15Q LOSS WILD-TYPE     63     63     39     49
D50V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 63
  CLUS_3                3                 39
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED        1      0      0      3      0      1      0
  15Q LOSS WILD-TYPE     45     28     33     26     47     26      9
D50V4, 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                 47
  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        0      8      0      0
  15Q LOSS WILD-TYPE    158    159     58    114
D50V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                8                159
  CLUS_3                0                 58
  CLUS_4                0                114
[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        0      8      0      0      0
  15Q LOSS WILD-TYPE    104    126     86     95     78
D50V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                8                126
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  15Q LOSS MUTATED        1      3      0      4
  15Q LOSS WILD-TYPE    164    142    119     65
D50V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                164
  CLUS_2                3                142
  CLUS_3                0                119
  CLUS_4                4                 65
[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
  15Q LOSS MUTATED        0      8      0
  15Q LOSS WILD-TYPE    178    120    192
D50V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                178
  CLUS_2                8                120
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      6      0      0
  15Q LOSS WILD-TYPE    130    119    108    104
D50V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                130
  CLUS_2                6                119
  CLUS_3                0                108
  CLUS_4                0                104
[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
  15Q LOSS MUTATED        0      7      0
  15Q LOSS WILD-TYPE    163    113    185
D50V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                7                113
  CLUS_3                0                185
[1] 3 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 = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        3      0      5
  17P LOSS WILD-TYPE    129    138    224
D51V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                129
  CLUS_2                0                138
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P LOSS MUTATED        1      3      1      1      2
  17P LOSS WILD-TYPE     45    144     83     41    178
D51V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 45
  CLUS_2                3                144
  CLUS_3                1                 83
  CLUS_4                1                 41
  CLUS_5                2                178
[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 CLUS_4
  17P LOSS MUTATED        2      1      0      0
  17P LOSS WILD-TYPE     62     63     42     49
D51V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                 63
  CLUS_3                0                 42
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P LOSS MUTATED        2      0      0      0      0      1      0
  17P LOSS WILD-TYPE     44     28     33     29     47     26      9
D51V4, 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                 47
  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        3      4      0      1
  17P LOSS WILD-TYPE    155    163     58    113
D51V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                155
  CLUS_2                4                163
  CLUS_3                0                 58
  CLUS_4                1                113
[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        2      4      0      1      1
  17P LOSS WILD-TYPE    102    130     86     94     77
D51V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                102
  CLUS_2                4                130
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  17P LOSS MUTATED        3      3      0      2
  17P LOSS WILD-TYPE    162    142    119     67
D51V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                162
  CLUS_2                3                142
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        3      4      1
  17P LOSS WILD-TYPE    175    124    191
D51V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                175
  CLUS_2                4                124
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        3      4      1      0
  17P LOSS WILD-TYPE    128    121    107    104
D51V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                128
  CLUS_2                4                121
  CLUS_3                1                107
  CLUS_4                0                104
[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
  17P LOSS MUTATED        3      4      1
  17P LOSS WILD-TYPE    160    116    184
D51V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                160
  CLUS_2                4                116
  CLUS_3                1                184
[1] 3 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 = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        1      0      3
  17Q LOSS WILD-TYPE    131    138    226
D52V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                3                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        0      1      1      1      1
  17Q LOSS WILD-TYPE     46    146     83     41    179
D52V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                1                146
  CLUS_3                1                 83
  CLUS_4                1                 41
  CLUS_5                1                179
[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 CLUS_4
  17Q LOSS MUTATED        0      0      0      0
  17Q LOSS WILD-TYPE     64     64     42     49
D52V3, 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     47     27      9
D52V4, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        1      2      0      1
  17Q LOSS WILD-TYPE    157    165     58    113
D52V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                157
  CLUS_2                2                165
  CLUS_3                0                 58
  CLUS_4                1                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        0      2      0      1      1
  17Q LOSS WILD-TYPE    104    132     86     94     77
D52V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                2                132
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  17Q LOSS MUTATED        1      1      0      2
  17Q LOSS WILD-TYPE    164    144    119     67
D52V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                164
  CLUS_2                1                144
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        1      2      1
  17Q LOSS WILD-TYPE    177    126    191
D52V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                177
  CLUS_2                2                126
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      2      1      0
  17Q LOSS WILD-TYPE    130    123    107    104
D52V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                130
  CLUS_2                2                123
  CLUS_3                1                107
  CLUS_4                0                104
[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
  17Q LOSS MUTATED        1      2      1
  17Q LOSS WILD-TYPE    162    118    184
D52V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                2                118
  CLUS_3                1                184
[1] 3 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 = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      0      3
  18P LOSS WILD-TYPE    131    138    226
D53V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                3                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      1      0
  18P LOSS WILD-TYPE     46    144     84     41    180
D53V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                3                144
  CLUS_3                0                 84
  CLUS_4                1                 41
  CLUS_5                0                180
[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 CLUS_4
  18P LOSS MUTATED        2      1      0      0
  18P LOSS WILD-TYPE     62     63     42     49
D53V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                 63
  CLUS_3                0                 42
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED        2      0      0      0      0      1      0
  18P LOSS WILD-TYPE     44     28     33     29     47     26      9
D53V4, 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                 47
  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        0      3      0      1
  18P LOSS WILD-TYPE    158    164     58    113
D53V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                3                164
  CLUS_3                0                 58
  CLUS_4                1                113
[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        0      3      0      1      0
  18P LOSS WILD-TYPE    104    131     86     94     78
D53V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                3                131
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  18P LOSS MUTATED        0      2      1      1
  18P LOSS WILD-TYPE    165    143    118     68
D53V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                165
  CLUS_2                2                143
  CLUS_3                1                118
  CLUS_4                1                 68
[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
  18P LOSS MUTATED        0      3      1
  18P LOSS WILD-TYPE    178    125    191
D53V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                178
  CLUS_2                3                125
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      2      0      1
  18P LOSS WILD-TYPE    131    123    108    103
D53V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                131
  CLUS_2                2                123
  CLUS_3                0                108
  CLUS_4                1                103
[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
  18P LOSS MUTATED        0      2      1
  18P LOSS WILD-TYPE    163    118    184
D53V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                2                118
  CLUS_3                1                184
[1] 3 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 = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      0      3
  18Q LOSS WILD-TYPE    131    138    226
D54V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                138
  CLUS_3                3                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      1      0
  18Q LOSS WILD-TYPE     46    144     84     41    180
D54V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                3                144
  CLUS_3                0                 84
  CLUS_4                1                 41
  CLUS_5                0                180
[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 CLUS_4
  18Q LOSS MUTATED        2      1      0      0
  18Q LOSS WILD-TYPE     62     63     42     49
D54V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                 63
  CLUS_3                0                 42
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q LOSS MUTATED        2      0      0      0      0      1      0
  18Q LOSS WILD-TYPE     44     28     33     29     47     26      9
D54V4, 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                 47
  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        0      3      0      1
  18Q LOSS WILD-TYPE    158    164     58    113
D54V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                3                164
  CLUS_3                0                 58
  CLUS_4                1                113
[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        0      3      0      1      0
  18Q LOSS WILD-TYPE    104    131     86     94     78
D54V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                3                131
  CLUS_3                0                 86
  CLUS_4                1                 94
  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 CLUS_4
  18Q LOSS MUTATED        0      2      1      1
  18Q LOSS WILD-TYPE    165    143    118     68
D54V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                165
  CLUS_2                2                143
  CLUS_3                1                118
  CLUS_4                1                 68
[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
  18Q LOSS MUTATED        0      3      1
  18Q LOSS WILD-TYPE    178    125    191
D54V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                178
  CLUS_2                3                125
  CLUS_3                1                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      2      0      1
  18Q LOSS WILD-TYPE    131    123    108    103
D54V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                131
  CLUS_2                2                123
  CLUS_3                0                108
  CLUS_4                1                103
[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
  18Q LOSS MUTATED        0      2      1
  18Q LOSS WILD-TYPE    163    118    184
D54V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                2                118
  CLUS_3                1                184
[1] 3 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 = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        2      1      2
  19P LOSS WILD-TYPE    130    137    227
D55V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                1                137
  CLUS_3                2                227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      5      0      0      0
  19P LOSS WILD-TYPE     46    142     84     42    180
D55V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                5                142
  CLUS_3                0                 84
  CLUS_4                0                 42
  CLUS_5                0                180
[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 CLUS_4
  19P LOSS MUTATED        2      0      2      0
  19P LOSS WILD-TYPE     62     64     40     49
D55V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                0                 64
  CLUS_3                2                 40
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P LOSS MUTATED        3      0      0      1      0      0      0
  19P LOSS WILD-TYPE     43     28     33     28     47     27      9
D55V4, 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                 47
  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        0      5      0      0
  19P LOSS WILD-TYPE    158    162     58    114
D55V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                158
  CLUS_2                5                162
  CLUS_3                0                 58
  CLUS_4                0                114
[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        0      5      0      0      0
  19P LOSS WILD-TYPE    104    129     86     95     78
D55V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                5                129
  CLUS_3                0                 86
  CLUS_4                0                 95
  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 CLUS_4
  19P LOSS MUTATED        0      4      0      1
  19P LOSS WILD-TYPE    165    141    119     68
D55V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                165
  CLUS_2                4                141
  CLUS_3                0                119
  CLUS_4                1                 68
[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
  19P LOSS MUTATED        0      5      0
  19P LOSS WILD-TYPE    178    123    192
D55V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                178
  CLUS_2                5                123
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      5      0      0
  19P LOSS WILD-TYPE    131    120    108    104
D55V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                131
  CLUS_2                5                120
  CLUS_3                0                108
  CLUS_4                0                104
[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
  19P LOSS MUTATED        0      5      0
  19P LOSS WILD-TYPE    163    115    185
D55V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                5                115
  CLUS_3                0                185
[1] 3 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 = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        2      1      5
  21Q LOSS WILD-TYPE    130    137    224
D56V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                1                137
  CLUS_3                5                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      4      2      0      2
  21Q LOSS WILD-TYPE     46    143     82     42    178
D56V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 46
  CLUS_2                4                143
  CLUS_3                2                 82
  CLUS_4                0                 42
  CLUS_5                2                178
[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 CLUS_4
  21Q LOSS MUTATED        1      2      0      0
  21Q LOSS WILD-TYPE     63     62     42     49
D56V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 62
  CLUS_3                0                 42
  CLUS_4                0                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED        1      0      0      0      0      2      0
  21Q LOSS WILD-TYPE     45     28     33     29     47     25      9
D56V4, 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                 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
  21Q LOSS MUTATED        1      4      2      1
  21Q LOSS WILD-TYPE    157    163     56    113
D56V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                157
  CLUS_2                4                163
  CLUS_3                2                 56
  CLUS_4                1                113
[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        0      4      2      1      1
  21Q LOSS WILD-TYPE    104    130     84     94     77
D56V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                104
  CLUS_2                4                130
  CLUS_3                2                 84
  CLUS_4                1                 94
  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 CLUS_4
  21Q LOSS MUTATED        5      1      0      2
  21Q LOSS WILD-TYPE    160    144    119     67
D56V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                160
  CLUS_2                1                144
  CLUS_3                0                119
  CLUS_4                2                 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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        4      4      0
  21Q LOSS WILD-TYPE    174    124    192
D56V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                174
  CLUS_2                4                124
  CLUS_3                0                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      0      1
  21Q LOSS WILD-TYPE    127    123    108    103
D56V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                127
  CLUS_2                2                123
  CLUS_3                0                108
  CLUS_4                1                103
[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
  21Q LOSS MUTATED        4      3      0
  21Q LOSS WILD-TYPE    159    117    185
D56V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                159
  CLUS_2                3                117
  CLUS_3                0                185
[1] 3 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 = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       75      0     14
  22Q LOSS WILD-TYPE     57    138    215
D57V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               75                 57
  CLUS_2                0                138
  CLUS_3               14                215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3     46      9      2     29
  22Q LOSS WILD-TYPE     43    101     75     40    151
D57V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 43
  CLUS_2               46                101
  CLUS_3                9                 75
  CLUS_4                2                 40
  CLUS_5               29                151
[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 CLUS_4
  22Q LOSS MUTATED       15      9      5      9
  22Q LOSS WILD-TYPE     49     55     37     40
D57V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               15                 49
  CLUS_2                9                 55
  CLUS_3                5                 37
  CLUS_4                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  22Q LOSS MUTATED       11      5      2      5      8      6      1
  22Q LOSS WILD-TYPE     35     23     31     24     39     21      8
D57V4, 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                 39
  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        8     47      8     26
  22Q LOSS WILD-TYPE    150    120     50     88
D57V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                8                150
  CLUS_2               47                120
  CLUS_3                8                 50
  CLUS_4               26                 88
[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        9     42     13     23      2
  22Q LOSS WILD-TYPE     95     92     73     72     76
D57V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                9                 95
  CLUS_2               42                 92
  CLUS_3               13                 73
  CLUS_4               23                 72
  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 CLUS_4
  22Q LOSS MUTATED       21     40     19      9
  22Q LOSS WILD-TYPE    144    105    100     60
D57V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               21                144
  CLUS_2               40                105
  CLUS_3               19                100
  CLUS_4                9                 60
[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
  22Q LOSS MUTATED       21     40     28
  22Q LOSS WILD-TYPE    157     88    164
D57V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               21                157
  CLUS_2               40                 88
  CLUS_3               28                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 CLUS_4
  22Q LOSS MUTATED       17     39      8     17
  22Q LOSS WILD-TYPE    114     86    100     87
D57V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               17                114
  CLUS_2               39                 86
  CLUS_3                8                100
  CLUS_4               17                 87
[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
  22Q LOSS MUTATED       21     38     22
  22Q LOSS WILD-TYPE    142     82    163
D57V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               21                142
  CLUS_2               38                 82
  CLUS_3               22                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"

Clustering(58) Variable = XP LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED        1      0      3
  XP LOSS WILD-TYPE    131    138    226
D58V1, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               3               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP LOSS MUTATED        0      3      0      0      1
  XP LOSS WILD-TYPE     46    144     84     42    179
D58V2, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               0                84
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  XP LOSS MUTATED        3      0      0      0
  XP LOSS WILD-TYPE     61     64     42     49
D58V3, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               0                64
  CLUS_3               0                42
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XP LOSS MUTATED        3      0      0      0      0      0      0
  XP LOSS WILD-TYPE     43     28     33     29     47     27      9
D58V4, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               3                43
  CLUS_2               0                28
  CLUS_3               0                33
  CLUS_4               0                29
  CLUS_5               0                47
  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
  XP LOSS MUTATED        1      3      0      0
  XP LOSS WILD-TYPE    157    164     58    114
D58V5, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1               157
  CLUS_2               3               164
  CLUS_3               0                58
  CLUS_4               0               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP LOSS MUTATED        0      3      0      0      1
  XP LOSS WILD-TYPE    104    131     86     95     77
D58V6, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               3               131
  CLUS_3               0                86
  CLUS_4               0                95
  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 CLUS_4
  XP LOSS MUTATED        0      3      0      1
  XP LOSS WILD-TYPE    165    142    119     68
D58V7, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               3               142
  CLUS_3               0               119
  CLUS_4               1                68
[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
  XP LOSS MUTATED        0      3      1
  XP LOSS WILD-TYPE    178    125    191
D58V8, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               3               125
  CLUS_3               1               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED        0      3      1      0
  XP LOSS WILD-TYPE    131    122    107    104
D58V9, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0               131
  CLUS_2               3               122
  CLUS_3               1               107
  CLUS_4               0               104
[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
  XP LOSS MUTATED        0      3      1
  XP LOSS WILD-TYPE    163    117    184
D58V10, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               1               184
[1] 3 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(59) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        1      0      4
  XQ LOSS WILD-TYPE    131    138    225
D59V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               138
  CLUS_3               4               225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED        0      3      1      0      1
  XQ LOSS WILD-TYPE     46    144     83     42    179
D59V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                46
  CLUS_2               3               144
  CLUS_3               1                83
  CLUS_4               0                42
  CLUS_5               1               179
[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 CLUS_4
  XQ LOSS MUTATED        3      0      0      0
  XQ LOSS WILD-TYPE     61     64     42     49
D59V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               0                64
  CLUS_3               0                42
  CLUS_4               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ LOSS MUTATED        3      0      0      0      0      0      0
  XQ LOSS WILD-TYPE     43     28     33     29     47     27      9
D59V4, 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                47
  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        1      3      1      0
  XQ LOSS WILD-TYPE    157    164     57    114
D59V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               157
  CLUS_2               3               164
  CLUS_3               1                57
  CLUS_4               0               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED        0      3      1      0      1
  XQ LOSS WILD-TYPE    104    131     85     95     77
D59V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               3               131
  CLUS_3               1                85
  CLUS_4               0                95
  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 CLUS_4
  XQ LOSS MUTATED        0      3      1      1
  XQ LOSS WILD-TYPE    165    142    118     68
D59V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               3               142
  CLUS_3               1               118
  CLUS_4               1                68
[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
  XQ LOSS MUTATED        0      3      2
  XQ LOSS WILD-TYPE    178    125    190
D59V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               178
  CLUS_2               3               125
  CLUS_3               2               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      2      0
  XQ LOSS WILD-TYPE    131    122    106    104
D59V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               131
  CLUS_2               3               122
  CLUS_3               2               106
  CLUS_4               0               104
[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
  XQ LOSS MUTATED        0      3      2
  XQ LOSS WILD-TYPE    163    117    183
D59V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               117
  CLUS_3               2               183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
