[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-oTLGG-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/LGG-TP/10668119/LGG-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/10013775/transformed.cor.cli.txt"

nPatients in clinical file=516, in cluster file=512, common to both=512
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 512
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               499 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               499 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               489 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               489 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               498 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               498 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               499 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               499 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               501 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               501 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               504 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               504 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               499 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               499 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               506 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               506 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               501 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               501 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               504 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               504 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               505 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               505 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120               392 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120               392 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               362 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               362 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               467 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               467 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               55               457 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               55               457 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               495 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               495 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               489 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               489 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                56                456 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                56                456 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                500 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                500 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                481 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                481 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                454 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                454 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                480 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                480 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                496 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                496 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                506 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                506 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                508 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                508 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                501 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                501 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                496 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                496 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                493 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                493 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                492 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                492 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                489 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                489 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                496 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                496 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                499 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                499 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               101                411 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               101                411 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                487 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                487 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                469 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                469 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                469 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                469 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                488 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                488 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                489 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                489 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40               472 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40               472 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              183               329 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              183               329 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               489 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               489 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               491 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               491 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               494 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               494 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               482 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               482 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               484 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               484 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               441 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               441 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               91               421 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               91               421 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               478 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               478 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               479 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               479 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               482 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               482 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               63               449 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               63               449 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               509 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               509 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               509 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               509 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               495 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               495 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               501 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               501 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              118               394 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              118               394 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               461 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               461 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                429 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                429 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                96                416 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                96                416 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                449 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                449 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                491 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                491 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                26                486 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                26                486 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                51                461 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                51                461 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                397 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                397 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                80                432 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                80                432 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                461 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                461 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                498 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                498 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                490 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                490 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                499 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                499 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                504 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                504 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                444 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                444 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                450 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                450 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                489 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                489 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                303 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                303 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                505 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                505 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                509 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                509 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                476 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                476 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                455 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                455 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               443 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               443 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 512 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 512 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        0      1      0
  1P GAIN WILD-TYPE      9      9      8
D1V1, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        0      1      0      0
  1P GAIN WILD-TYPE      7      6      7      6
D1V2, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        5      8      0
  1P GAIN WILD-TYPE    163    110    226
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5               163
  CLUS_2               8               110
  CLUS_3               0               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
  1P GAIN MUTATED        5      8      0      0
  1P GAIN WILD-TYPE    218     64     57    155
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5               218
  CLUS_2               8                64
  CLUS_3               0                57
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        1      5      1      0
  1P GAIN WILD-TYPE     51     57     67     74
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                51
  CLUS_2               5                57
  CLUS_3               1                67
  CLUS_4               0                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        2      4      1
  1P GAIN WILD-TYPE     65    127     57
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               4               127
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0     13      0      0      0
  1P GAIN WILD-TYPE    135     99    108    127     28
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2              13                99
  CLUS_3               0               108
  CLUS_4               0               127
  CLUS_5               0                28
[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     13      0      0
  1P GAIN WILD-TYPE    135    100    125    137
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2              13               100
  CLUS_3               0               125
  CLUS_4               0               137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      5      1      0
  1P GAIN WILD-TYPE    129     99    186     72
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7               129
  CLUS_2               5                99
  CLUS_3               1               186
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      0     10
  1P GAIN WILD-TYPE    152    107    137     90
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               152
  CLUS_2               0               107
  CLUS_3               0               137
  CLUS_4              10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  1P GAIN MUTATED        2      8      0      0      0      3      0
  1P GAIN WILD-TYPE    111     86     69    146     34     15     25
D1V11, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               111
  CLUS_2               8                86
  CLUS_3               0                69
  CLUS_4               0               146
  CLUS_5               0                34
  CLUS_6               3                15
  CLUS_7               0                25
[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
  1P GAIN MUTATED        3      0      0     10
  1P GAIN WILD-TYPE    145    141    112     88
D1V12, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               145
  CLUS_2               0               141
  CLUS_3               0               112
  CLUS_4              10                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"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        0      1      0
  1Q GAIN WILD-TYPE      9      9      8
D2V1, multiclass
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        0      1      0      0
  1Q GAIN WILD-TYPE      7      6      7      6
D2V2, multiclass
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        8     12      3
  1Q GAIN WILD-TYPE    160    106    223
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8               160
  CLUS_2              12               106
  CLUS_3               3               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
  1Q GAIN MUTATED        9     11      1      2
  1Q GAIN WILD-TYPE    214     61     56    153
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9               214
  CLUS_2              11                61
  CLUS_3               1                56
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      5      2      3
  1Q GAIN WILD-TYPE     51     57     66     71
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                51
  CLUS_2               5                57
  CLUS_3               2                66
  CLUS_4               3                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        2      5      4
  1Q GAIN WILD-TYPE     65    126     54
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               5               126
  CLUS_3               4                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q GAIN MUTATED        2     14      0      5      2
  1Q GAIN WILD-TYPE    133     98    108    122     26
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2              14                98
  CLUS_3               0               108
  CLUS_4               5               122
  CLUS_5               2                26
[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        3     14      2      4
  1Q GAIN WILD-TYPE    132     99    123    133
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3               132
  CLUS_2              14                99
  CLUS_3               2               123
  CLUS_4               4               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9      5      7      1
  1Q GAIN WILD-TYPE    127     99    180     71
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9               127
  CLUS_2               5                99
  CLUS_3               7               180
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      0      6     10
  1Q GAIN WILD-TYPE    149    107    131     90
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6               149
  CLUS_2               0               107
  CLUS_3               6               131
  CLUS_4              10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3      9      0      6      0      4      0
  1Q GAIN WILD-TYPE    110     85     69    140     34     14     25
D2V11, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3               110
  CLUS_2               9                85
  CLUS_3               0                69
  CLUS_4               6               140
  CLUS_5               0                34
  CLUS_6               4                14
  CLUS_7               0                25
[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        6      1      5     10
  1Q GAIN WILD-TYPE    142    140    107     88
D2V12, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6               142
  CLUS_2               1               140
  CLUS_3               5               107
  CLUS_4              10                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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        0      2      0
  2P GAIN WILD-TYPE      9      8      8
D3V1, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"2P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED        0      1      1      0
  2P GAIN WILD-TYPE      7      6      6      6
D3V2, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"2P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        4      7      3
  2P GAIN WILD-TYPE    164    111    223
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4               164
  CLUS_2               7               111
  CLUS_3               3               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
  2P GAIN MUTATED        4      6      0      4
  2P GAIN WILD-TYPE    219     66     57    151
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4               219
  CLUS_2               6                66
  CLUS_3               0                57
  CLUS_4               4               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        0      2      0      2
  2P GAIN WILD-TYPE     52     60     68     72
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                52
  CLUS_2               2                60
  CLUS_3               0                68
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 GAIN MUTATED        1      1      2
  2P GAIN WILD-TYPE     66    130     56
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               1               130
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P GAIN MUTATED        1      9      2      2      0
  2P GAIN WILD-TYPE    134    103    106    125     28
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               9               103
  CLUS_3               2               106
  CLUS_4               2               125
  CLUS_5               0                28
[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 GAIN MUTATED        0      9      3      2
  2P GAIN WILD-TYPE    135    104    122    135
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               9               104
  CLUS_3               3               122
  CLUS_4               2               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        4      5      3      2
  2P GAIN WILD-TYPE    132     99    184     70
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4               132
  CLUS_2               5                99
  CLUS_3               3               184
  CLUS_4               2                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        5      1      2      6
  2P GAIN WILD-TYPE    150    106    135     94
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5               150
  CLUS_2               1               106
  CLUS_3               2               135
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        1      7      2      3      0      1      0
  2P GAIN WILD-TYPE    112     87     67    143     34     17     25
D3V11, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1               112
  CLUS_2               7                87
  CLUS_3               2                67
  CLUS_4               3               143
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               0                25
[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 GAIN MUTATED        4      3      1      6
  2P GAIN WILD-TYPE    144    138    111     92
D3V12, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               3               138
  CLUS_3               1               111
  CLUS_4               6                92
[1] 4 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 = 2Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        0      2      0
  2Q GAIN WILD-TYPE      9      8      8
D4V1, multiclass
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"2Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED        0      1      1      0
  2Q GAIN WILD-TYPE      7      6      6      6
D4V2, multiclass
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"2Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        4      6      3
  2Q GAIN WILD-TYPE    164    112    223
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4               164
  CLUS_2               6               112
  CLUS_3               3               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
  2Q GAIN MUTATED        4      6      0      3
  2Q GAIN WILD-TYPE    219     66     57    152
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4               219
  CLUS_2               6                66
  CLUS_3               0                57
  CLUS_4               3               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        0      2      0      2
  2Q GAIN WILD-TYPE     52     60     68     72
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                52
  CLUS_2               2                60
  CLUS_3               0                68
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 GAIN MUTATED        1      1      2
  2Q GAIN WILD-TYPE     66    130     56
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               1               130
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q GAIN MUTATED        1      8      2      2      0
  2Q GAIN WILD-TYPE    134    104    106    125     28
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               8               104
  CLUS_3               2               106
  CLUS_4               2               125
  CLUS_5               0                28
[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 GAIN MUTATED        0      9      2      2
  2Q GAIN WILD-TYPE    135    104    123    135
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               9               104
  CLUS_3               2               123
  CLUS_4               2               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        4      5      3      1
  2Q GAIN WILD-TYPE    132     99    184     71
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4               132
  CLUS_2               5                99
  CLUS_3               3               184
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        5      0      2      6
  2Q GAIN WILD-TYPE    150    107    135     94
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5               150
  CLUS_2               0               107
  CLUS_3               2               135
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        1      7      1      3      0      1      0
  2Q GAIN WILD-TYPE    112     87     68    143     34     17     25
D4V11, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1               112
  CLUS_2               7                87
  CLUS_3               1                68
  CLUS_4               3               143
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               0                25
[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 GAIN MUTATED        4      2      1      6
  2Q GAIN WILD-TYPE    144    139    111     92
D4V12, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               2               139
  CLUS_3               1               111
  CLUS_4               6                92
[1] 4 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 = 3P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        0      1      0
  3P GAIN WILD-TYPE      9      9      8
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        0      1      0      0
  3P GAIN WILD-TYPE      7      6      7      6
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        4      4      3
  3P GAIN WILD-TYPE    164    114    223
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               164
  CLUS_2               4               114
  CLUS_3               3               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
  3P GAIN MUTATED        4      4      0      3
  3P GAIN WILD-TYPE    219     68     57    152
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               219
  CLUS_2               4                68
  CLUS_3               0                57
  CLUS_4               3               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      1      2
  3P GAIN WILD-TYPE     51     58     67     72
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                51
  CLUS_2               4                58
  CLUS_3               1                67
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        0      6      2
  3P GAIN WILD-TYPE     67    125     56
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               6               125
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED        1      6      3      1      0
  3P GAIN WILD-TYPE    134    106    105    126     28
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               6               106
  CLUS_3               3               105
  CLUS_4               1               126
  CLUS_5               0                28
[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        2      6      2      1
  3P GAIN WILD-TYPE    133    107    123    136
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               6               107
  CLUS_3               2               123
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      3      1      2
  3P GAIN WILD-TYPE    131    101    186     70
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5               131
  CLUS_2               3               101
  CLUS_3               1               186
  CLUS_4               2                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        4      3      0      4
  3P GAIN WILD-TYPE    151    104    137     96
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               151
  CLUS_2               3               104
  CLUS_3               0               137
  CLUS_4               4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  3P GAIN MUTATED        2      5      1      1      1      1      0
  3P GAIN WILD-TYPE    111     89     68    145     33     17     25
D5V11, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               111
  CLUS_2               5                89
  CLUS_3               1                68
  CLUS_4               1               145
  CLUS_5               1                33
  CLUS_6               1                17
  CLUS_7               0                25
[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
  3P GAIN MUTATED        4      3      0      4
  3P GAIN WILD-TYPE    144    138    112     94
D5V12, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               3               138
  CLUS_3               0               112
  CLUS_4               4                94
[1] 4 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 = 3Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        0      1      0
  3Q GAIN WILD-TYPE      9      9      8
D6V1, multiclass
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        0      1      0      0
  3Q GAIN WILD-TYPE      7      6      7      6
D6V2, multiclass
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        2      4      2
  3Q GAIN WILD-TYPE    166    114    224
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               166
  CLUS_2               4               114
  CLUS_3               2               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
  3Q GAIN MUTATED        2      4      0      2
  3Q GAIN WILD-TYPE    221     68     57    153
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               221
  CLUS_2               4                68
  CLUS_3               0                57
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        0      4      0      2
  3Q GAIN WILD-TYPE     52     58     68     72
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                52
  CLUS_2               4                58
  CLUS_3               0                68
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        0      4      2
  3Q GAIN WILD-TYPE     67    127     56
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               4               127
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q GAIN MUTATED        0      5      2      1      0
  3Q GAIN WILD-TYPE    135    107    106    126     28
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5               107
  CLUS_3               2               106
  CLUS_4               1               126
  CLUS_5               0                28
[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 GAIN MUTATED        0      6      1      1
  3Q GAIN WILD-TYPE    135    107    124    136
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               6               107
  CLUS_3               1               124
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        3      3      1      1
  3Q GAIN WILD-TYPE    133    101    186     71
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3               133
  CLUS_2               3               101
  CLUS_3               1               186
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        2      2      0      4
  3Q GAIN WILD-TYPE    153    105    137     96
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               153
  CLUS_2               2               105
  CLUS_3               0               137
  CLUS_4               4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        1      4      0      1      1      1      0
  3Q GAIN WILD-TYPE    112     90     69    145     33     17     25
D6V11, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1               112
  CLUS_2               4                90
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               1                33
  CLUS_6               1                17
  CLUS_7               0                25
[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 GAIN MUTATED        2      2      0      4
  3Q GAIN WILD-TYPE    146    139    112     94
D6V12, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               146
  CLUS_2               2               139
  CLUS_3               0               112
  CLUS_4               4                94
[1] 4 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 = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        1      0      0
  4P GAIN WILD-TYPE      8     10      8
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5394 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        0      1      0      0
  4P GAIN WILD-TYPE      7      6      7      6
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5394 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        8      4      1
  4P GAIN WILD-TYPE    160    114    225
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8               160
  CLUS_2               4               114
  CLUS_3               1               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
  4P GAIN MUTATED        8      4      1      0
  4P GAIN WILD-TYPE    215     68     56    155
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8               215
  CLUS_2               4                68
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      1
  4P GAIN WILD-TYPE     50     57     68     73
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                50
  CLUS_2               5                57
  CLUS_3               0                68
  CLUS_4               1                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        2      5      1
  4P GAIN WILD-TYPE     65    126     57
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               5               126
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      8      0      1      0
  4P GAIN WILD-TYPE    131    104    108    126     28
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               131
  CLUS_2               8               104
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               0                28
[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        4      8      0      1
  4P GAIN WILD-TYPE    131    105    125    136
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               131
  CLUS_2               8               105
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      4      2      1
  4P GAIN WILD-TYPE    130    100    185     71
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               130
  CLUS_2               4               100
  CLUS_3               2               185
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      1      2      5
  4P GAIN WILD-TYPE    150    106    135     95
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               150
  CLUS_2               1               106
  CLUS_3               2               135
  CLUS_4               5                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  4P GAIN MUTATED        3      5      1      1      0      1      2
  4P GAIN WILD-TYPE    110     89     68    145     34     17     23
D7V11, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               110
  CLUS_2               5                89
  CLUS_3               1                68
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               2                23
[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
  4P GAIN MUTATED        6      1      1      5
  4P GAIN WILD-TYPE    142    140    111     93
D7V12, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               142
  CLUS_2               1               140
  CLUS_3               1               111
  CLUS_4               5                93
[1] 4 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 = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        0      0      0
  4Q GAIN WILD-TYPE      9     10      8
D8V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        0      0      0      0
  4Q GAIN WILD-TYPE      7      7      7      6
D8V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        3      3      0
  4Q GAIN WILD-TYPE    165    115    226
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               165
  CLUS_2               3               115
  CLUS_3               0               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
  4Q GAIN MUTATED        2      3      1      0
  4Q GAIN WILD-TYPE    221     69     56    155
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               221
  CLUS_2               3                69
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      1
  4Q GAIN WILD-TYPE     52     59     68     73
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                52
  CLUS_2               3                59
  CLUS_3               0                68
  CLUS_4               1                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        0      3      1
  4Q GAIN WILD-TYPE     67    128     57
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               3               128
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      1      0
  4Q GAIN WILD-TYPE    135    107    108    126     28
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5               107
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               0                28
[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        0      5      0      1
  4Q GAIN WILD-TYPE    135    108    125    136
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5               108
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      0
  4Q GAIN WILD-TYPE    134    101    186     72
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               134
  CLUS_2               3               101
  CLUS_3               1               186
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      3
  4Q GAIN WILD-TYPE    154    107    135     97
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               154
  CLUS_2               0               107
  CLUS_3               2               135
  CLUS_4               3                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  4Q GAIN MUTATED        0      5      0      1      0      0      0
  4Q GAIN WILD-TYPE    113     89     69    145     34     18     25
D8V11, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               113
  CLUS_2               5                89
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               0                18
  CLUS_7               0                25
[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
  4Q GAIN MUTATED        2      0      1      3
  4Q GAIN WILD-TYPE    146    141    111     95
D8V12, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               146
  CLUS_2               0               141
  CLUS_3               1               111
  CLUS_4               3                95
[1] 4 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 = 5P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        0      1      0
  5P GAIN WILD-TYPE      9      9      8
D9V1, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        0      1      0      0
  5P GAIN WILD-TYPE      7      6      7      6
D9V2, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        4      6      1
  5P GAIN WILD-TYPE    164    112    225
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               164
  CLUS_2               6               112
  CLUS_3               1               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
  5P GAIN MUTATED        4      6      1      0
  5P GAIN WILD-TYPE    219     66     56    155
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               219
  CLUS_2               6                66
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      3      0      0
  5P GAIN WILD-TYPE     52     59     68     74
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                52
  CLUS_2               3                59
  CLUS_3               0                68
  CLUS_4               0                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        0      2      1
  5P GAIN WILD-TYPE     67    129     57
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2               129
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P GAIN MUTATED        0      9      0      1      1
  5P GAIN WILD-TYPE    135    103    108    126     27
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               9               103
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               1                27
[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        1      9      0      1
  5P GAIN WILD-TYPE    134    104    125    136
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               9               104
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      1      0
  5P GAIN WILD-TYPE    131     99    186     72
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5               131
  CLUS_2               5                99
  CLUS_3               1               186
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      2      6
  5P GAIN WILD-TYPE    152    107    135     94
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3               152
  CLUS_2               0               107
  CLUS_3               2               135
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      9      0      1      0      1      0
  5P GAIN WILD-TYPE    113     85     69    145     34     17     25
D9V11, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0               113
  CLUS_2               9                85
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               0                25
[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        4      1      0      6
  5P GAIN WILD-TYPE    144    140    112     92
D9V12, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               1               140
  CLUS_3               0               112
  CLUS_4               6                92
[1] 4 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 = 5Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        0      0      0
  5Q GAIN WILD-TYPE      9     10      8
D10V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED        0      0      0      0
  5Q GAIN WILD-TYPE      7      7      7      6
D10V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        1      6      1
  5Q GAIN WILD-TYPE    167    112    225
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1               167
  CLUS_2               6               112
  CLUS_3               1               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
  5Q GAIN MUTATED        1      6      1      0
  5Q GAIN WILD-TYPE    222     66     56    155
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1               222
  CLUS_2               6                66
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      1      0      0
  5Q GAIN WILD-TYPE     52     61     68     74
D10V5, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TU 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        0      1      0
  5Q GAIN WILD-TYPE     67    130     58
D10V6, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TU 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED        0      7      0      0      1
  5Q GAIN WILD-TYPE    135    105    108    127     27
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               7               105
  CLUS_3               0               108
  CLUS_4               0               127
  CLUS_5               1                27
[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        1      7      0      0
  5Q GAIN WILD-TYPE    134    106    125    137
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               7               106
  CLUS_3               0               125
  CLUS_4               0               137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      3      0      0
  5Q GAIN WILD-TYPE    131    101    187     72
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5               131
  CLUS_2               3               101
  CLUS_3               0               187
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      0      6
  5Q GAIN WILD-TYPE    153    107    137     94
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               153
  CLUS_2               0               107
  CLUS_3               0               137
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      8      0      0      0      0      0
  5Q GAIN WILD-TYPE    113     86     69    146     34     18     25
D10V11, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0               113
  CLUS_2               8                86
  CLUS_3               0                69
  CLUS_4               0               146
  CLUS_5               0                34
  CLUS_6               0                18
  CLUS_7               0                25
[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      0      0      6
  5Q GAIN WILD-TYPE    146    141    112     92
D10V12, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               146
  CLUS_2               0               141
  CLUS_3               0               112
  CLUS_4               6                92
[1] 4 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 = 6P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        0      0      0
  6P GAIN WILD-TYPE      9     10      8
D11V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        0      0      0      0
  6P GAIN WILD-TYPE      7      7      7      6
D11V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        7      0      0
  6P GAIN WILD-TYPE    161    118    226
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               7               161
  CLUS_2               0               118
  CLUS_3               0               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
  6P GAIN MUTATED        7      0      0      0
  6P GAIN WILD-TYPE    216     72     57    155
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               7               216
  CLUS_2               0                72
  CLUS_3               0                57
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        2      3      0      0
  6P GAIN WILD-TYPE     50     59     68     74
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                50
  CLUS_2               3                59
  CLUS_3               0                68
  CLUS_4               0                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        1      4      0
  6P GAIN WILD-TYPE     66    127     58
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               4               127
  CLUS_3               0                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P GAIN MUTATED        1      4      1      1      0
  6P GAIN WILD-TYPE    134    108    107    126     28
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               4               108
  CLUS_3               1               107
  CLUS_4               1               126
  CLUS_5               0                28
[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 GAIN MUTATED        2      4      0      1
  6P GAIN WILD-TYPE    133    109    125    136
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               4               109
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        4      3      0      0
  6P GAIN WILD-TYPE    132    101    187     72
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               132
  CLUS_2               3               101
  CLUS_3               0               187
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        4      0      0      3
  6P GAIN WILD-TYPE    151    107    137     97
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               151
  CLUS_2               0               107
  CLUS_3               0               137
  CLUS_4               3                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  6P GAIN MUTATED        2      2      0      0      1      2      0
  6P GAIN WILD-TYPE    111     92     69    146     33     16     25
D11V11, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               111
  CLUS_2               2                92
  CLUS_3               0                69
  CLUS_4               0               146
  CLUS_5               1                33
  CLUS_6               2                16
  CLUS_7               0                25
[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
  6P GAIN MUTATED        5      0      0      2
  6P GAIN WILD-TYPE    143    141    112     96
D11V12, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               5               143
  CLUS_2               0               141
  CLUS_3               0               112
  CLUS_4               2                96
[1] 4 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 = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2      2      3
  7P GAIN WILD-TYPE      7      8      5
D12V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 8
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        2      3      1      1
  7P GAIN WILD-TYPE      5      4      6      5
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               3                 4
  CLUS_3               1                 6
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       21     90      9
  7P GAIN WILD-TYPE    147     28    217
D12V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              21               147
  CLUS_2              90                28
  CLUS_3               9               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
  7P GAIN MUTATED       38     54     11     15
  7P GAIN WILD-TYPE    185     18     46    140
D12V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              38               185
  CLUS_2              54                18
  CLUS_3              11                46
  CLUS_4              15               140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11     27     12     10
  7P GAIN WILD-TYPE     41     35     56     64
D12V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              11                41
  CLUS_2              27                35
  CLUS_3              12                56
  CLUS_4              10                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
  7P GAIN MUTATED       15     39      6
  7P GAIN WILD-TYPE     52     92     52
D12V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              15                52
  CLUS_2              39                92
  CLUS_3               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       22     59      9     22      6
  7P GAIN WILD-TYPE    113     53     99    105     22
D12V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22               113
  CLUS_2              59                53
  CLUS_3               9                99
  CLUS_4              22               105
  CLUS_5               6                22
[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       19     58     11     30
  7P GAIN WILD-TYPE    116     55    114    107
D12V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              19               116
  CLUS_2              58                55
  CLUS_3              11               114
  CLUS_4              30               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       42     32     31     13
  7P GAIN WILD-TYPE     94     72    156     59
D12V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              42                94
  CLUS_2              32                72
  CLUS_3              31               156
  CLUS_4              13                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       29     18     16     55
  7P GAIN WILD-TYPE    126     89    121     45
D12V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              29               126
  CLUS_2              18                89
  CLUS_3              16               121
  CLUS_4              55                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
  7P GAIN MUTATED       22     49      6     24      8      6      3
  7P GAIN WILD-TYPE     91     45     63    122     26     12     22
D12V11, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22                91
  CLUS_2              49                45
  CLUS_3               6                63
  CLUS_4              24               122
  CLUS_5               8                26
  CLUS_6               6                12
  CLUS_7               3                22
[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       26     25     12     55
  7P GAIN WILD-TYPE    122    116    100     43
D12V12, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              26               122
  CLUS_2              25               116
  CLUS_3              12               100
  CLUS_4              55                43
[1] 4 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 = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        3      2      3
  7Q GAIN WILD-TYPE      6      8      5
D13V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               2                 8
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        3      3      1      1
  7Q GAIN WILD-TYPE      4      4      6      5
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               3                 4
  CLUS_3               1                 6
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       36     97     17
  7Q GAIN WILD-TYPE    132     21    209
D13V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              36               132
  CLUS_2              97                21
  CLUS_3              17               209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       56     56     13     23
  7Q GAIN WILD-TYPE    167     16     44    132
D13V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              56               167
  CLUS_2              56                16
  CLUS_3              13                44
  CLUS_4              23               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       16     30     14     18
  7Q GAIN WILD-TYPE     36     32     54     56
D13V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16                36
  CLUS_2              30                32
  CLUS_3              14                54
  CLUS_4              18                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       19     46     13
  7Q GAIN WILD-TYPE     48     85     45
D13V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              19                48
  CLUS_2              46                85
  CLUS_3              13                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       36     62     12     30      8
  7Q GAIN WILD-TYPE     99     50     96     97     20
D13V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              36                99
  CLUS_2              62                50
  CLUS_3              12                96
  CLUS_4              30                97
  CLUS_5               8                20
[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       32     60     16     40
  7Q GAIN WILD-TYPE    103     53    109     97
D13V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32               103
  CLUS_2              60                53
  CLUS_3              16               109
  CLUS_4              40                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       49     39     45     15
  7Q GAIN WILD-TYPE     87     65    142     57
D13V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              49                87
  CLUS_2              39                65
  CLUS_3              45               142
  CLUS_4              15                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       40     24     24     60
  7Q GAIN WILD-TYPE    115     83    113     40
D13V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              40               115
  CLUS_2              24                83
  CLUS_3              24               113
  CLUS_4              60                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
  7Q GAIN MUTATED       30     52      7     34     14      6      5
  7Q GAIN WILD-TYPE     83     42     62    112     20     12     20
D13V11, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              30                83
  CLUS_2              52                42
  CLUS_3               7                62
  CLUS_4              34               112
  CLUS_5              14                20
  CLUS_6               6                12
  CLUS_7               5                20
[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       38     32     18     60
  7Q GAIN WILD-TYPE    110    109     94     38
D13V12, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              38               110
  CLUS_2              32               109
  CLUS_3              18                94
  CLUS_4              60                38
[1] 4 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 = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        1      0      1
  8P GAIN WILD-TYPE      8     10      7
D14V1, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        1      0      0      1
  8P GAIN WILD-TYPE      6      7      7      5
D14V2, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       29     10      6
  8P GAIN WILD-TYPE    139    108    220
D14V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              29               139
  CLUS_2              10               108
  CLUS_3               6               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
  8P GAIN MUTATED       32      3      2      8
  8P GAIN WILD-TYPE    191     69     55    147
D14V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              32               191
  CLUS_2               3                69
  CLUS_3               2                55
  CLUS_4               8               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      7      9      2
  8P GAIN WILD-TYPE     45     55     59     72
D14V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7                45
  CLUS_2               7                55
  CLUS_3               9                59
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8     15      2
  8P GAIN WILD-TYPE     59    116     56
D14V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                59
  CLUS_2              15               116
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       21      8      4      9      3
  8P GAIN WILD-TYPE    114    104    104    118     25
D14V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              21               114
  CLUS_2               8               104
  CLUS_3               4               104
  CLUS_4               9               118
  CLUS_5               3                25
[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       22      8      5     10
  8P GAIN WILD-TYPE    113    105    120    127
D14V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              22               113
  CLUS_2               8               105
  CLUS_3               5               120
  CLUS_4              10               127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15      9     14      4
  8P GAIN WILD-TYPE    121     95    173     68
D14V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              15               121
  CLUS_2               9                95
  CLUS_3              14               173
  CLUS_4               4                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 CLUS_4
  8P GAIN MUTATED       19      8      9      6
  8P GAIN WILD-TYPE    136     99    128     94
D14V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              19               136
  CLUS_2               8                99
  CLUS_3               9               128
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       19      5      3     10      2      1      2
  8P GAIN WILD-TYPE     94     89     66    136     32     17     23
D14V11, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              19                94
  CLUS_2               5                89
  CLUS_3               3                66
  CLUS_4              10               136
  CLUS_5               2                32
  CLUS_6               1                17
  CLUS_7               2                23
[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       20     11      4      7
  8P GAIN WILD-TYPE    128    130    108     91
D14V12, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              20               128
  CLUS_2              11               130
  CLUS_3               4               108
  CLUS_4               7                91
[1] 4 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 = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        1      0      3
  8Q GAIN WILD-TYPE      8     10      5
D15V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                10
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        1      1      0      2
  8Q GAIN WILD-TYPE      6      6      7      4
D15V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 6
  CLUS_3               0                 7
  CLUS_4               2                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       35     13      7
  8Q GAIN WILD-TYPE    133    105    219
D15V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              35               133
  CLUS_2              13               105
  CLUS_3               7               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
  8Q GAIN MUTATED       40      3      4      8
  8Q GAIN WILD-TYPE    183     69     53    147
D15V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              40               183
  CLUS_2               3                69
  CLUS_3               4                53
  CLUS_4               8               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10      8     10      2
  8Q GAIN WILD-TYPE     42     54     58     72
D15V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                42
  CLUS_2               8                54
  CLUS_3              10                58
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       10     18      2
  8Q GAIN WILD-TYPE     57    113     56
D15V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                57
  CLUS_2              18               113
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       27      9      4     12      3
  8Q GAIN WILD-TYPE    108    103    104    115     25
D15V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27               108
  CLUS_2               9               103
  CLUS_3               4               104
  CLUS_4              12               115
  CLUS_5               3                25
[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       27      9      5     14
  8Q GAIN WILD-TYPE    108    104    120    123
D15V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27               108
  CLUS_2               9               104
  CLUS_3               5               120
  CLUS_4              14               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       20     10     18      4
  8Q GAIN WILD-TYPE    116     94    169     68
D15V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              20               116
  CLUS_2              10                94
  CLUS_3              18               169
  CLUS_4               4                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 CLUS_4
  8Q GAIN MUTATED       26      9     11      6
  8Q GAIN WILD-TYPE    129     98    126     94
D15V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              26               129
  CLUS_2               9                98
  CLUS_3              11               126
  CLUS_4               6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       25      6      3     13      2      1      2
  8Q GAIN WILD-TYPE     88     88     66    133     32     17     23
D15V11, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              25                88
  CLUS_2               6                88
  CLUS_3               3                66
  CLUS_4              13               133
  CLUS_5               2                32
  CLUS_6               1                17
  CLUS_7               2                23
[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       27     13      5      7
  8Q GAIN WILD-TYPE    121    128    107     91
D15V12, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27               121
  CLUS_2              13               128
  CLUS_3               5               107
  CLUS_4               7                91
[1] 4 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 = 9P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      1      0
  9P GAIN WILD-TYPE      8      9      8
D16V1, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        1      0      1      0
  9P GAIN WILD-TYPE      6      7      6      6
D16V2, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E1-5322 
"9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        9      6      2
  9P GAIN WILD-TYPE    159    112    224
D16V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               9               159
  CLUS_2               6               112
  CLUS_3               2               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
  9P GAIN MUTATED        8      5      2      2
  9P GAIN WILD-TYPE    215     67     55    153
D16V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8               215
  CLUS_2               5                67
  CLUS_3               2                55
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      1      2
  9P GAIN WILD-TYPE     50     57     67     72
D16V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                50
  CLUS_2               5                57
  CLUS_3               1                67
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      5      1
  9P GAIN WILD-TYPE     63    126     57
D16V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                63
  CLUS_2               5               126
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        2      9      2      4      0
  9P GAIN WILD-TYPE    133    103    106    123     28
D16V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               9               103
  CLUS_3               2               106
  CLUS_4               4               123
  CLUS_5               0                28
[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      9      2      4
  9P GAIN WILD-TYPE    133    104    123    133
D16V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               9               104
  CLUS_3               2               123
  CLUS_4               4               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      4      5      2
  9P GAIN WILD-TYPE    130    100    182     70
D16V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6               130
  CLUS_2               4               100
  CLUS_3               5               182
  CLUS_4               2                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      3      3      8
  9P GAIN WILD-TYPE    152    104    134     92
D16V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               152
  CLUS_2               3               104
  CLUS_3               3               134
  CLUS_4               8                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        3      6      2      4      0      2      0
  9P GAIN WILD-TYPE    110     88     67    142     34     16     25
D16V11, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               110
  CLUS_2               6                88
  CLUS_3               2                67
  CLUS_4               4               142
  CLUS_5               0                34
  CLUS_6               2                16
  CLUS_7               0                25
[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 GAIN MUTATED        2      4      3      8
  9P GAIN WILD-TYPE    146    137    109     90
D16V12, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               146
  CLUS_2               4               137
  CLUS_3               3               109
  CLUS_4               8                90
[1] 4 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 = 9Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        1      1      0
  9Q GAIN WILD-TYPE      8      9      8
D17V1, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        1      0      1      0
  9Q GAIN WILD-TYPE      6      7      6      6
D17V2, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED       11      8      4
  9Q GAIN WILD-TYPE    157    110    222
D17V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11               157
  CLUS_2               8               110
  CLUS_3               4               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
  9Q GAIN MUTATED       12      6      2      3
  9Q GAIN WILD-TYPE    211     66     55    152
D17V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              12               211
  CLUS_2               6                66
  CLUS_3               2                55
  CLUS_4               3               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      6      2      2
  9Q GAIN WILD-TYPE     49     56     66     72
D17V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                49
  CLUS_2               6                56
  CLUS_3               2                66
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        6      7      0
  9Q GAIN WILD-TYPE     61    124     58
D17V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6                61
  CLUS_2               7               124
  CLUS_3               0                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4     12      3      4      0
  9Q GAIN WILD-TYPE    131    100    105    123     28
D17V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               131
  CLUS_2              12               100
  CLUS_3               3               105
  CLUS_4               4               123
  CLUS_5               0                28
[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        3     12      3      5
  9Q GAIN WILD-TYPE    132    101    122    132
D17V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               132
  CLUS_2              12               101
  CLUS_3               3               122
  CLUS_4               5               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      7      6      3
  9Q GAIN WILD-TYPE    129     97    181     69
D17V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               129
  CLUS_2               7                97
  CLUS_3               6               181
  CLUS_4               3                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 CLUS_4
  9Q GAIN MUTATED        5      4      4     10
  9Q GAIN WILD-TYPE    150    103    133     90
D17V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               150
  CLUS_2               4               103
  CLUS_3               4               133
  CLUS_4              10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        4      9      2      4      0      3      1
  9Q GAIN WILD-TYPE    109     85     67    142     34     15     24
D17V11, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               109
  CLUS_2               9                85
  CLUS_3               2                67
  CLUS_4               4               142
  CLUS_5               0                34
  CLUS_6               3                15
  CLUS_7               1                24
[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 GAIN MUTATED        4      6      3     10
  9Q GAIN WILD-TYPE    144    135    109     88
D17V12, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               6               135
  CLUS_3               3               109
  CLUS_4              10                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"

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        1      1      1
  10P GAIN WILD-TYPE      8      9      7
D18V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  9
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED        0      3      0      0
  10P GAIN WILD-TYPE      7      4      7      6
D18V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                3                  4
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       48      2      6
  10P GAIN WILD-TYPE    120    116    220
D18V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               48                120
  CLUS_2                2                116
  CLUS_3                6                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
  10P GAIN MUTATED       52      2      2      0
  10P GAIN WILD-TYPE    171     70     55    155
D18V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               52                171
  CLUS_2                2                 70
  CLUS_3                2                 55
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED       11      5      8      3
  10P GAIN WILD-TYPE     41     57     60     71
D18V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               11                 41
  CLUS_2                5                 57
  CLUS_3                8                 60
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        7     16      4
  10P GAIN WILD-TYPE     60    115     54
D18V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                7                 60
  CLUS_2               16                115
  CLUS_3                4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P GAIN MUTATED       29     14      0     12      1
  10P GAIN WILD-TYPE    106     98    108    115     27
D18V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               29                106
  CLUS_2               14                 98
  CLUS_3                0                108
  CLUS_4               12                115
  CLUS_5                1                 27
[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 GAIN MUTATED       29     14      0     13
  10P GAIN WILD-TYPE    106     99    125    124
D18V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               29                106
  CLUS_2               14                 99
  CLUS_3                0                125
  CLUS_4               13                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED       15     18     16      4
  10P GAIN WILD-TYPE    121     86    171     68
D18V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               15                121
  CLUS_2               18                 86
  CLUS_3               16                171
  CLUS_4                4                 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 CLUS_4
  10P GAIN MUTATED       24      7     11     11
  10P GAIN WILD-TYPE    131    100    126     89
D18V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               24                131
  CLUS_2                7                100
  CLUS_3               11                126
  CLUS_4               11                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED       19      8      2     13      2      6      3
  10P GAIN WILD-TYPE     94     86     67    133     32     12     22
D18V11, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               19                 94
  CLUS_2                8                 86
  CLUS_3                2                 67
  CLUS_4               13                133
  CLUS_5                2                 32
  CLUS_6                6                 12
  CLUS_7                3                 22
[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 GAIN MUTATED       29      9      8      7
  10P GAIN WILD-TYPE    119    132    104     91
D18V12, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               29                119
  CLUS_2                9                132
  CLUS_3                8                104
  CLUS_4                7                 91
[1] 4 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 = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        0      0      1
  10Q GAIN WILD-TYPE      9     10      7
D19V1, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        0      1      0      0
  10Q GAIN WILD-TYPE      7      6      7      6
D19V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       11      0      1
  10Q GAIN WILD-TYPE    157    118    225
D19V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               11                157
  CLUS_2                0                118
  CLUS_3                1                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
  10Q GAIN MUTATED        9      2      1      0
  10Q GAIN WILD-TYPE    214     70     56    155
D19V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                9                214
  CLUS_2                2                 70
  CLUS_3                1                 56
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        1      1      3      0
  10Q GAIN WILD-TYPE     51     61     65     74
D19V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                1                 61
  CLUS_3                3                 65
  CLUS_4                0                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        1      4      0
  10Q GAIN WILD-TYPE     66    127     58
D19V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                4                127
  CLUS_3                0                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q GAIN MUTATED        2      6      0      4      0
  10Q GAIN WILD-TYPE    133    106    108    123     28
D19V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                6                106
  CLUS_3                0                108
  CLUS_4                4                123
  CLUS_5                0                 28
[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 GAIN MUTATED        2      6      0      4
  10Q GAIN WILD-TYPE    133    107    125    133
D19V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                6                107
  CLUS_3                0                125
  CLUS_4                4                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        0      3      6      2
  10Q GAIN WILD-TYPE    136    101    181     70
D19V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                136
  CLUS_2                3                101
  CLUS_3                6                181
  CLUS_4                2                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        2      2      3      4
  10Q GAIN WILD-TYPE    153    105    134     96
D19V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                153
  CLUS_2                2                105
  CLUS_3                3                134
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  10Q GAIN MUTATED        0      2      2      4      0      2      1
  10Q GAIN WILD-TYPE    113     92     67    142     34     16     24
D19V11, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                113
  CLUS_2                2                 92
  CLUS_3                2                 67
  CLUS_4                4                142
  CLUS_5                0                 34
  CLUS_6                2                 16
  CLUS_7                1                 24
[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
  10Q GAIN MUTATED        2      2      3      4
  10Q GAIN WILD-TYPE    146    139    109     94
D19V12, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                146
  CLUS_2                2                139
  CLUS_3                3                109
  CLUS_4                4                 94
[1] 4 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 = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        0      2      0
  11P GAIN WILD-TYPE      9      8      8
D20V1, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-E1-5302         TCGA-E1-5303 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"11P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        0      0      2      0
  11P GAIN WILD-TYPE      7      7      5      6
D20V2, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-E1-5302         TCGA-E1-5303 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"11P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        5      7     19
  11P GAIN WILD-TYPE    163    111    207
D20V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                163
  CLUS_2                7                111
  CLUS_3               19                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9      1      1     20
  11P GAIN WILD-TYPE    214     71     56    135
D20V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                9                214
  CLUS_2                1                 71
  CLUS_3                1                 56
  CLUS_4               20                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      9      5
  11P GAIN WILD-TYPE     52     59     59     69
D20V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 52
  CLUS_2                3                 59
  CLUS_3                9                 59
  CLUS_4                5                 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        1     11      5
  11P GAIN WILD-TYPE     66    120     53
D20V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2               11                120
  CLUS_3                5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8      1     13      7      2
  11P GAIN WILD-TYPE    127    111     95    120     26
D20V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                127
  CLUS_2                1                111
  CLUS_3               13                 95
  CLUS_4                7                120
  CLUS_5                2                 26
[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        7      1     15      8
  11P GAIN WILD-TYPE    128    112    110    129
D20V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                128
  CLUS_2                1                112
  CLUS_3               15                110
  CLUS_4                8                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        5      5     12      9
  11P GAIN WILD-TYPE    131     99    175     63
D20V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                131
  CLUS_2                5                 99
  CLUS_3               12                175
  CLUS_4                9                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12     11      7      1
  11P GAIN WILD-TYPE    143     96    130     99
D20V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               12                143
  CLUS_2               11                 96
  CLUS_3                7                130
  CLUS_4                1                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8      2      7      9      4      1      0
  11P GAIN WILD-TYPE    105     92     62    137     30     17     25
D20V11, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                105
  CLUS_2                2                 92
  CLUS_3                7                 62
  CLUS_4                9                137
  CLUS_5                4                 30
  CLUS_6                1                 17
  CLUS_7                0                 25
[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        7     18      5      1
  11P GAIN WILD-TYPE    141    123    107     97
D20V12, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                141
  CLUS_2               18                123
  CLUS_3                5                107
  CLUS_4                1                 97
[1] 4 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 = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        0      2      1
  11Q GAIN WILD-TYPE      9      8      7
D21V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                  8
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        0      1      2      0
  11Q GAIN WILD-TYPE      7      6      5      6
D21V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  6
  CLUS_3                2                  5
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       22      9     27
  11Q GAIN WILD-TYPE    146    109    199
D21V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               22                146
  CLUS_2                9                109
  CLUS_3               27                199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       29      3      2     23
  11Q GAIN WILD-TYPE    194     69     55    132
D21V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               29                194
  CLUS_2                3                 69
  CLUS_3                2                 55
  CLUS_4               23                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      4     13      8
  11Q GAIN WILD-TYPE     49     58     55     66
D21V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                4                 58
  CLUS_3               13                 55
  CLUS_4                8                 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
  11Q GAIN MUTATED        2     19      7
  11Q GAIN WILD-TYPE     65    112     51
D21V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2               19                112
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       16      5     17     15      4
  11Q GAIN WILD-TYPE    119    107     91    112     24
D21V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               16                119
  CLUS_2                5                107
  CLUS_3               17                 91
  CLUS_4               15                112
  CLUS_5                4                 24
[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       17      5     19     16
  11Q GAIN WILD-TYPE    118    108    106    121
D21V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               17                118
  CLUS_2                5                108
  CLUS_3               19                106
  CLUS_4               16                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       13      9     22     12
  11Q GAIN WILD-TYPE    123     95    165     60
D21V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               13                123
  CLUS_2                9                 95
  CLUS_3               22                165
  CLUS_4               12                 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 CLUS_4
  11Q GAIN MUTATED       24     13     15      4
  11Q GAIN WILD-TYPE    131     94    122     96
D21V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               24                131
  CLUS_2               13                 94
  CLUS_3               15                122
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       14      5      9     18      6      2      2
  11Q GAIN WILD-TYPE     99     89     60    128     28     16     23
D21V11, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               14                 99
  CLUS_2                5                 89
  CLUS_3                9                 60
  CLUS_4               18                128
  CLUS_5                6                 28
  CLUS_6                2                 16
  CLUS_7                2                 23
[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       19     24     10      3
  11Q GAIN WILD-TYPE    129    117    102     95
D21V12, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               19                129
  CLUS_2               24                117
  CLUS_3               10                102
  CLUS_4                3                 95
[1] 4 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 = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        1      2      0
  12P GAIN WILD-TYPE      8      8      8
D22V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                  8
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED        1      2      0      0
  12P GAIN WILD-TYPE      6      5      7      6
D22V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                  5
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       19     10      3
  12P GAIN WILD-TYPE    149    108    223
D22V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               19                149
  CLUS_2               10                108
  CLUS_3                3                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
  12P GAIN MUTATED       20      6      2      4
  12P GAIN WILD-TYPE    203     66     55    151
D22V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               20                203
  CLUS_2                6                 66
  CLUS_3                2                 55
  CLUS_4                4                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      8      3      4
  12P GAIN WILD-TYPE     47     54     65     70
D22V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                5                 47
  CLUS_2                8                 54
  CLUS_3                3                 65
  CLUS_4                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7     11      2
  12P GAIN WILD-TYPE     60    120     56
D22V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 60
  CLUS_2               11                120
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED       12     11      3      3      3
  12P GAIN WILD-TYPE    123    101    105    124     25
D22V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                123
  CLUS_2               11                101
  CLUS_3                3                105
  CLUS_4                3                124
  CLUS_5                3                 25
[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       13     10      4      5
  12P GAIN WILD-TYPE    122    103    121    132
D22V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               13                122
  CLUS_2               10                103
  CLUS_3                4                121
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10     11      5      5
  12P GAIN WILD-TYPE    126     93    182     67
D22V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               10                126
  CLUS_2               11                 93
  CLUS_3                5                182
  CLUS_4                5                 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 CLUS_4
  12P GAIN MUTATED       12      7      2     10
  12P GAIN WILD-TYPE    143    100    135     90
D22V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                143
  CLUS_2                7                100
  CLUS_3                2                135
  CLUS_4               10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8      8      3      2      4      4      2
  12P GAIN WILD-TYPE    105     86     66    144     30     14     23
D22V11, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                105
  CLUS_2                8                 86
  CLUS_3                3                 66
  CLUS_4                2                144
  CLUS_5                4                 30
  CLUS_6                4                 14
  CLUS_7                2                 23
[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       11     10      1      9
  12P GAIN WILD-TYPE    137    131    111     89
D22V12, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                137
  CLUS_2               10                131
  CLUS_3                1                111
  CLUS_4                9                 89
[1] 4 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 = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        0      1      0
  12Q GAIN WILD-TYPE      9      9      8
D23V1, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED        0      1      0      0
  12Q GAIN WILD-TYPE      7      6      7      6
D23V2, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        6      9      1
  12Q GAIN WILD-TYPE    162    109    225
D23V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                162
  CLUS_2                9                109
  CLUS_3                1                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
  12Q GAIN MUTATED        7      6      0      3
  12Q GAIN WILD-TYPE    216     66     57    152
D23V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                7                216
  CLUS_2                6                 66
  CLUS_3                0                 57
  CLUS_4                3                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      1      2
  12Q GAIN WILD-TYPE     50     57     67     72
D23V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 50
  CLUS_2                5                 57
  CLUS_3                1                 67
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      5      1
  12Q GAIN WILD-TYPE     63    126     57
D23V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                5                126
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      9      2      0      1
  12Q GAIN WILD-TYPE    131    103    106    127     27
D23V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                9                103
  CLUS_3                2                106
  CLUS_4                0                127
  CLUS_5                1                 27
[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      8      3      2
  12Q GAIN WILD-TYPE    132    105    122    135
D23V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                8                105
  CLUS_3                3                122
  CLUS_4                2                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      5      1      4
  12Q GAIN WILD-TYPE    130     99    186     68
D23V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                130
  CLUS_2                5                 99
  CLUS_3                1                186
  CLUS_4                4                 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 CLUS_4
  12Q GAIN MUTATED        5      3      1      7
  12Q GAIN WILD-TYPE    150    104    136     93
D23V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                150
  CLUS_2                3                104
  CLUS_3                1                136
  CLUS_4                7                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      7      1      0      4      1      0
  12Q GAIN WILD-TYPE    110     87     68    146     30     17     25
D23V11, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                110
  CLUS_2                7                 87
  CLUS_3                1                 68
  CLUS_4                0                146
  CLUS_5                4                 30
  CLUS_6                1                 17
  CLUS_7                0                 25
[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        4      5      0      7
  12Q GAIN WILD-TYPE    144    136    112     91
D23V12, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                144
  CLUS_2                5                136
  CLUS_3                0                112
  CLUS_4                7                 91
[1] 4 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 = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        0      0      0
  13Q GAIN WILD-TYPE      9     10      8
D24V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        0      0      0      0
  13Q GAIN WILD-TYPE      7      7      7      6
D24V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3      2      1
  13Q GAIN WILD-TYPE    165    116    225
D24V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                165
  CLUS_2                2                116
  CLUS_3                1                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
  13Q GAIN MUTATED        5      0      0      1
  13Q GAIN WILD-TYPE    218     72     57    154
D24V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                218
  CLUS_2                0                 72
  CLUS_3                0                 57
  CLUS_4                1                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      0      1
  13Q GAIN WILD-TYPE     51     61     68     73
D24V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                1                 61
  CLUS_3                0                 68
  CLUS_4                1                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        1      1      1
  13Q GAIN WILD-TYPE     66    130     57
D24V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                1                130
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      1      0      3      1
  13Q GAIN WILD-TYPE    134    111    108    124     27
D24V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2                1                111
  CLUS_3                0                108
  CLUS_4                3                124
  CLUS_5                1                 27
[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      1      0      3
  13Q GAIN WILD-TYPE    133    112    125    134
D24V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                1                112
  CLUS_3                0                125
  CLUS_4                3                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        3      0      3      0
  13Q GAIN WILD-TYPE    133    104    184     72
D24V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                133
  CLUS_2                0                104
  CLUS_3                3                184
  CLUS_4                0                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        3      0      3      0
  13Q GAIN WILD-TYPE    152    107    134    100
D24V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                152
  CLUS_2                0                107
  CLUS_3                3                134
  CLUS_4                0                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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q GAIN MUTATED        1      2      0      3      0      0      0
  13Q GAIN WILD-TYPE    112     92     69    143     34     18     25
D24V11, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                112
  CLUS_2                2                 92
  CLUS_3                0                 69
  CLUS_4                3                143
  CLUS_5                0                 34
  CLUS_6                0                 18
  CLUS_7                0                 25
[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        3      1      2      0
  13Q GAIN WILD-TYPE    145    140    110     98
D24V12, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                145
  CLUS_2                1                140
  CLUS_3                2                110
  CLUS_4                0                 98
[1] 4 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 = 14Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        0      0      0
  14Q GAIN WILD-TYPE      9     10      8
D25V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        0      0      0      0
  14Q GAIN WILD-TYPE      7      7      7      6
D25V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      1      2
  14Q GAIN WILD-TYPE    167    117    224
D25V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                167
  CLUS_2                1                117
  CLUS_3                2                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
  14Q GAIN MUTATED        3      0      0      1
  14Q GAIN WILD-TYPE    220     72     57    154
D25V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                220
  CLUS_2                0                 72
  CLUS_3                0                 57
  CLUS_4                1                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      1      0
  14Q GAIN WILD-TYPE     51     62     67     74
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                254 
        TCGA-CS-4938         TCGA-CS-4942         TCGA-CS-4943 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-4944         TCGA-CS-5390         TCGA-CS-5393 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5396         TCGA-CS-5397 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6186         TCGA-CS-6188         TCGA-CS-6666 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6668         TCGA-CS-6669         TCGA-CS-6670 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5279         TCGA-DB-5280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DB-A4X9         TCGA-DB-A4XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XB         TCGA-DB-A4XC         TCGA-DB-A4XD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XE         TCGA-DB-A4XF         TCGA-DB-A4XG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XH         TCGA-DH-5140         TCGA-DH-5141 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5847         TCGA-DU-5849         TCGA-DU-5851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5872         TCGA-DU-5874         TCGA-DU-6392 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6393         TCGA-DU-6394         TCGA-DU-6395 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6397         TCGA-DU-6399 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6400         TCGA-DU-6401         TCGA-DU-6402 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6406         TCGA-DU-6407         TCGA-DU-6408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-6542         TCGA-DU-7006 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7007         TCGA-DU-7008         TCGA-DU-7009 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7010         TCGA-DU-7011         TCGA-DU-7012 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7290         TCGA-DU-7292 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7294         TCGA-DU-7298         TCGA-DU-7300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7301         TCGA-DU-7302         TCGA-DU-7304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7306         TCGA-DU-7309         TCGA-DU-8158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8161         TCGA-DU-8162         TCGA-DU-8163 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8164         TCGA-DU-8165         TCGA-DU-8166 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8167         TCGA-DU-8168         TCGA-DU-A5TP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TR         TCGA-DU-A5TS         TCGA-DU-A5TT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TU         TCGA-DU-A5TW         TCGA-DU-A5TY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EZ-7264         TCGA-FG-5962         TCGA-FG-5963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-5964         TCGA-FG-5965         TCGA-FG-6688 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-7634         TCGA-FG-7636         TCGA-FG-7638 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-7641         TCGA-FG-7643         TCGA-FG-8181 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8182         TCGA-FG-8185         TCGA-FG-8186 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8191         TCGA-FG-A4MT         TCGA-FG-A4MU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A4MY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A60J         TCGA-HT-7467         TCGA-HT-7468 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7469         TCGA-HT-7470         TCGA-HT-7471 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7472         TCGA-HT-7473         TCGA-HT-7474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7476         TCGA-HT-7477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7478         TCGA-HT-7479         TCGA-HT-7480 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7481         TCGA-HT-7482         TCGA-HT-7483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7601         TCGA-HT-7602 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7603         TCGA-HT-7604         TCGA-HT-7605 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7606         TCGA-HT-7607         TCGA-HT-7608 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7610         TCGA-HT-7611 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7616         TCGA-HT-7620         TCGA-HT-7676 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7677         TCGA-HT-7680         TCGA-HT-7681 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7684         TCGA-HT-7686         TCGA-HT-7687 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7688         TCGA-HT-7689         TCGA-HT-7690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7691         TCGA-HT-7692         TCGA-HT-7693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7695         TCGA-HT-7854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7855         TCGA-HT-7856         TCGA-HT-7857 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7858         TCGA-HT-7860         TCGA-HT-7873 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7874         TCGA-HT-7875         TCGA-HT-7877 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7879         TCGA-HT-7880         TCGA-HT-7881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7882         TCGA-HT-7884         TCGA-HT-7902 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8010         TCGA-HT-8011         TCGA-HT-8012 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8013         TCGA-HT-8015         TCGA-HT-8018 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8019         TCGA-HT-8104         TCGA-HT-8105 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8106         TCGA-HT-8107         TCGA-HT-8109 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8110         TCGA-HT-8111         TCGA-HT-8113 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8114         TCGA-HT-8564         TCGA-HT-A4DV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5R5         TCGA-HT-A5R7         TCGA-HT-A5R9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5RB         TCGA-HW-7486         TCGA-HW-7487 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-7489         TCGA-HW-7490         TCGA-HW-7491 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-7493         TCGA-HW-7495         TCGA-HW-8319 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-8320         TCGA-HW-8321         TCGA-HW-8322 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-A5KJ         TCGA-HW-A5KK         TCGA-HW-A5KM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IK-7675         TCGA-IK-8125         TCGA-P5-A5ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EU         TCGA-P5-A5EV         TCGA-P5-A5EW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EX         TCGA-P5-A5EY         TCGA-P5-A5EZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F0         TCGA-P5-A5F1         TCGA-P5-A5F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F4         TCGA-P5-A5F6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      1      0
  14Q GAIN WILD-TYPE     66    130     58
D25V6, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                254 
        TCGA-CS-4938         TCGA-CS-4942         TCGA-CS-4943 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-4944         TCGA-CS-5390         TCGA-CS-5393 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5396         TCGA-CS-5397 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6186         TCGA-CS-6188         TCGA-CS-6666 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6668         TCGA-CS-6669         TCGA-CS-6670 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5279         TCGA-DB-5280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DB-A4X9         TCGA-DB-A4XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XB         TCGA-DB-A4XC         TCGA-DB-A4XD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XE         TCGA-DB-A4XF         TCGA-DB-A4XG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XH         TCGA-DH-5140         TCGA-DH-5141 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5847         TCGA-DU-5849         TCGA-DU-5851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5872         TCGA-DU-5874         TCGA-DU-6392 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6393         TCGA-DU-6394         TCGA-DU-6395 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6397         TCGA-DU-6399 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6400         TCGA-DU-6401         TCGA-DU-6402 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6406         TCGA-DU-6407         TCGA-DU-6408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-6542         TCGA-DU-7006 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7007         TCGA-DU-7008         TCGA-DU-7009 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7010         TCGA-DU-7011         TCGA-DU-7012 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7290         TCGA-DU-7292 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7294         TCGA-DU-7298         TCGA-DU-7300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7301         TCGA-DU-7302         TCGA-DU-7304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7306         TCGA-DU-7309         TCGA-DU-8158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8161         TCGA-DU-8162         TCGA-DU-8163 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8164         TCGA-DU-8165         TCGA-DU-8166 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8167         TCGA-DU-8168         TCGA-DU-A5TP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TR         TCGA-DU-A5TS         TCGA-DU-A5TT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TU         TCGA-DU-A5TW         TCGA-DU-A5TY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EZ-7264         TCGA-FG-5962         TCGA-FG-5963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-5964         TCGA-FG-5965         TCGA-FG-6688 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-7634         TCGA-FG-7636         TCGA-FG-7638 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-7641         TCGA-FG-7643         TCGA-FG-8181 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8182         TCGA-FG-8185         TCGA-FG-8186 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8191         TCGA-FG-A4MT         TCGA-FG-A4MU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A4MY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A60J         TCGA-HT-7467         TCGA-HT-7468 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7469         TCGA-HT-7470         TCGA-HT-7471 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7472         TCGA-HT-7473         TCGA-HT-7474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7476         TCGA-HT-7477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7478         TCGA-HT-7479         TCGA-HT-7480 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7481         TCGA-HT-7482         TCGA-HT-7483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7601         TCGA-HT-7602 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7603         TCGA-HT-7604         TCGA-HT-7605 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7606         TCGA-HT-7607         TCGA-HT-7608 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7610         TCGA-HT-7611 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7616         TCGA-HT-7620         TCGA-HT-7676 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7677         TCGA-HT-7680         TCGA-HT-7681 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7684         TCGA-HT-7686         TCGA-HT-7687 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7688         TCGA-HT-7689         TCGA-HT-7690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7691         TCGA-HT-7692         TCGA-HT-7693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7695         TCGA-HT-7854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7855         TCGA-HT-7856         TCGA-HT-7857 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7858         TCGA-HT-7860         TCGA-HT-7873 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7874         TCGA-HT-7875         TCGA-HT-7877 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7879         TCGA-HT-7880         TCGA-HT-7881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7882         TCGA-HT-7884         TCGA-HT-7902 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8010         TCGA-HT-8011         TCGA-HT-8012 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8013         TCGA-HT-8015         TCGA-HT-8018 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8019         TCGA-HT-8104         TCGA-HT-8105 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8106         TCGA-HT-8107         TCGA-HT-8109 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8110         TCGA-HT-8111         TCGA-HT-8113 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-8114         TCGA-HT-8564         TCGA-HT-A4DV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5R5         TCGA-HT-A5R7         TCGA-HT-A5R9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5RB         TCGA-HW-7486         TCGA-HW-7487 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-7489         TCGA-HW-7490         TCGA-HW-7491 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-7493         TCGA-HW-7495         TCGA-HW-8319 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-8320         TCGA-HW-8321         TCGA-HW-8322 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HW-A5KJ         TCGA-HW-A5KK         TCGA-HW-A5KM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IK-7675         TCGA-IK-8125         TCGA-P5-A5ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EU         TCGA-P5-A5EV         TCGA-P5-A5EW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EX         TCGA-P5-A5EY         TCGA-P5-A5EZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F0         TCGA-P5-A5F1         TCGA-P5-A5F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F4         TCGA-P5-A5F6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q GAIN MUTATED        1      2      0      1      0
  14Q GAIN WILD-TYPE    134    110    108    126     28
D25V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2                2                110
  CLUS_3                0                108
  CLUS_4                1                126
  CLUS_5                0                 28
[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        2      1      1      0
  14Q GAIN WILD-TYPE    133    112    124    137
D25V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                1                112
  CLUS_3                1                124
  CLUS_4                0                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      1      1      1
  14Q GAIN WILD-TYPE    136    103    186     71
D25V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                136
  CLUS_2                1                103
  CLUS_3                1                186
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      1      1      1
  14Q GAIN WILD-TYPE    155    106    136     99
D25V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                155
  CLUS_2                1                106
  CLUS_3                1                136
  CLUS_4                1                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      0      1      1      0      1      0
  14Q GAIN WILD-TYPE    113     94     68    145     34     17     25
D25V11, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                113
  CLUS_2                0                 94
  CLUS_3                1                 68
  CLUS_4                1                145
  CLUS_5                0                 34
  CLUS_6                1                 17
  CLUS_7                0                 25
[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        0      2      0      1
  14Q GAIN WILD-TYPE    148    139    112     97
D25V12, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                148
  CLUS_2                2                139
  CLUS_3                0                112
  CLUS_4                1                 97
[1] 4 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 = 15Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        1      1      0
  15Q GAIN WILD-TYPE      8      9      8
D26V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4944         TCGA-CS-5390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"15Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        0      2      0      0
  15Q GAIN WILD-TYPE      7      5      7      6
D26V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4944         TCGA-CS-5390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"15Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        7      4      0
  15Q GAIN WILD-TYPE    161    114    226
D26V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                7                161
  CLUS_2                4                114
  CLUS_3                0                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
  15Q GAIN MUTATED        8      3      0      0
  15Q GAIN WILD-TYPE    215     69     57    155
D26V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                215
  CLUS_2                3                 69
  CLUS_3                0                 57
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        0      4      2      0
  15Q GAIN WILD-TYPE     52     58     66     74
D26V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 52
  CLUS_2                4                 58
  CLUS_3                2                 66
  CLUS_4                0                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        0      5      1
  15Q GAIN WILD-TYPE     67    126     57
D26V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                5                126
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        4      6      0      1      0
  15Q GAIN WILD-TYPE    131    106    108    126     28
D26V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                6                106
  CLUS_3                0                108
  CLUS_4                1                126
  CLUS_5                0                 28
[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 GAIN MUTATED        4      6      0      1
  15Q GAIN WILD-TYPE    131    107    125    136
D26V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                6                107
  CLUS_3                0                125
  CLUS_4                1                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        4      5      2      0
  15Q GAIN WILD-TYPE    132     99    185     72
D26V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                132
  CLUS_2                5                 99
  CLUS_3                2                185
  CLUS_4                0                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        4      1      1      5
  15Q GAIN WILD-TYPE    151    106    136     95
D26V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                151
  CLUS_2                1                106
  CLUS_3                1                136
  CLUS_4                5                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        3      5      0      1      0      2      0
  15Q GAIN WILD-TYPE    110     89     69    145     34     16     25
D26V11, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                110
  CLUS_2                5                 89
  CLUS_3                0                 69
  CLUS_4                1                145
  CLUS_5                0                 34
  CLUS_6                2                 16
  CLUS_7                0                 25
[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 GAIN MUTATED        5      2      0      4
  15Q GAIN WILD-TYPE    143    139    112     94
D26V12, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                2                139
  CLUS_3                0                112
  CLUS_4                4                 94
[1] 4 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 = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        0      1      0
  16P GAIN WILD-TYPE      9      9      8
D27V1, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        0      1      0      0
  16P GAIN WILD-TYPE      7      6      7      6
D27V2, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        7      4      5
  16P GAIN WILD-TYPE    161    114    221
D27V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                7                161
  CLUS_2                4                114
  CLUS_3                5                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
  16P GAIN MUTATED        8      3      0      5
  16P GAIN WILD-TYPE    215     69     57    150
D27V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                8                215
  CLUS_2                3                 69
  CLUS_3                0                 57
  CLUS_4                5                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        2      4      1      3
  16P GAIN WILD-TYPE     50     58     67     71
D27V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 50
  CLUS_2                4                 58
  CLUS_3                1                 67
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        3      4      3
  16P GAIN WILD-TYPE     64    127     55
D27V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                4                127
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      8      3      3      0
  16P GAIN WILD-TYPE    133    104    105    124     28
D27V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                8                104
  CLUS_3                3                105
  CLUS_4                3                124
  CLUS_5                0                 28
[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        1      7      3      5
  16P GAIN WILD-TYPE    134    106    122    132
D27V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2                7                106
  CLUS_3                3                122
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      8      2
  16P GAIN WILD-TYPE    135     99    179     70
D27V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                135
  CLUS_2                5                 99
  CLUS_3                8                179
  CLUS_4                2                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      5      4
  16P GAIN WILD-TYPE    153    102    132     96
D27V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                153
  CLUS_2                5                102
  CLUS_3                5                132
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      1      5      1      2      1
  16P GAIN WILD-TYPE    111     90     68    141     33     16     24
D27V11, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                111
  CLUS_2                4                 90
  CLUS_3                1                 68
  CLUS_4                5                141
  CLUS_5                1                 33
  CLUS_6                2                 16
  CLUS_7                1                 24
[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        3      8      1      4
  16P GAIN WILD-TYPE    145    133    111     94
D27V12, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                145
  CLUS_2                8                133
  CLUS_3                1                111
  CLUS_4                4                 94
[1] 4 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 = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        1      1      0
  16Q GAIN WILD-TYPE      8      9      8
D28V1, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"16Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        1      1      0      0
  16Q GAIN WILD-TYPE      6      6      7      6
D28V2, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"16Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       11      4      4
  16Q GAIN WILD-TYPE    157    114    222
D28V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               11                157
  CLUS_2                4                114
  CLUS_3                4                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
  16Q GAIN MUTATED       12      3      0      4
  16Q GAIN WILD-TYPE    211     69     57    151
D28V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               12                211
  CLUS_2                3                 69
  CLUS_3                0                 57
  CLUS_4                4                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      1      3
  16Q GAIN WILD-TYPE     49     58     67     71
D28V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                4                 58
  CLUS_3                1                 67
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      4      3
  16Q GAIN WILD-TYPE     63    127     55
D28V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                4                127
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      9      2      4      0
  16Q GAIN WILD-TYPE    131    103    106    123     28
D28V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                9                103
  CLUS_3                2                106
  CLUS_4                4                123
  CLUS_5                0                 28
[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      9      2      6
  16Q GAIN WILD-TYPE    133    104    123    131
D28V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                9                104
  CLUS_3                2                123
  CLUS_4                6                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      9      2
  16Q GAIN WILD-TYPE    135     97    178     70
D28V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                135
  CLUS_2                7                 97
  CLUS_3                9                178
  CLUS_4                2                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      4      6      4
  16Q GAIN WILD-TYPE    150    103    131     96
D28V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                150
  CLUS_2                4                103
  CLUS_3                6                131
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      3      1      6      1      3      1
  16Q GAIN WILD-TYPE    109     91     68    140     33     15     24
D28V11, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                109
  CLUS_2                3                 91
  CLUS_3                1                 68
  CLUS_4                6                140
  CLUS_5                1                 33
  CLUS_6                3                 15
  CLUS_7                1                 24
[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        5      7      2      5
  16Q GAIN WILD-TYPE    143    134    110     93
D28V12, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                7                134
  CLUS_3                2                110
  CLUS_4                5                 93
[1] 4 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 = 17P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        0      1      0
  17P GAIN WILD-TYPE      9      9      8
D29V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        0      1      0      0
  17P GAIN WILD-TYPE      7      6      7      6
D29V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        7      7      6
  17P GAIN WILD-TYPE    161    111    220
D29V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                161
  CLUS_2                7                111
  CLUS_3                6                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
  17P GAIN MUTATED        8      4      0      8
  17P GAIN WILD-TYPE    215     68     57    147
D29V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                215
  CLUS_2                4                 68
  CLUS_3                0                 57
  CLUS_4                8                147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      1      1
  17P GAIN WILD-TYPE     51     58     67     73
D29V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                4                 58
  CLUS_3                1                 67
  CLUS_4                1                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        2      3      2
  17P GAIN WILD-TYPE     65    128     56
D29V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                3                128
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3      9      4      4      0
  17P GAIN WILD-TYPE    132    103    104    123     28
D29V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                9                103
  CLUS_3                4                104
  CLUS_4                4                123
  CLUS_5                0                 28
[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      9      6      3
  17P GAIN WILD-TYPE    133    104    119    134
D29V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                9                104
  CLUS_3                6                119
  CLUS_4                3                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      8      4      3
  17P GAIN WILD-TYPE    131     96    183     69
D29V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                131
  CLUS_2                8                 96
  CLUS_3                4                183
  CLUS_4                3                 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 CLUS_4
  17P GAIN MUTATED        5      6      3      6
  17P GAIN WILD-TYPE    150    101    134     94
D29V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                150
  CLUS_2                6                101
  CLUS_3                3                134
  CLUS_4                6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      5      4      4      2      3      0
  17P GAIN WILD-TYPE    111     89     65    142     32     15     25
D29V11, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                111
  CLUS_2                5                 89
  CLUS_3                4                 65
  CLUS_4                4                142
  CLUS_5                2                 32
  CLUS_6                3                 15
  CLUS_7                0                 25
[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        6      8      1      5
  17P GAIN WILD-TYPE    142    133    111     93
D29V12, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                142
  CLUS_2                8                133
  CLUS_3                1                111
  CLUS_4                5                 93
[1] 4 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 = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        0      1      0
  17Q GAIN WILD-TYPE      9      9      8
D30V1, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        0      1      0      0
  17Q GAIN WILD-TYPE      7      6      7      6
D30V2, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        8      7      8
  17Q GAIN WILD-TYPE    160    111    218
D30V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                160
  CLUS_2                7                111
  CLUS_3                8                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
  17Q GAIN MUTATED        9      5      0      9
  17Q GAIN WILD-TYPE    214     67     57    146
D30V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                214
  CLUS_2                5                 67
  CLUS_3                0                 57
  CLUS_4                9                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      1      1
  17Q GAIN WILD-TYPE     51     58     67     73
D30V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                4                 58
  CLUS_3                1                 67
  CLUS_4                1                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        2      3      2
  17Q GAIN WILD-TYPE     65    128     56
D30V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                3                128
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5      9      5      4      0
  17Q GAIN WILD-TYPE    130    103    103    123     28
D30V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                130
  CLUS_2                9                103
  CLUS_3                5                103
  CLUS_4                4                123
  CLUS_5                0                 28
[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        4      9      7      3
  17Q GAIN WILD-TYPE    131    104    118    134
D30V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                9                104
  CLUS_3                7                118
  CLUS_4                3                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      9      4      4
  17Q GAIN WILD-TYPE    130     95    183     68
D30V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                130
  CLUS_2                9                 95
  CLUS_3                4                183
  CLUS_4                4                 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 CLUS_4
  17Q GAIN MUTATED        7      7      3      6
  17Q GAIN WILD-TYPE    148    100    134     94
D30V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                7                148
  CLUS_2                7                100
  CLUS_3                3                134
  CLUS_4                6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      6      5      4      2      2      0
  17Q GAIN WILD-TYPE    109     88     64    142     32     16     25
D30V11, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                109
  CLUS_2                6                 88
  CLUS_3                5                 64
  CLUS_4                4                142
  CLUS_5                2                 32
  CLUS_6                2                 16
  CLUS_7                0                 25
[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        8      9      1      5
  17Q GAIN WILD-TYPE    140    132    111     93
D30V12, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                140
  CLUS_2                9                132
  CLUS_3                1                111
  CLUS_4                5                 93
[1] 4 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 = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        0      1      1
  18P GAIN WILD-TYPE      9      9      7
D31V1, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"18P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        0      2      0      0
  18P GAIN WILD-TYPE      7      5      7      6
D31V2, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"18P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       11      5      0
  18P GAIN WILD-TYPE    157    113    226
D31V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               11                157
  CLUS_2                5                113
  CLUS_3                0                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
  18P GAIN MUTATED       11      4      1      0
  18P GAIN WILD-TYPE    212     68     56    155
D31V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               11                212
  CLUS_2                4                 68
  CLUS_3                1                 56
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        3      5      1      0
  18P GAIN WILD-TYPE     49     57     67     74
D31V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                5                 57
  CLUS_3                1                 67
  CLUS_4                0                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        4      4      1
  18P GAIN WILD-TYPE     63    127     57
D31V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                4                127
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3      8      0      3      1
  18P GAIN WILD-TYPE    132    104    108    124     27
D31V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                8                104
  CLUS_3                0                108
  CLUS_4                3                124
  CLUS_5                1                 27
[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        4      8      0      3
  18P GAIN WILD-TYPE    131    105    125    134
D31V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                8                105
  CLUS_3                0                125
  CLUS_4                3                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      2      6      1
  18P GAIN WILD-TYPE    130    102    181     71
D31V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                130
  CLUS_2                2                102
  CLUS_3                6                181
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      2      2      5
  18P GAIN WILD-TYPE    149    105    135     95
D31V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                149
  CLUS_2                2                105
  CLUS_3                2                135
  CLUS_4                5                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        3      5      1      3      0      1      2
  18P GAIN WILD-TYPE    110     89     68    143     34     17     23
D31V11, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                110
  CLUS_2                5                 89
  CLUS_3                1                 68
  CLUS_4                3                143
  CLUS_5                0                 34
  CLUS_6                1                 17
  CLUS_7                2                 23
[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 GAIN MUTATED        5      2      2      6
  18P GAIN WILD-TYPE    143    139    110     92
D31V12, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                2                139
  CLUS_3                2                110
  CLUS_4                6                 92
[1] 4 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 = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        0      1      0
  18Q GAIN WILD-TYPE      9      9      8
D32V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        0      1      0      0
  18Q GAIN WILD-TYPE      7      6      7      6
D32V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        8      5      0
  18Q GAIN WILD-TYPE    160    113    226
D32V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                8                160
  CLUS_2                5                113
  CLUS_3                0                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
  18Q GAIN MUTATED        7      5      1      0
  18Q GAIN WILD-TYPE    216     67     56    155
D32V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                216
  CLUS_2                5                 67
  CLUS_3                1                 56
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      0
  18Q GAIN WILD-TYPE     50     58     67     74
D32V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 50
  CLUS_2                4                 58
  CLUS_3                1                 67
  CLUS_4                0                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        3      3      1
  18Q GAIN WILD-TYPE     64    128     57
D32V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                3                128
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      9      0      1      0
  18Q GAIN WILD-TYPE    133    103    108    126     28
D32V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                9                103
  CLUS_3                0                108
  CLUS_4                1                126
  CLUS_5                0                 28
[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      9      0      1
  18Q GAIN WILD-TYPE    133    104    125    136
D32V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                9                104
  CLUS_3                0                125
  CLUS_4                1                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      3      3      1
  18Q GAIN WILD-TYPE    131    101    184     71
D32V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                131
  CLUS_2                3                101
  CLUS_3                3                184
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        4      1      1      6
  18Q GAIN WILD-TYPE    151    106    136     94
D32V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                151
  CLUS_2                1                106
  CLUS_3                1                136
  CLUS_4                6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        2      6      1      1      0      1      1
  18Q GAIN WILD-TYPE    111     88     68    145     34     17     24
D32V11, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                111
  CLUS_2                6                 88
  CLUS_3                1                 68
  CLUS_4                1                145
  CLUS_5                0                 34
  CLUS_6                1                 17
  CLUS_7                1                 24
[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 GAIN MUTATED        3      1      1      7
  18Q GAIN WILD-TYPE    145    140    111     91
D32V12, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                145
  CLUS_2                1                140
  CLUS_3                1                111
  CLUS_4                7                 91
[1] 4 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 = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      3      2
  19P GAIN WILD-TYPE      9      7      6
D33V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                3                  7
  CLUS_3                2                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        1      1      2      1
  19P GAIN WILD-TYPE      6      6      5      5
D33V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  6
  CLUS_3                2                  5
  CLUS_4                1                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7     37     57
  19P GAIN WILD-TYPE    161     81    169
D33V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                161
  CLUS_2               37                 81
  CLUS_3               57                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED       10     27      5     57
  19P GAIN WILD-TYPE    213     45     52     98
D33V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                213
  CLUS_2               27                 45
  CLUS_3                5                 52
  CLUS_4               57                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        8     13      9     13
  19P GAIN WILD-TYPE     44     49     59     61
D33V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 44
  CLUS_2               13                 49
  CLUS_3                9                 59
  CLUS_4               13                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       10     26      7
  19P GAIN WILD-TYPE     57    105     51
D33V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                 57
  CLUS_2               26                105
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5     30     45     20      1
  19P GAIN WILD-TYPE    130     82     63    107     27
D33V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                5                130
  CLUS_2               30                 82
  CLUS_3               45                 63
  CLUS_4               20                107
  CLUS_5                1                 27
[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        6     28     45     22
  19P GAIN WILD-TYPE    129     85     80    115
D33V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                129
  CLUS_2               28                 85
  CLUS_3               45                 80
  CLUS_4               22                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       21     18     35     25
  19P GAIN WILD-TYPE    115     86    152     47
D33V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               21                115
  CLUS_2               18                 86
  CLUS_3               35                152
  CLUS_4               25                 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
  19P GAIN MUTATED       18     30     24     27
  19P GAIN WILD-TYPE    137     77    113     73
D33V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               18                137
  CLUS_2               30                 77
  CLUS_3               24                113
  CLUS_4               27                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P GAIN MUTATED        4     26     30     27      8      2      2
  19P GAIN WILD-TYPE    109     68     39    119     26     16     23
D33V11, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                109
  CLUS_2               26                 68
  CLUS_3               30                 39
  CLUS_4               27                119
  CLUS_5                8                 26
  CLUS_6                2                 16
  CLUS_7                2                 23
[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 GAIN MUTATED       12     40     19     28
  19P GAIN WILD-TYPE    136    101     93     70
D33V12, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               12                136
  CLUS_2               40                101
  CLUS_3               19                 93
  CLUS_4               28                 70
[1] 4 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 = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      0      1
  19Q GAIN WILD-TYPE      9     10      7
D34V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        1      0      0      0
  19Q GAIN WILD-TYPE      6      7      7      6
D34V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        1     23      1
  19Q GAIN WILD-TYPE    167     95    225
D34V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                167
  CLUS_2               23                 95
  CLUS_3                1                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
  19Q GAIN MUTATED        2     20      2      0
  19Q GAIN WILD-TYPE    221     52     55    155
D34V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                221
  CLUS_2               20                 52
  CLUS_3                2                 55
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      6      1      1
  19Q GAIN WILD-TYPE     49     56     67     73
D34V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                6                 56
  CLUS_3                1                 67
  CLUS_4                1                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        2      8      1
  19Q GAIN WILD-TYPE     65    123     57
D34V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                8                123
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1     19      0      4      1
  19Q GAIN WILD-TYPE    134     93    108    123     27
D34V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2               19                 93
  CLUS_3                0                108
  CLUS_4                4                123
  CLUS_5                1                 27
[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        2     19      0      4
  19Q GAIN WILD-TYPE    133     94    125    133
D34V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2               19                 94
  CLUS_3                0                125
  CLUS_4                4                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7     12      6      0
  19Q GAIN WILD-TYPE    129     92    181     72
D34V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                129
  CLUS_2               12                 92
  CLUS_3                6                181
  CLUS_4                0                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      0      2     20
  19Q GAIN WILD-TYPE    152    107    135     80
D34V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                152
  CLUS_2                0                107
  CLUS_3                2                135
  CLUS_4               20                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     19      0      5      1      0      0
  19Q GAIN WILD-TYPE    113     75     69    141     33     18     25
D34V11, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                113
  CLUS_2               19                 75
  CLUS_3                0                 69
  CLUS_4                5                141
  CLUS_5                1                 33
  CLUS_6                0                 18
  CLUS_7                0                 25
[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        2      1      1     21
  19Q GAIN WILD-TYPE    146    140    111     77
D34V12, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                146
  CLUS_2                1                140
  CLUS_3                1                111
  CLUS_4               21                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        0      1      1
  20P GAIN WILD-TYPE      9      9      7
D35V1, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        1      1      0      0
  20P GAIN WILD-TYPE      6      6      7      6
D35V2, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        8     31      4
  20P GAIN WILD-TYPE    160     87    222
D35V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                160
  CLUS_2               31                 87
  CLUS_3                4                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
  20P GAIN MUTATED        7     26      4      6
  20P GAIN WILD-TYPE    216     46     53    149
D35V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                216
  CLUS_2               26                 46
  CLUS_3                4                 53
  CLUS_4                6                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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     14      2      5
  20P GAIN WILD-TYPE     50     48     66     69
D35V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 50
  CLUS_2               14                 48
  CLUS_3                2                 66
  CLUS_4                5                 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
  20P GAIN MUTATED        3     16      4
  20P GAIN WILD-TYPE     64    115     54
D35V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 64
  CLUS_2               16                115
  CLUS_3                4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3     28      3      8      1
  20P GAIN WILD-TYPE    132     84    105    119     27
D35V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2               28                 84
  CLUS_3                3                105
  CLUS_4                8                119
  CLUS_5                1                 27
[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     26      4     10
  20P GAIN WILD-TYPE    132     87    121    127
D35V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2               26                 87
  CLUS_3                4                121
  CLUS_4               10                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       17     11     12      3
  20P GAIN WILD-TYPE    119     93    175     69
D35V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               17                119
  CLUS_2               11                 93
  CLUS_3               12                175
  CLUS_4                3                 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 CLUS_4
  20P GAIN MUTATED        5      4      8     26
  20P GAIN WILD-TYPE    150    103    129     74
D35V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                150
  CLUS_2                4                103
  CLUS_3                8                129
  CLUS_4               26                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P GAIN MUTATED        2     22      2     10      5      2      0
  20P GAIN WILD-TYPE    111     72     67    136     29     16     25
D35V11, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                111
  CLUS_2               22                 72
  CLUS_3                2                 67
  CLUS_4               10                136
  CLUS_5                5                 29
  CLUS_6                2                 16
  CLUS_7                0                 25
[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        7      6      4     26
  20P GAIN WILD-TYPE    141    135    108     72
D35V12, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                141
  CLUS_2                6                135
  CLUS_3                4                108
  CLUS_4               26                 72
[1] 4 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 = 20Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        0      1      1
  20Q GAIN WILD-TYPE      9      9      7
D36V1, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        1      1      0      0
  20Q GAIN WILD-TYPE      6      6      7      6
D36V2, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        8     31      4
  20Q GAIN WILD-TYPE    160     87    222
D36V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                160
  CLUS_2               31                 87
  CLUS_3                4                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
  20Q GAIN MUTATED        8     27      2      6
  20Q GAIN WILD-TYPE    215     45     55    149
D36V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                215
  CLUS_2               27                 45
  CLUS_3                2                 55
  CLUS_4                6                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5     14      2      3
  20Q GAIN WILD-TYPE     47     48     66     71
D36V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                 47
  CLUS_2               14                 48
  CLUS_3                2                 66
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4     17      3
  20Q GAIN WILD-TYPE     63    114     55
D36V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 63
  CLUS_2               17                114
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4     29      3      6      1
  20Q GAIN WILD-TYPE    131     83    105    121     27
D36V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2               29                 83
  CLUS_3                3                105
  CLUS_4                6                121
  CLUS_5                1                 27
[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        4     27      4      8
  20Q GAIN WILD-TYPE    131     86    121    129
D36V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2               27                 86
  CLUS_3                4                121
  CLUS_4                8                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       19     10     10      4
  20Q GAIN WILD-TYPE    117     94    177     68
D36V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               19                117
  CLUS_2               10                 94
  CLUS_3               10                177
  CLUS_4                4                 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 CLUS_4
  20Q GAIN MUTATED        8      4      6     25
  20Q GAIN WILD-TYPE    147    103    131     75
D36V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                147
  CLUS_2                4                103
  CLUS_3                6                131
  CLUS_4               25                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2     23      2      8      6      2      0
  20Q GAIN WILD-TYPE    111     71     67    138     28     16     25
D36V11, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                111
  CLUS_2               23                 71
  CLUS_3                2                 67
  CLUS_4                8                138
  CLUS_5                6                 28
  CLUS_6                2                 16
  CLUS_7                0                 25
[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        9      6      2     26
  20Q GAIN WILD-TYPE    139    135    110     72
D36V12, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                139
  CLUS_2                6                135
  CLUS_3                2                110
  CLUS_4               26                 72
[1] 4 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 = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        0      1      1
  21Q GAIN WILD-TYPE      9      9      7
D37V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        0      2      0      0
  21Q GAIN WILD-TYPE      7      5      7      6
D37V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        4     12      8
  21Q GAIN WILD-TYPE    164    106    218
D37V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                164
  CLUS_2               12                106
  CLUS_3                8                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
  21Q GAIN MUTATED        6      9      0      9
  21Q GAIN WILD-TYPE    217     63     57    146
D37V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                6                217
  CLUS_2                9                 63
  CLUS_3                0                 57
  CLUS_4                9                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      6      3      3
  21Q GAIN WILD-TYPE     52     56     65     71
D37V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 52
  CLUS_2                6                 56
  CLUS_3                3                 65
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      8      3
  21Q GAIN WILD-TYPE     66    123     55
D37V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                8                123
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        3      8      5      7      1
  21Q GAIN WILD-TYPE    132    104    103    120     27
D37V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                8                104
  CLUS_3                5                103
  CLUS_4                7                120
  CLUS_5                1                 27
[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        3      9      6      6
  21Q GAIN WILD-TYPE    132    104    119    131
D37V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                9                104
  CLUS_3                6                119
  CLUS_4                6                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      3      9      4
  21Q GAIN WILD-TYPE    128    101    178     68
D37V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                8                128
  CLUS_2                3                101
  CLUS_3                9                178
  CLUS_4                4                 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 CLUS_4
  21Q GAIN MUTATED        6      6      3      9
  21Q GAIN WILD-TYPE    149    101    134     91
D37V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                6                149
  CLUS_2                6                101
  CLUS_3                3                134
  CLUS_4                9                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        3      6      2      8      3      2      0
  21Q GAIN WILD-TYPE    110     88     67    138     31     16     25
D37V11, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                110
  CLUS_2                6                 88
  CLUS_3                2                 67
  CLUS_4                8                138
  CLUS_5                3                 31
  CLUS_6                2                 16
  CLUS_7                0                 25
[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 GAIN MUTATED        5      6      4      9
  21Q GAIN WILD-TYPE    143    135    108     89
D37V12, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                6                135
  CLUS_3                4                108
  CLUS_4                9                 89
[1] 4 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 = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        0      0      0
  22Q GAIN WILD-TYPE      9     10      8
D38V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        0      0      0      0
  22Q GAIN WILD-TYPE      7      7      7      6
D38V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        3      3     17
  22Q GAIN WILD-TYPE    165    115    209
D38V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                165
  CLUS_2                3                115
  CLUS_3               17                209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        2      3      0     18
  22Q GAIN WILD-TYPE    221     69     57    137
D38V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                221
  CLUS_2                3                 69
  CLUS_3                0                 57
  CLUS_4               18                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        1      2      2      2
  22Q GAIN WILD-TYPE     51     60     66     72
D38V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                2                 60
  CLUS_3                2                 66
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 GAIN MUTATED        1      5      1
  22Q GAIN WILD-TYPE     66    126     57
D38V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                5                126
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        1      4     13      5      0
  22Q GAIN WILD-TYPE    134    108     95    122     28
D38V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2                4                108
  CLUS_3               13                 95
  CLUS_4                5                122
  CLUS_5                0                 28
[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 GAIN MUTATED        0      4     13      6
  22Q GAIN WILD-TYPE    135    109    112    131
D38V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                135
  CLUS_2                4                109
  CLUS_3               13                112
  CLUS_4                6                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED        4      3      8      6
  22Q GAIN WILD-TYPE    132    101    179     66
D38V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                132
  CLUS_2                3                101
  CLUS_3                8                179
  CLUS_4                6                 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 CLUS_4
  22Q GAIN MUTATED        3     10      5      3
  22Q GAIN WILD-TYPE    152     97    132     97
D38V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                152
  CLUS_2               10                 97
  CLUS_3                5                132
  CLUS_4                3                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED        1      3      8      6      2      1      0
  22Q GAIN WILD-TYPE    112     91     61    140     32     17     25
D38V11, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                112
  CLUS_2                3                 91
  CLUS_3                8                 61
  CLUS_4                6                140
  CLUS_5                2                 32
  CLUS_6                1                 17
  CLUS_7                0                 25
[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 GAIN MUTATED        1     15      2      3
  22Q GAIN WILD-TYPE    147    126    110     95
D38V12, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                147
  CLUS_2               15                126
  CLUS_3                2                110
  CLUS_4                3                 95
[1] 4 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 = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1      0      1
  XQ GAIN WILD-TYPE      8     10      7
D39V1, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-E1-5318 
"XQ GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        0      1      0      1
  XQ GAIN WILD-TYPE      7      6      7      5
D39V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-E1-5318 
"XQ GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       32      6      2
  XQ GAIN WILD-TYPE    136    112    224
D39V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              32               136
  CLUS_2               6               112
  CLUS_3               2               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
  XQ GAIN MUTATED       34      3      3      0
  XQ GAIN WILD-TYPE    189     69     54    155
D39V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              34               189
  CLUS_2               3                69
  CLUS_3               3                54
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        3      5      9      3
  XQ GAIN WILD-TYPE     49     57     59     71
D39V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                49
  CLUS_2               5                57
  CLUS_3               9                59
  CLUS_4               3                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        5     12      3
  XQ GAIN WILD-TYPE     62    119     55
D39V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5                62
  CLUS_2              12               119
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       19      7      0     10      4
  XQ GAIN WILD-TYPE    116    105    108    117     24
D39V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              19               116
  CLUS_2               7               105
  CLUS_3               0               108
  CLUS_4              10               117
  CLUS_5               4                24
[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       23      7      0     10
  XQ GAIN WILD-TYPE    112    106    125    127
D39V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              23               112
  CLUS_2               7               106
  CLUS_3               0               125
  CLUS_4              10               127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15      8     13      1
  XQ GAIN WILD-TYPE    121     96    174     71
D39V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              15               121
  CLUS_2               8                96
  CLUS_3              13               174
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       18      2     10      7
  XQ GAIN WILD-TYPE    137    105    127     93
D39V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              18               137
  CLUS_2               2               105
  CLUS_3              10               127
  CLUS_4               7                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       15      7      0      9      2      2      2
  XQ GAIN WILD-TYPE     98     87     69    137     32     16     23
D39V11, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              15                98
  CLUS_2               7                87
  CLUS_3               0                69
  CLUS_4               9               137
  CLUS_5               2                32
  CLUS_6               2                16
  CLUS_7               2                23
[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       20      4      7      6
  XQ GAIN WILD-TYPE    128    137    105     92
D39V12, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              20               128
  CLUS_2               4               137
  CLUS_3               7               105
  CLUS_4               6                92
[1] 4 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 = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      7      2
  1P LOSS WILD-TYPE      8      3      6
D40V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               7                 3
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        0      1      7      2
  1P LOSS WILD-TYPE      7      6      0      4
D40V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 6
  CLUS_3               7                 0
  CLUS_4               2                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        6     16    161
  1P LOSS WILD-TYPE    162    102     65
D40V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6               162
  CLUS_2              16               102
  CLUS_3             161                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        4      4     18    154
  1P LOSS WILD-TYPE    219     68     39      1
D40V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4               219
  CLUS_2               4                68
  CLUS_3              18                39
  CLUS_4             154                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8     14     26     36
  1P LOSS WILD-TYPE     44     48     42     38
D40V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               8                44
  CLUS_2              14                48
  CLUS_3              26                42
  CLUS_4              36                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       24     38     22
  1P LOSS WILD-TYPE     43     93     36
D40V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              24                43
  CLUS_2              38                93
  CLUS_3              22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED        3      9    106     55     10
  1P LOSS WILD-TYPE    132    103      2     72     18
D40V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               132
  CLUS_2               9               103
  CLUS_3             106                 2
  CLUS_4              55                72
  CLUS_5              10                18
[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        3      7    122     51
  1P LOSS WILD-TYPE    132    106      3     86
D40V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               132
  CLUS_2               7               106
  CLUS_3             122                 3
  CLUS_4              51                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       27      8     89     57
  1P LOSS WILD-TYPE    109     96     98     15
D40V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              27               109
  CLUS_2               8                96
  CLUS_3              89                98
  CLUS_4              57                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       32     80     62      7
  1P LOSS WILD-TYPE    123     27     75     93
D40V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              32               123
  CLUS_2              80                27
  CLUS_3              62                75
  CLUS_4               7                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  1P LOSS MUTATED        4     16     64     70     13      1     13
  1P LOSS WILD-TYPE    109     78      5     76     21     17     12
D40V11, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4               109
  CLUS_2              16                78
  CLUS_3              64                 5
  CLUS_4              70                76
  CLUS_5              13                21
  CLUS_6               1                17
  CLUS_7              13                12
[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
  1P LOSS MUTATED       19     99     56      7
  1P LOSS WILD-TYPE    129     42     56     91
D40V12, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              19               129
  CLUS_2              99                42
  CLUS_3              56                56
  CLUS_4               7                91
[1] 4 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 = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        1      3      0
  1Q LOSS WILD-TYPE      8      7      8
D41V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               3                 7
  CLUS_3               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        0      1      3      0
  1Q LOSS WILD-TYPE      7      6      4      6
D41V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 6
  CLUS_3               3                 4
  CLUS_4               0                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        7      4     12
  1Q LOSS WILD-TYPE    161    114    214
D41V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               161
  CLUS_2               4               114
  CLUS_3              12               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
  1Q LOSS MUTATED        5      2      5     11
  1Q LOSS WILD-TYPE    218     70     52    144
D41V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5               218
  CLUS_2               2                70
  CLUS_3               5                52
  CLUS_4              11               144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      4      5
  1Q LOSS WILD-TYPE     51     58     64     69
D41V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                51
  CLUS_2               4                58
  CLUS_3               4                64
  CLUS_4               5                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        2      9      3
  1Q LOSS WILD-TYPE     65    122     55
D41V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                65
  CLUS_2               9               122
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q LOSS MUTATED        3      4      7      8      1
  1Q LOSS WILD-TYPE    132    108    101    119     27
D41V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               132
  CLUS_2               4               108
  CLUS_3               7               101
  CLUS_4               8               119
  CLUS_5               1                27
[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        4      3     10      6
  1Q LOSS WILD-TYPE    131    110    115    131
D41V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               131
  CLUS_2               3               110
  CLUS_3              10               115
  CLUS_4               6               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      3      9      7
  1Q LOSS WILD-TYPE    132    101    178     65
D41V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               132
  CLUS_2               3               101
  CLUS_3               9               178
  CLUS_4               7                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 CLUS_4
  1Q LOSS MUTATED        6      9      5      3
  1Q LOSS WILD-TYPE    149     98    132     97
D41V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6               149
  CLUS_2               9                98
  CLUS_3               5               132
  CLUS_4               3                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        2      4      6      7      3      0      1
  1Q LOSS WILD-TYPE    111     90     63    139     31     18     24
D41V11, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               111
  CLUS_2               4                90
  CLUS_3               6                63
  CLUS_4               7               139
  CLUS_5               3                31
  CLUS_6               0                18
  CLUS_7               1                24
[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 LOSS MUTATED        4     10      6      3
  1Q LOSS WILD-TYPE    144    131    106     95
D41V12, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               144
  CLUS_2              10               131
  CLUS_3               6               106
  CLUS_4               3                95
[1] 4 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 = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        1      0      0
  2P LOSS WILD-TYPE      8     10      8
D42V1, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5143        TCGA-DH-5144 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        0      1      0      0
  2P LOSS WILD-TYPE      7      6      7      6
D42V2, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5143        TCGA-DH-5144 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       17      2      2
  2P LOSS WILD-TYPE    151    116    224
D42V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              17               151
  CLUS_2               2               116
  CLUS_3               2               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
  2P LOSS MUTATED       15      2      2      2
  2P LOSS WILD-TYPE    208     70     55    153
D42V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              15               208
  CLUS_2               2                70
  CLUS_3               2                55
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      5      1      3
  2P LOSS WILD-TYPE     49     57     67     71
D42V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                49
  CLUS_2               5                57
  CLUS_3               1                67
  CLUS_4               3                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      6      3
  2P LOSS WILD-TYPE     64    125     55
D42V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                64
  CLUS_2               6               125
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        6      9      2      3      1
  2P LOSS WILD-TYPE    129    103    106    124     27
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               129
  CLUS_2               9               103
  CLUS_3               2               106
  CLUS_4               3               124
  CLUS_5               1                27
[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        6     10      2      3
  2P LOSS WILD-TYPE    129    103    123    134
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               129
  CLUS_2              10               103
  CLUS_3               2               123
  CLUS_4               3               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      8      5      1
  2P LOSS WILD-TYPE    131     96    182     71
D42V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5               131
  CLUS_2               8                96
  CLUS_3               5               182
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      1      5      5
  2P LOSS WILD-TYPE    147    106    132     95
D42V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               8               147
  CLUS_2               1               106
  CLUS_3               5               132
  CLUS_4               5                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        6      5      1      4      1      2      0
  2P LOSS WILD-TYPE    107     89     68    142     33     16     25
D42V11, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               107
  CLUS_2               5                89
  CLUS_3               1                68
  CLUS_4               4               142
  CLUS_5               1                33
  CLUS_6               2                16
  CLUS_7               0                25
[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        9      2      3      5
  2P LOSS WILD-TYPE    139    139    109     93
D42V12, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9               139
  CLUS_2               2               139
  CLUS_3               3               109
  CLUS_4               5                93
[1] 4 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 = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        1      0      1
  2Q LOSS WILD-TYPE      8     10      7
D43V1, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        0      2      0      0
  2Q LOSS WILD-TYPE      7      5      7      6
D43V2, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       15      1      2
  2Q LOSS WILD-TYPE    153    117    224
D43V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              15               153
  CLUS_2               1               117
  CLUS_3               2               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
  2Q LOSS MUTATED       15      0      1      2
  2Q LOSS WILD-TYPE    208     72     56    153
D43V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              15               208
  CLUS_2               0                72
  CLUS_3               1                56
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      2
  2Q LOSS WILD-TYPE     50     57     68     72
D43V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                50
  CLUS_2               5                57
  CLUS_3               0                68
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        1      6      2
  2Q LOSS WILD-TYPE     66    125     56
D43V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                66
  CLUS_2               6               125
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5      7      2      3      1
  2Q LOSS WILD-TYPE    130    105    106    124     27
D43V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               130
  CLUS_2               7               105
  CLUS_3               2               106
  CLUS_4               3               124
  CLUS_5               1                27
[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        5      8      2      3
  2Q LOSS WILD-TYPE    130    105    123    134
D43V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               130
  CLUS_2               8               105
  CLUS_3               2               123
  CLUS_4               3               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      9      4      1
  2Q LOSS WILD-TYPE    133     95    183     71
D43V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               133
  CLUS_2               9                95
  CLUS_3               4               183
  CLUS_4               1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      1      5      4
  2Q LOSS WILD-TYPE    148    106    132     96
D43V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               7               148
  CLUS_2               1               106
  CLUS_3               5               132
  CLUS_4               4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3      6      1      4      2      1      0
  2Q LOSS WILD-TYPE    110     88     68    142     32     17     25
D43V11, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               110
  CLUS_2               6                88
  CLUS_3               1                68
  CLUS_4               4               142
  CLUS_5               2                32
  CLUS_6               1                17
  CLUS_7               0                25
[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        9      3      2      3
  2Q LOSS WILD-TYPE    139    138    110     95
D43V12, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9               139
  CLUS_2               3               138
  CLUS_3               2               110
  CLUS_4               3                95
[1] 4 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 = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        0      0      1
  3P LOSS WILD-TYPE      9     10      7
D44V1, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      1      0      0
  3P LOSS WILD-TYPE      7      6      7      6
D44V2, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       18      8      4
  3P LOSS WILD-TYPE    150    110    222
D44V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              18               150
  CLUS_2               8               110
  CLUS_3               4               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
  3P LOSS MUTATED       16      7      2      5
  3P LOSS WILD-TYPE    207     65     55    150
D44V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              16               207
  CLUS_2               7                65
  CLUS_3               2                55
  CLUS_4               5               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        2      8      0      3
  3P LOSS WILD-TYPE     50     54     68     71
D44V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                50
  CLUS_2               8                54
  CLUS_3               0                68
  CLUS_4               3                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        1      9      3
  3P LOSS WILD-TYPE     66    122     55
D44V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                66
  CLUS_2               9               122
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9     13      3      5      0
  3P LOSS WILD-TYPE    126     99    105    122     28
D44V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2              13                99
  CLUS_3               3               105
  CLUS_4               5               122
  CLUS_5               0                28
[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        9     13      4      4
  3P LOSS WILD-TYPE    126    100    121    133
D44V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2              13               100
  CLUS_3               4               121
  CLUS_4               4               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9     12      4      3
  3P LOSS WILD-TYPE    127     92    183     69
D44V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               127
  CLUS_2              12                92
  CLUS_3               4               183
  CLUS_4               3                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 CLUS_4
  3P LOSS MUTATED       13      4      2      9
  3P LOSS WILD-TYPE    142    103    135     91
D44V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              13               142
  CLUS_2               4               103
  CLUS_3               2               135
  CLUS_4               9                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  3P LOSS MUTATED        7     12      2      3      2      2      0
  3P LOSS WILD-TYPE    106     82     67    143     32     16     25
D44V11, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               7               106
  CLUS_2              12                82
  CLUS_3               2                67
  CLUS_4               3               143
  CLUS_5               2                32
  CLUS_6               2                16
  CLUS_7               0                25
[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
  3P LOSS MUTATED       14      6      1      7
  3P LOSS WILD-TYPE    134    135    111     91
D44V12, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              14               134
  CLUS_2               6               135
  CLUS_3               1               111
  CLUS_4               7                91
[1] 4 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 = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        1      0      2
  3Q LOSS WILD-TYPE      8     10      6
D45V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                10
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        1      1      0      1
  3Q LOSS WILD-TYPE      6      6      7      5
D45V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 6
  CLUS_3               0                 7
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       18      5      5
  3Q LOSS WILD-TYPE    150    113    221
D45V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              18               150
  CLUS_2               5               113
  CLUS_3               5               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
  3Q LOSS MUTATED       17      5      2      4
  3Q LOSS WILD-TYPE    206     67     55    151
D45V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              17               206
  CLUS_2               5                67
  CLUS_3               2                55
  CLUS_4               4               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      8      4      3
  3Q LOSS WILD-TYPE     49     54     64     71
D45V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                49
  CLUS_2               8                54
  CLUS_3               4                64
  CLUS_4               3                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        4     11      3
  3Q LOSS WILD-TYPE     63    120     55
D45V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4                63
  CLUS_2              11               120
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9     11      2      6      0
  3Q LOSS WILD-TYPE    126    101    106    121     28
D45V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2              11               101
  CLUS_3               2               106
  CLUS_4               6               121
  CLUS_5               0                28
[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        9     11      3      5
  3Q LOSS WILD-TYPE    126    102    122    132
D45V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2              11               102
  CLUS_3               3               122
  CLUS_4               5               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8     10      7      2
  3Q LOSS WILD-TYPE    128     94    180     70
D45V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8               128
  CLUS_2              10                94
  CLUS_3               7               180
  CLUS_4               2                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10      4      4      9
  3Q LOSS WILD-TYPE    145    103    133     91
D45V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              10               145
  CLUS_2               4               103
  CLUS_3               4               133
  CLUS_4               9                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7     10      2      5      1      2      0
  3Q LOSS WILD-TYPE    106     84     67    141     33     16     25
D45V11, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               7               106
  CLUS_2              10                84
  CLUS_3               2                67
  CLUS_4               5               141
  CLUS_5               1                33
  CLUS_6               2                16
  CLUS_7               0                25
[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       13      4      2      8
  3Q LOSS WILD-TYPE    135    137    110     90
D45V12, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              13               135
  CLUS_2               4               137
  CLUS_3               2               110
  CLUS_4               8                90
[1] 4 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 = 4P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        2      3      2
  4P LOSS WILD-TYPE      7      7      6
D46V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                 7
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        2      3      1      1
  4P LOSS WILD-TYPE      5      4      6      5
D46V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               3                 4
  CLUS_3               1                 6
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       18     12     41
  4P LOSS WILD-TYPE    150    106    185
D46V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              18               150
  CLUS_2              12               106
  CLUS_3              41               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED       25      1      1     44
  4P LOSS WILD-TYPE    198     71     56    111
D46V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              25               198
  CLUS_2               1                71
  CLUS_3               1                56
  CLUS_4              44               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
  4P LOSS MUTATED        4      9     13     12
  4P LOSS WILD-TYPE     48     53     55     62
D46V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                48
  CLUS_2               9                53
  CLUS_3              13                55
  CLUS_4              12                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       10     20      8
  4P LOSS WILD-TYPE     57    111     50
D46V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              10                57
  CLUS_2              20               111
  CLUS_3               8                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P LOSS MUTATED       15      5     30     17      3
  4P LOSS WILD-TYPE    120    107     78    110     25
D46V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              15               120
  CLUS_2               5               107
  CLUS_3              30                78
  CLUS_4              17               110
  CLUS_5               3                25
[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 LOSS MUTATED       13      4     37     16
  4P LOSS WILD-TYPE    122    109     88    121
D46V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13               122
  CLUS_2               4               109
  CLUS_3              37                88
  CLUS_4              16               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       10     12     24     24
  4P LOSS WILD-TYPE    126     92    163     48
D46V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              10               126
  CLUS_2              12                92
  CLUS_3              24               163
  CLUS_4              24                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
  4P LOSS MUTATED       21     31     13      5
  4P LOSS WILD-TYPE    134     76    124     95
D46V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              21               134
  CLUS_2              31                76
  CLUS_3              13               124
  CLUS_4               5                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  4P LOSS MUTATED       12      8     19     20      7      1      3
  4P LOSS WILD-TYPE    101     86     50    126     27     17     22
D46V11, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              12               101
  CLUS_2               8                86
  CLUS_3              19                50
  CLUS_4              20               126
  CLUS_5               7                27
  CLUS_6               1                17
  CLUS_7               3                22
[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
  4P LOSS MUTATED       16     39     12      3
  4P LOSS WILD-TYPE    132    102    100     95
D46V12, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              16               132
  CLUS_2              39               102
  CLUS_3              12               100
  CLUS_4               3                95
[1] 4 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 = 4Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        3      3      2
  4Q LOSS WILD-TYPE      6      7      6
D47V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               3                 7
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        2      4      1      1
  4Q LOSS WILD-TYPE      5      3      6      5
D47V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               4                 3
  CLUS_3               1                 6
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       32     11     48
  4Q LOSS WILD-TYPE    136    107    178
D47V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              32               136
  CLUS_2              11               107
  CLUS_3              48               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       39      1      4     47
  4Q LOSS WILD-TYPE    184     71     53    108
D47V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              39               184
  CLUS_2               1                71
  CLUS_3               4                53
  CLUS_4              47               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        5     11     15     16
  4Q LOSS WILD-TYPE     47     51     53     58
D47V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                47
  CLUS_2              11                51
  CLUS_3              15                53
  CLUS_4              16                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       13     23     11
  4Q LOSS WILD-TYPE     54    108     47
D47V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              13                54
  CLUS_2              23               108
  CLUS_3              11                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q LOSS MUTATED       21     10     32     25      2
  4Q LOSS WILD-TYPE    114    102     76    102     26
D47V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              21               114
  CLUS_2              10               102
  CLUS_3              32                76
  CLUS_4              25               102
  CLUS_5               2                26
[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 LOSS MUTATED       18      9     39     24
  4Q LOSS WILD-TYPE    117    104     86    113
D47V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              18               117
  CLUS_2               9               104
  CLUS_3              39                86
  CLUS_4              24               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
  4Q LOSS MUTATED       11     17     37     25
  4Q LOSS WILD-TYPE    125     87    150     47
D47V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               125
  CLUS_2              17                87
  CLUS_3              37               150
  CLUS_4              25                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
  4Q LOSS MUTATED       25     37     20      8
  4Q LOSS WILD-TYPE    130     70    117     92
D47V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              25               130
  CLUS_2              37                70
  CLUS_3              20               117
  CLUS_4               8                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  4Q LOSS MUTATED       15     10     19     30      7      5      4
  4Q LOSS WILD-TYPE     98     84     50    116     27     13     21
D47V11, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              15                98
  CLUS_2              10                84
  CLUS_3              19                50
  CLUS_4              30               116
  CLUS_5               7                27
  CLUS_6               5                13
  CLUS_7               4                21
[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
  4Q LOSS MUTATED       22     45     19      4
  4Q LOSS WILD-TYPE    126     96     93     94
D47V12, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              22               126
  CLUS_2              45                96
  CLUS_3              19                93
  CLUS_4               4                94
[1] 4 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 = 5P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED        2      2      3
  5P LOSS WILD-TYPE      7      8      5
D48V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 8
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED        1      4      0      2
  5P LOSS WILD-TYPE      6      3      7      4
D48V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               4                 3
  CLUS_3               0                 7
  CLUS_4               2                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       26      5      3
  5P LOSS WILD-TYPE    142    113    223
D48V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              26               142
  CLUS_2               5               113
  CLUS_3               3               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
  5P LOSS MUTATED       26      3      3      2
  5P LOSS WILD-TYPE    197     69     54    153
D48V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              26               197
  CLUS_2               3                69
  CLUS_3               3                54
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        3      5      5      7
  5P LOSS WILD-TYPE     49     57     63     67
D48V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                49
  CLUS_2               5                57
  CLUS_3               5                63
  CLUS_4               7                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
  5P LOSS MUTATED        5     10      5
  5P LOSS WILD-TYPE     62    121     53
D48V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                62
  CLUS_2              10               121
  CLUS_3               5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       10     10      2      9      2
  5P LOSS WILD-TYPE    125    102    106    118     26
D48V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2              10               102
  CLUS_3               2               106
  CLUS_4               9               118
  CLUS_5               2                26
[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 LOSS MUTATED       10     10      2     11
  5P LOSS WILD-TYPE    125    103    123    126
D48V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2              10               103
  CLUS_3               2               123
  CLUS_4              11               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        7     13     12      2
  5P LOSS WILD-TYPE    129     91    175     70
D48V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               7               129
  CLUS_2              13                91
  CLUS_3              12               175
  CLUS_4               2                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       11      4      9     10
  5P LOSS WILD-TYPE    144    103    128     90
D48V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              11               144
  CLUS_2               4               103
  CLUS_3               9               128
  CLUS_4              10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        7      6      3     10      2      4      2
  5P LOSS WILD-TYPE    106     88     66    136     32     14     23
D48V11, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               7               106
  CLUS_2               6                88
  CLUS_3               3                66
  CLUS_4              10               136
  CLUS_5               2                32
  CLUS_6               4                14
  CLUS_7               2                23
[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 LOSS MUTATED       12      6      5     11
  5P LOSS WILD-TYPE    136    135    107     87
D48V12, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              12               136
  CLUS_2               6               135
  CLUS_3               5               107
  CLUS_4              11                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"

Clustering(49) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        1      2      3
  5Q LOSS WILD-TYPE      8      8      5
D49V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 8
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        1      3      0      2
  5Q LOSS WILD-TYPE      6      4      7      4
D49V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                 4
  CLUS_3               0                 7
  CLUS_4               2                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       27      3      3
  5Q LOSS WILD-TYPE    141    115    223
D49V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              27               141
  CLUS_2               3               115
  CLUS_3               3               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
  5Q LOSS MUTATED       26      3      2      2
  5Q LOSS WILD-TYPE    197     69     55    153
D49V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              26               197
  CLUS_2               3                69
  CLUS_3               2                55
  CLUS_4               2               153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        5      9      4      1
  5Q LOSS WILD-TYPE     47     53     64     73
D49V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               5                47
  CLUS_2               9                53
  CLUS_3               4                64
  CLUS_4               1                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        7     11      1
  5Q LOSS WILD-TYPE     60    120     57
D49V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7                60
  CLUS_2              11               120
  CLUS_3               1                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       10     13      2      5      2
  5Q LOSS WILD-TYPE    125     99    106    122     26
D49V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2              13                99
  CLUS_3               2               106
  CLUS_4               5               122
  CLUS_5               2                26
[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 LOSS MUTATED        9     14      2      7
  5Q LOSS WILD-TYPE    126     99    123    130
D49V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2              14                99
  CLUS_3               2               123
  CLUS_4               7               130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        6     18      9      0
  5Q LOSS WILD-TYPE    130     86    178     72
D49V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6               130
  CLUS_2              18                86
  CLUS_3               9               178
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       12      3      7     11
  5Q LOSS WILD-TYPE    143    104    130     89
D49V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              12               143
  CLUS_2               3               104
  CLUS_3               7               130
  CLUS_4              11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        8      8      1      7      3      4      2
  5Q LOSS WILD-TYPE    105     86     68    139     31     14     23
D49V11, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8               105
  CLUS_2               8                86
  CLUS_3               1                68
  CLUS_4               7               139
  CLUS_5               3                31
  CLUS_6               4                14
  CLUS_7               2                23
[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 LOSS MUTATED       15      6      1     11
  5Q LOSS WILD-TYPE    133    135    111     87
D49V12, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              15               133
  CLUS_2               6               135
  CLUS_3               1               111
  CLUS_4              11                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"

Clustering(50) Variable = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        0      0      1
  6P LOSS WILD-TYPE      9     10      7
D50V1, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        0      1      0      0
  6P LOSS WILD-TYPE      7      6      7      6
D50V2, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       11     14      5
  6P LOSS WILD-TYPE    157    104    221
D50V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               157
  CLUS_2              14               104
  CLUS_3               5               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
  6P LOSS MUTATED       11      7      6      6
  6P LOSS WILD-TYPE    212     65     51    149
D50V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               212
  CLUS_2               7                65
  CLUS_3               6                51
  CLUS_4               6               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      5      1      4
  6P LOSS WILD-TYPE     47     57     67     70
D50V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                47
  CLUS_2               5                57
  CLUS_3               1                67
  CLUS_4               4                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      8      2
  6P LOSS WILD-TYPE     62    123     56
D50V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                62
  CLUS_2               8               123
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7     11      5      5      1
  6P LOSS WILD-TYPE    128    101    103    122     27
D50V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               128
  CLUS_2              11               101
  CLUS_3               5               103
  CLUS_4               5               122
  CLUS_5               1                27
[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        7     10      6      6
  6P LOSS WILD-TYPE    128    103    119    131
D50V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               128
  CLUS_2              10               103
  CLUS_3               6               119
  CLUS_4               6               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      6      9      4
  6P LOSS WILD-TYPE    125     98    178     68
D50V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               125
  CLUS_2               6                98
  CLUS_3               9               178
  CLUS_4               4                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 CLUS_4
  6P LOSS MUTATED        8      5      6     11
  6P LOSS WILD-TYPE    147    102    131     89
D50V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8               147
  CLUS_2               5               102
  CLUS_3               6               131
  CLUS_4              11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  6P LOSS MUTATED        6      9      3      8      1      2      1
  6P LOSS WILD-TYPE    107     85     66    138     33     16     24
D50V11, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6               107
  CLUS_2               9                85
  CLUS_3               3                66
  CLUS_4               8               138
  CLUS_5               1                33
  CLUS_6               2                16
  CLUS_7               1                24
[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
  6P LOSS MUTATED        8      7      2     13
  6P LOSS WILD-TYPE    140    134    110     85
D50V12, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8               140
  CLUS_2               7               134
  CLUS_3               2               110
  CLUS_4              13                85
[1] 4 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 = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        2      0      0
  6Q LOSS WILD-TYPE      7     10      8
D51V1, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        2      0      0      0
  6Q LOSS WILD-TYPE      5      7      7      6
D51V2, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       29     26      8
  6Q LOSS WILD-TYPE    139     92    218
D51V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              29               139
  CLUS_2              26                92
  CLUS_3               8               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
  6Q LOSS MUTATED       36     11      9      7
  6Q LOSS WILD-TYPE    187     61     48    148
D51V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              36               187
  CLUS_2              11                61
  CLUS_3               9                48
  CLUS_4               7               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7     13      6      9
  6Q LOSS WILD-TYPE     45     49     62     65
D51V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                45
  CLUS_2              13                49
  CLUS_3               6                62
  CLUS_4               9                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
  6Q LOSS MUTATED        7     21      7
  6Q LOSS WILD-TYPE     60    110     51
D51V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                60
  CLUS_2              21               110
  CLUS_3               7                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       18     21      7     13      3
  6Q LOSS WILD-TYPE    117     91    101    114     25
D51V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              18               117
  CLUS_2              21                91
  CLUS_3               7               101
  CLUS_4              13               114
  CLUS_5               3                25
[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       20     20      7     15
  6Q LOSS WILD-TYPE    115     93    118    122
D51V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              20               115
  CLUS_2              20                93
  CLUS_3               7               118
  CLUS_4              15               122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       27     15     16      4
  6Q LOSS WILD-TYPE    109     89    171     68
D51V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              27               109
  CLUS_2              15                89
  CLUS_3              16               171
  CLUS_4               4                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 CLUS_4
  6Q LOSS MUTATED       21      7     13     21
  6Q LOSS WILD-TYPE    134    100    124     79
D51V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              21               134
  CLUS_2               7               100
  CLUS_3              13               124
  CLUS_4              21                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       19     19      3     15      2      3      1
  6Q LOSS WILD-TYPE     94     75     66    131     32     15     24
D51V11, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              19                94
  CLUS_2              19                75
  CLUS_3               3                66
  CLUS_4              15               131
  CLUS_5               2                32
  CLUS_6               3                15
  CLUS_7               1                24
[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       25      9     10     18
  6Q LOSS WILD-TYPE    123    132    102     80
D51V12, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              25               123
  CLUS_2               9               132
  CLUS_3              10               102
  CLUS_4              18                80
[1] 4 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 = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        0      0      0
  7P LOSS WILD-TYPE      9     10      8
D52V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        0      0      0      0
  7P LOSS WILD-TYPE      7      7      7      6
D52V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        2      0      1
  7P LOSS WILD-TYPE    166    118    225
D52V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               166
  CLUS_2               0               118
  CLUS_3               1               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
  7P LOSS MUTATED        2      0      1      0
  7P LOSS WILD-TYPE    221     72     56    155
D52V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               221
  CLUS_2               0                72
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      0      0      0
  7P LOSS WILD-TYPE     51     62     68     74
D52V5, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-7641        TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8107        TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8113        TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5R5        TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7486        TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7491        TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8320        TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-A5KK        TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5ET        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5F1        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        0      1      0
  7P LOSS WILD-TYPE     67    130     58
D52V6, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-7641        TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8107        TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8113        TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5R5        TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7486        TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7491        TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8320        TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-A5KK        TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5ET        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5F1        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P LOSS MUTATED        1      1      0      1      0
  7P LOSS WILD-TYPE    134    111    108    126     28
D52V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               1               111
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               0                28
[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 LOSS MUTATED        1      1      0      1
  7P LOSS WILD-TYPE    134    112    125    136
D52V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               1               112
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      1      1      0
  7P LOSS WILD-TYPE    135    103    186     72
D52V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               135
  CLUS_2               1               103
  CLUS_3               1               186
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        2      0      1      0
  7P LOSS WILD-TYPE    153    107    136    100
D52V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               153
  CLUS_2               0               107
  CLUS_3               1               136
  CLUS_4               0               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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P LOSS MUTATED        1      1      0      1      0      0      0
  7P LOSS WILD-TYPE    112     93     69    145     34     18     25
D52V11, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               112
  CLUS_2               1                93
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               0                18
  CLUS_7               0                25
[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 LOSS MUTATED        2      1      0      0
  7P LOSS WILD-TYPE    146    140    112     98
D52V12, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               1               140
  CLUS_3               0               112
  CLUS_4               0                98
[1] 4 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 = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        0      0      0
  7Q LOSS WILD-TYPE      9     10      8
D53V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        0      0      0      0
  7Q LOSS WILD-TYPE      7      7      7      6
D53V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        3      0      0
  7Q LOSS WILD-TYPE    165    118    226
D53V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3               165
  CLUS_2               0               118
  CLUS_3               0               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
  7Q LOSS MUTATED        2      0      1      0
  7Q LOSS WILD-TYPE    221     72     56    155
D53V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2               221
  CLUS_2               0                72
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      0      0      0
  7Q LOSS WILD-TYPE     51     62     68     74
D53V5, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-7641        TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8107        TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8113        TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-A5R5        TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-7486        TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-7491        TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-8320        TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-A5KK        TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5ET        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5F1        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        0      1      0
  7Q LOSS WILD-TYPE     67    130     58
D53V6, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1               255 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7298        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-8165        TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7634        TCGA-FG-7636        TCGA-FG-7638 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-7641        TCGA-FG-7643        TCGA-FG-8181        TCGA-FG-8182 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-8191        TCGA-FG-A4MT        TCGA-FG-A4MU 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A4MY        TCGA-FG-A60J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8107        TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-8113        TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HT-A5R5        TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-7486        TCGA-HW-7487        TCGA-HW-7489        TCGA-HW-7490 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-7491        TCGA-HW-7493        TCGA-HW-7495        TCGA-HW-8319 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-8320        TCGA-HW-8321        TCGA-HW-8322        TCGA-HW-A5KJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HW-A5KK        TCGA-HW-A5KM        TCGA-IK-7675        TCGA-IK-8125 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5ET        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-P5-A5F1        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED        0      2      0      1      0
  7Q LOSS WILD-TYPE    135    110    108    126     28
D53V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               135
  CLUS_2               2               110
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               0                28
[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 LOSS MUTATED        0      2      0      1
  7Q LOSS WILD-TYPE    135    111    125    136
D53V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               135
  CLUS_2               2               111
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      1      1      0
  7Q LOSS WILD-TYPE    135    103    186     72
D53V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               135
  CLUS_2               1               103
  CLUS_3               1               186
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      0      1      1
  7Q LOSS WILD-TYPE    154    107    136     99
D53V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               154
  CLUS_2               0               107
  CLUS_3               1               136
  CLUS_4               1                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        0      2      0      1      0      0      0
  7Q LOSS WILD-TYPE    113     92     69    145     34     18     25
D53V11, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               113
  CLUS_2               2                92
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               0                18
  CLUS_7               0                25
[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 LOSS MUTATED        2      1      0      0
  7Q LOSS WILD-TYPE    146    140    112     98
D53V12, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               1               140
  CLUS_3               0               112
  CLUS_4               0                98
[1] 4 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 = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      2      1
  8P LOSS WILD-TYPE      9      8      7
D54V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                 8
  CLUS_3               1                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        0      3      0      0
  8P LOSS WILD-TYPE      7      4      7      6
D54V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               3                 4
  CLUS_3               0                 7
  CLUS_4               0                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        7     10      0
  8P LOSS WILD-TYPE    161    108    226
D54V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7               161
  CLUS_2              10               108
  CLUS_3               0               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
  8P LOSS MUTATED        7      9      1      0
  8P LOSS WILD-TYPE    216     63     56    155
D54V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7               216
  CLUS_2               9                63
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      0      2
  8P LOSS WILD-TYPE     51     56     68     72
D54V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                51
  CLUS_2               6                56
  CLUS_3               0                68
  CLUS_4               2                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      6      3
  8P LOSS WILD-TYPE     67    125     55
D54V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               6               125
  CLUS_3               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     13      0      3      1
  8P LOSS WILD-TYPE    135     99    108    124     27
D54V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               135
  CLUS_2              13                99
  CLUS_3               0               108
  CLUS_4               3               124
  CLUS_5               1                27
[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     13      0      3
  8P LOSS WILD-TYPE    134    100    125    134
D54V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2              13               100
  CLUS_3               0               125
  CLUS_4               3               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      6      4      0
  8P LOSS WILD-TYPE    129     98    183     72
D54V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7               129
  CLUS_2               6                98
  CLUS_3               4               183
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      1      1     10
  8P LOSS WILD-TYPE    150    106    136     90
D54V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5               150
  CLUS_2               1               106
  CLUS_3               1               136
  CLUS_4              10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        0     12      0      3      0      1      1
  8P LOSS WILD-TYPE    113     82     69    143     34     17     24
D54V11, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               113
  CLUS_2              12                82
  CLUS_3               0                69
  CLUS_4               3               143
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               1                24
[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 LOSS MUTATED        6      1      1      9
  8P LOSS WILD-TYPE    142    140    111     89
D54V12, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               6               142
  CLUS_2               1               140
  CLUS_3               1               111
  CLUS_4               9                89
[1] 4 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 = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      2      0
  8Q LOSS WILD-TYPE      9      8      8
D55V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        0      2      0      0
  8Q LOSS WILD-TYPE      7      5      7      6
D55V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        3      8      0
  8Q LOSS WILD-TYPE    165    110    226
D55V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3               165
  CLUS_2               8               110
  CLUS_3               0               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
  8Q LOSS MUTATED        2      8      1      0
  8Q LOSS WILD-TYPE    221     64     56    155
D55V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2               221
  CLUS_2               8                64
  CLUS_3               1                56
  CLUS_4               0               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      0      1
  8Q LOSS WILD-TYPE     51     58     68     73
D55V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                51
  CLUS_2               4                58
  CLUS_3               0                68
  CLUS_4               1                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      4      2
  8Q LOSS WILD-TYPE     67    127     56
D55V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               4               127
  CLUS_3               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      9      0      1      1
  8Q LOSS WILD-TYPE    135    103    108    126     27
D55V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               135
  CLUS_2               9               103
  CLUS_3               0               108
  CLUS_4               1               126
  CLUS_5               1                27
[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      9      0      1
  8Q LOSS WILD-TYPE    134    104    125    136
D55V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               9               104
  CLUS_3               0               125
  CLUS_4               1               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      3      2      0
  8Q LOSS WILD-TYPE    130    101    185     72
D55V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6               130
  CLUS_2               3               101
  CLUS_3               2               185
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      1      0      7
  8Q LOSS WILD-TYPE    152    106    137     93
D55V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3               152
  CLUS_2               1               106
  CLUS_3               0               137
  CLUS_4               7                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        0      8      0      1      0      1      1
  8Q LOSS WILD-TYPE    113     86     69    145     34     17     24
D55V11, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               113
  CLUS_2               8                86
  CLUS_3               0                69
  CLUS_4               1               145
  CLUS_5               0                34
  CLUS_6               1                17
  CLUS_7               1                24
[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 LOSS MUTATED        3      1      0      7
  8Q LOSS WILD-TYPE    145    140    112     91
D55V12, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3               145
  CLUS_2               1               140
  CLUS_3               0               112
  CLUS_4               7                91
[1] 4 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 = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        1      1      3
  9P LOSS WILD-TYPE      8      9      5
D56V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 9
  CLUS_3               3                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED        1      3      0      1
  9P LOSS WILD-TYPE      6      4      7      5
D56V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                 4
  CLUS_3               0                 7
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       47     45     26
  9P LOSS WILD-TYPE    121     73    200
D56V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              47               121
  CLUS_2              45                73
  CLUS_3              26               200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       61     27      7     21
  9P LOSS WILD-TYPE    162     45     50    134
D56V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              61               162
  CLUS_2              27                45
  CLUS_3               7                50
  CLUS_4              21               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9     24     17     14
  9P LOSS WILD-TYPE     43     38     51     60
D56V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                43
  CLUS_2              24                38
  CLUS_3              17                51
  CLUS_4              14                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
  9P LOSS MUTATED        9     41     14
  9P LOSS WILD-TYPE     58     90     44
D56V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                58
  CLUS_2              41                90
  CLUS_3              14                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       30     34     16     31      7
  9P LOSS WILD-TYPE    105     78     92     96     21
D56V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              30               105
  CLUS_2              34                78
  CLUS_3              16                92
  CLUS_4              31                96
  CLUS_5               7                21
[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       33     34     19     32
  9P LOSS WILD-TYPE    102     79    106    105
D56V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              33               102
  CLUS_2              34                79
  CLUS_3              19               106
  CLUS_4              32               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       28     24     45     18
  9P LOSS WILD-TYPE    108     80    142     54
D56V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              28               108
  CLUS_2              24                80
  CLUS_3              45               142
  CLUS_4              18                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       35     18     32     30
  9P LOSS WILD-TYPE    120     89    105     70
D56V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              35               120
  CLUS_2              18                89
  CLUS_3              32               105
  CLUS_4              30                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       28     23     10     36     10      5      3
  9P LOSS WILD-TYPE     85     71     59    110     24     13     22
D56V11, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              28                85
  CLUS_2              23                71
  CLUS_3              10                59
  CLUS_4              36               110
  CLUS_5              10                24
  CLUS_6               5                13
  CLUS_7               3                22
[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       40     23     23     29
  9P LOSS WILD-TYPE    108    118     89     69
D56V12, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              40               108
  CLUS_2              23               118
  CLUS_3              23                89
  CLUS_4              29                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"

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        0      1      1
  9Q LOSS WILD-TYPE      9      9      7
D57V1, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"9Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED        0      2      0      0
  9Q LOSS WILD-TYPE      7      5      7      6
D57V2, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311        TCGA-E1-5318 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"9Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       19     17     15
  9Q LOSS WILD-TYPE    149    101    211
D57V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              19               149
  CLUS_2              17               101
  CLUS_3              15               211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       20     12      4     14
  9Q LOSS WILD-TYPE    203     60     53    141
D57V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              20               203
  CLUS_2              12                60
  CLUS_3               4                53
  CLUS_4              14               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      8      5      5
  9Q LOSS WILD-TYPE     47     54     63     69
D57V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                47
  CLUS_2               8                54
  CLUS_3               5                63
  CLUS_4               5                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 LOSS MUTATED        3     14      6
  9Q LOSS WILD-TYPE     64    117     52
D57V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                64
  CLUS_2              14               117
  CLUS_3               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       10     16     11     11      3
  9Q LOSS WILD-TYPE    125     96     97    116     25
D57V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2              16                96
  CLUS_3              11                97
  CLUS_4              11               116
  CLUS_5               3                25
[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       11     17     14      9
  9Q LOSS WILD-TYPE    124     96    111    128
D57V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               124
  CLUS_2              17                96
  CLUS_3              14               111
  CLUS_4               9               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       14      8     16     11
  9Q LOSS WILD-TYPE    122     96    171     61
D57V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              14               122
  CLUS_2               8                96
  CLUS_3              16               171
  CLUS_4              11                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       16      9     13     11
  9Q LOSS WILD-TYPE    139     98    124     89
D57V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              16               139
  CLUS_2               9                98
  CLUS_3              13               124
  CLUS_4              11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8     10      7     15      5      2      2
  9Q LOSS WILD-TYPE    105     84     62    131     29     16     23
D57V11, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               8               105
  CLUS_2              10                84
  CLUS_3               7                62
  CLUS_4              15               131
  CLUS_5               5                29
  CLUS_6               2                16
  CLUS_7               2                23
[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       17     10      9     13
  9Q LOSS WILD-TYPE    131    131    103     85
D57V12, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              17               131
  CLUS_2              10               131
  CLUS_3               9               103
  CLUS_4              13                85
[1] 4 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 = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        0      1      2
  10P LOSS WILD-TYPE      9      9      6
D58V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                  9
  CLUS_3                2                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        1      1      0      1
  10P LOSS WILD-TYPE      6      6      7      5
D58V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  6
  CLUS_3                0                  7
  CLUS_4                1                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7     71      5
  10P LOSS WILD-TYPE    161     47    221
D58V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                161
  CLUS_2               71                 47
  CLUS_3                5                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
  10P LOSS MUTATED        4     62     10      6
  10P LOSS WILD-TYPE    219     10     47    149
D58V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                219
  CLUS_2               62                 10
  CLUS_3               10                 47
  CLUS_4                6                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4     24      3      6
  10P LOSS WILD-TYPE     48     38     65     68
D58V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 48
  CLUS_2               24                 38
  CLUS_3                3                 65
  CLUS_4                6                 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        3     29      5
  10P LOSS WILD-TYPE     64    102     53
D58V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2               29                102
  CLUS_3                5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1     64      1     12      4
  10P LOSS WILD-TYPE    134     48    107    115     24
D58V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2               64                 48
  CLUS_3                1                107
  CLUS_4               12                115
  CLUS_5                4                 24
[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        1     63      6     12
  10P LOSS WILD-TYPE    134     50    119    125
D58V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2               63                 50
  CLUS_3                6                119
  CLUS_4               12                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       34     24     19      4
  10P LOSS WILD-TYPE    102     80    168     68
D58V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               34                102
  CLUS_2               24                 80
  CLUS_3               19                168
  CLUS_4                4                 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 CLUS_4
  10P LOSS MUTATED        8      5      9     59
  10P LOSS WILD-TYPE    147    102    128     41
D58V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                147
  CLUS_2                5                102
  CLUS_3                9                128
  CLUS_4               59                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     52      2     15      6      2      2
  10P LOSS WILD-TYPE    111     42     67    131     28     16     23
D58V11, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                111
  CLUS_2               52                 42
  CLUS_3                2                 67
  CLUS_4               15                131
  CLUS_5                6                 28
  CLUS_6                2                 16
  CLUS_7                2                 23
[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        8      4      6     63
  10P LOSS WILD-TYPE    140    137    106     35
D58V12, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                140
  CLUS_2                4                137
  CLUS_3                6                106
  CLUS_4               63                 35
[1] 4 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 = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        0      1      2
  10Q LOSS WILD-TYPE      9      9      6
D59V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                  9
  CLUS_3                2                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        1      1      0      1
  10Q LOSS WILD-TYPE      6      6      7      5
D59V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  6
  CLUS_3                0                  7
  CLUS_4                1                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       18     72      6
  10Q LOSS WILD-TYPE    150     46    220
D59V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               18                150
  CLUS_2               72                 46
  CLUS_3                6                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
  10Q LOSS MUTATED       17     62     10      6
  10Q LOSS WILD-TYPE    206     10     47    149
D59V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               17                206
  CLUS_2               62                 10
  CLUS_3               10                 47
  CLUS_4                6                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6     27      7      7
  10Q LOSS WILD-TYPE     46     35     61     67
D59V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 46
  CLUS_2               27                 35
  CLUS_3                7                 61
  CLUS_4                7                 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
  10Q LOSS MUTATED        5     36      6
  10Q LOSS WILD-TYPE     62     95     52
D59V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                 62
  CLUS_2               36                 95
  CLUS_3                6                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q LOSS MUTATED        5     70      1     15      4
  10Q LOSS WILD-TYPE    130     42    107    112     24
D59V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                130
  CLUS_2               70                 42
  CLUS_3                1                107
  CLUS_4               15                112
  CLUS_5                4                 24
[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        6     68      6     15
  10Q LOSS WILD-TYPE    129     45    119    122
D59V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                129
  CLUS_2               68                 45
  CLUS_3                6                119
  CLUS_4               15                122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       37     30     23      5
  10Q LOSS WILD-TYPE     99     74    164     67
D59V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               37                 99
  CLUS_2               30                 74
  CLUS_3               23                164
  CLUS_4                5                 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 CLUS_4
  10Q LOSS MUTATED       12      7     11     65
  10Q LOSS WILD-TYPE    143    100    126     35
D59V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                143
  CLUS_2                7                100
  CLUS_3               11                126
  CLUS_4               65                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  10Q LOSS MUTATED        5     55      2     17      8      5      3
  10Q LOSS WILD-TYPE    108     39     67    129     26     13     22
D59V11, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                108
  CLUS_2               55                 39
  CLUS_3                2                 67
  CLUS_4               17                129
  CLUS_5                8                 26
  CLUS_6                5                 13
  CLUS_7                3                 22
[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
  10Q LOSS MUTATED       13      4      8     70
  10Q LOSS WILD-TYPE    135    137    104     28
D59V12, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                4                137
  CLUS_3                8                104
  CLUS_4               70                 28
[1] 4 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(60) Variable = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        2      2      1
  11P LOSS WILD-TYPE      7      8      7
D60V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                2                  8
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        1      4      0      0
  11P LOSS WILD-TYPE      6      3      7      6
D60V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                4                  3
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       49     11      3
  11P LOSS WILD-TYPE    119    107    223
D60V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               49                119
  CLUS_2               11                107
  CLUS_3                3                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
  11P LOSS MUTATED       47     12      4      0
  11P LOSS WILD-TYPE    176     60     53    155
D60V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               47                176
  CLUS_2               12                 60
  CLUS_3                4                 53
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10     15      5      6
  11P LOSS WILD-TYPE     42     47     63     68
D60V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 42
  CLUS_2               15                 47
  CLUS_3                5                 63
  CLUS_4                6                 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
  11P LOSS MUTATED        8     21      7
  11P LOSS WILD-TYPE     59    110     51
D60V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2               21                110
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       14     31      0     11      6
  11P LOSS WILD-TYPE    121     81    108    116     22
D60V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               14                121
  CLUS_2               31                 81
  CLUS_3                0                108
  CLUS_4               11                116
  CLUS_5                6                 22
[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       17     34      0     11
  11P LOSS WILD-TYPE    118     79    125    126
D60V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               17                118
  CLUS_2               34                 79
  CLUS_3                0                125
  CLUS_4               11                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12     25     18      4
  11P LOSS WILD-TYPE    124     79    169     68
D60V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               12                124
  CLUS_2               25                 79
  CLUS_3               18                169
  CLUS_4                4                 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 CLUS_4
  11P LOSS MUTATED       18      5     12     24
  11P LOSS WILD-TYPE    137    102    125     76
D60V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               18                137
  CLUS_2                5                102
  CLUS_3               12                125
  CLUS_4               24                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED       10     19      2     13      5      6      4
  11P LOSS WILD-TYPE    103     75     67    133     29     12     21
D60V11, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                103
  CLUS_2               19                 75
  CLUS_3                2                 67
  CLUS_4               13                133
  CLUS_5                5                 29
  CLUS_6                6                 12
  CLUS_7                4                 21
[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       22      6     10     21
  11P LOSS WILD-TYPE    126    135    102     77
D60V12, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               22                126
  CLUS_2                6                135
  CLUS_3               10                102
  CLUS_4               21                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        0      2      0
  11Q LOSS WILD-TYPE      9      8      8
D61V1, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5141         TCGA-DH-5142 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"11Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        0      2      0      0
  11Q LOSS WILD-TYPE      7      5      7      6
D61V2, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5141         TCGA-DH-5142 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"11Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       11      9      1
  11Q LOSS WILD-TYPE    157    109    225
D61V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               11                157
  CLUS_2                9                109
  CLUS_3                1                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
  11Q LOSS MUTATED        9      9      3      0
  11Q LOSS WILD-TYPE    214     63     54    155
D61V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                9                214
  CLUS_2                9                 63
  CLUS_3                3                 54
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      7      0      3
  11Q LOSS WILD-TYPE     49     55     68     71
D61V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                7                 55
  CLUS_3                0                 68
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        2      7      4
  11Q LOSS WILD-TYPE     65    124     54
D61V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                7                124
  CLUS_3                4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     16      0      3      1
  11Q LOSS WILD-TYPE    134     96    108    124     27
D61V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2               16                 96
  CLUS_3                0                108
  CLUS_4                3                124
  CLUS_5                1                 27
[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     16      0      3
  11Q LOSS WILD-TYPE    133     97    125    134
D61V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                133
  CLUS_2               16                 97
  CLUS_3                0                125
  CLUS_4                3                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      8      6      0
  11Q LOSS WILD-TYPE    130     96    181     72
D61V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                130
  CLUS_2                8                 96
  CLUS_3                6                181
  CLUS_4                0                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      1      3     12
  11Q LOSS WILD-TYPE    151    106    134     88
D61V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                151
  CLUS_2                1                106
  CLUS_3                3                134
  CLUS_4               12                 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 CLUS_6 CLUS_7
  11Q LOSS MUTATED        2     11      0      4      0      2      1
  11Q LOSS WILD-TYPE    111     83     69    142     34     16     24
D61V11, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                111
  CLUS_2               11                 83
  CLUS_3                0                 69
  CLUS_4                4                142
  CLUS_5                0                 34
  CLUS_6                2                 16
  CLUS_7                1                 24
[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        5      1      2     12
  11Q LOSS WILD-TYPE    143    140    110     86
D61V12, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                143
  CLUS_2                1                140
  CLUS_3                2                110
  CLUS_4               12                 86
[1] 4 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(62) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED        1      0      0
  12P LOSS WILD-TYPE      8     10      8
D62V1, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        1      0      0      0
  12P LOSS WILD-TYPE      6      7      7      6
D62V2, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       16      3      7
  12P LOSS WILD-TYPE    152    115    219
D62V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               16                152
  CLUS_2                3                115
  CLUS_3                7                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
  12P LOSS MUTATED       19      0      2      5
  12P LOSS WILD-TYPE    204     72     55    150
D62V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               19                204
  CLUS_2                0                 72
  CLUS_3                2                 55
  CLUS_4                5                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        4      2      5      3
  12P LOSS WILD-TYPE     48     60     63     71
D62V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 48
  CLUS_2                2                 60
  CLUS_3                5                 63
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED        4      7      3
  12P LOSS WILD-TYPE     63    124     55
D62V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                7                124
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        8      8      2      7      1
  12P LOSS WILD-TYPE    127    104    106    120     27
D62V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                127
  CLUS_2                8                104
  CLUS_3                2                106
  CLUS_4                7                120
  CLUS_5                1                 27
[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 LOSS MUTATED        8      9      4      5
  12P LOSS WILD-TYPE    127    104    121    132
D62V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                127
  CLUS_2                9                104
  CLUS_3                4                121
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        4     11      7      3
  12P LOSS WILD-TYPE    132     93    180     69
D62V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                132
  CLUS_2               11                 93
  CLUS_3                7                180
  CLUS_4                3                 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 CLUS_4
  12P LOSS MUTATED        6      4      7      8
  12P LOSS WILD-TYPE    149    103    130     92
D62V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                6                149
  CLUS_2                4                103
  CLUS_3                7                130
  CLUS_4                8                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        8      5      2      5      3      2      0
  12P LOSS WILD-TYPE    105     89     67    141     31     16     25
D62V11, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                105
  CLUS_2                5                 89
  CLUS_3                2                 67
  CLUS_4                5                141
  CLUS_5                3                 31
  CLUS_6                2                 16
  CLUS_7                0                 25
[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 LOSS MUTATED        8      5      4      8
  12P LOSS WILD-TYPE    140    136    108     90
D62V12, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                140
  CLUS_2                5                136
  CLUS_3                4                108
  CLUS_4                8                 90
[1] 4 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(63) Variable = 12Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED        1      1      1
  12Q LOSS WILD-TYPE      8      9      7
D63V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  9
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        1      2      0      0
  12Q LOSS WILD-TYPE      6      5      7      6
D63V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                  5
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       40      3      8
  12Q LOSS WILD-TYPE    128    115    218
D63V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               40                128
  CLUS_2                3                115
  CLUS_3                8                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
  12Q LOSS MUTATED       41      0      5      5
  12Q LOSS WILD-TYPE    182     72     52    150
D63V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               41                182
  CLUS_2                0                 72
  CLUS_3                5                 52
  CLUS_4                5                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        5      4      8      9
  12Q LOSS WILD-TYPE     47     58     60     65
D63V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 47
  CLUS_2                4                 58
  CLUS_3                8                 60
  CLUS_4                9                 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
  12Q LOSS MUTATED        4     12     10
  12Q LOSS WILD-TYPE     63    119     48
D63V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2               12                119
  CLUS_3               10                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       17     15      2     13      4
  12Q LOSS WILD-TYPE    118     97    106    114     24
D63V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               17                118
  CLUS_2               15                 97
  CLUS_3                2                106
  CLUS_4               13                114
  CLUS_5                4                 24
[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 LOSS MUTATED       21     15      4     11
  12Q LOSS WILD-TYPE    114     98    121    126
D63V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               21                114
  CLUS_2               15                 98
  CLUS_3                4                121
  CLUS_4               11                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        9     21     16      4
  12Q LOSS WILD-TYPE    127     83    171     68
D63V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                9                127
  CLUS_2               21                 83
  CLUS_3               16                171
  CLUS_4                4                 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 CLUS_4
  12Q LOSS MUTATED       17      6     14     13
  12Q LOSS WILD-TYPE    138    101    123     87
D63V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               17                138
  CLUS_2                6                101
  CLUS_3               14                123
  CLUS_4               13                 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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q LOSS MUTATED       16     11      3     10      5      3      2
  12Q LOSS WILD-TYPE     97     83     66    136     29     15     23
D63V11, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               16                 97
  CLUS_2               11                 83
  CLUS_3                3                 66
  CLUS_4               10                136
  CLUS_5                5                 29
  CLUS_6                3                 15
  CLUS_7                2                 23
[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 LOSS MUTATED       20      9      9     12
  12Q LOSS WILD-TYPE    128    132    103     86
D63V12, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               20                128
  CLUS_2                9                132
  CLUS_3                9                103
  CLUS_4               12                 86
[1] 4 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(64) Variable = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        5      3      1
  13Q LOSS WILD-TYPE      4      7      7
D64V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                  4
  CLUS_2                3                  7
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        2      7      0      0
  13Q LOSS WILD-TYPE      5      0      7      6
D64V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                7                  0
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       62     26     27
  13Q LOSS WILD-TYPE    106     92    199
D64V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               62                106
  CLUS_2               26                 92
  CLUS_3               27                199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       59     21      9     26
  13Q LOSS WILD-TYPE    164     51     48    129
D64V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               59                164
  CLUS_2               21                 51
  CLUS_3                9                 48
  CLUS_4               26                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7     23     16     15
  13Q LOSS WILD-TYPE     45     39     52     59
D64V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 45
  CLUS_2               23                 39
  CLUS_3               16                 52
  CLUS_4               15                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       13     34     14
  13Q LOSS WILD-TYPE     54     97     44
D64V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               13                 54
  CLUS_2               34                 97
  CLUS_3               14                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       31     38     16     25      5
  13Q LOSS WILD-TYPE    104     74     92    102     23
D64V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               31                104
  CLUS_2               38                 74
  CLUS_3               16                 92
  CLUS_4               25                102
  CLUS_5                5                 23
[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       33     38     19     25
  13Q LOSS WILD-TYPE    102     75    106    112
D64V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               33                102
  CLUS_2               38                 75
  CLUS_3               19                106
  CLUS_4               25                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
  13Q LOSS MUTATED       29     31     33     18
  13Q LOSS WILD-TYPE    107     73    154     54
D64V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               29                107
  CLUS_2               31                 73
  CLUS_3               33                154
  CLUS_4               18                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       37     24     22     28
  13Q LOSS WILD-TYPE    118     83    115     72
D64V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               37                118
  CLUS_2               24                 83
  CLUS_3               22                115
  CLUS_4               28                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       28     22     19     24      7      9      2
  13Q LOSS WILD-TYPE     85     72     50    122     27      9     23
D64V11, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               28                 85
  CLUS_2               22                 72
  CLUS_3               19                 50
  CLUS_4               24                122
  CLUS_5                7                 27
  CLUS_6                9                  9
  CLUS_7                2                 23
[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       37     26     19     29
  13Q LOSS WILD-TYPE    111    115     93     69
D64V12, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               37                111
  CLUS_2               26                115
  CLUS_3               19                 93
  CLUS_4               29                 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"

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED        3      1      1
  14Q LOSS WILD-TYPE      6      9      7
D65V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                1                  9
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED        1      3      0      1
  14Q LOSS WILD-TYPE      6      4      7      5
D65V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                3                  4
  CLUS_3                0                  7
  CLUS_4                1                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       26     32     22
  14Q LOSS WILD-TYPE    142     86    204
D65V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               26                142
  CLUS_2               32                 86
  CLUS_3               22                204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       29     24      7     19
  14Q LOSS WILD-TYPE    194     48     50    136
D65V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               29                194
  CLUS_2               24                 48
  CLUS_3                7                 50
  CLUS_4               19                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        5     16     11      7
  14Q LOSS WILD-TYPE     47     46     57     67
D65V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 47
  CLUS_2               16                 46
  CLUS_3               11                 57
  CLUS_4                7                 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
  14Q LOSS MUTATED        6     26      7
  14Q LOSS WILD-TYPE     61    105     51
D65V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 61
  CLUS_2               26                105
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       10     35     11     16      7
  14Q LOSS WILD-TYPE    125     77     97    111     21
D65V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               10                125
  CLUS_2               35                 77
  CLUS_3               11                 97
  CLUS_4               16                111
  CLUS_5                7                 21
[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 LOSS MUTATED       15     35     13     16
  14Q LOSS WILD-TYPE    120     78    112    121
D65V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               15                120
  CLUS_2               35                 78
  CLUS_3               13                112
  CLUS_4               16                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       33     12     21     10
  14Q LOSS WILD-TYPE    103     92    166     62
D65V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               33                103
  CLUS_2               12                 92
  CLUS_3               21                166
  CLUS_4               10                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       18     11     18     29
  14Q LOSS WILD-TYPE    137     96    119     71
D65V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               18                137
  CLUS_2               11                 96
  CLUS_3               18                119
  CLUS_4               29                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       12     31      9     16      4      2      2
  14Q LOSS WILD-TYPE    101     63     60    130     30     16     23
D65V11, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               12                101
  CLUS_2               31                 63
  CLUS_3                9                 60
  CLUS_4               16                130
  CLUS_5                4                 30
  CLUS_6                2                 16
  CLUS_7                2                 23
[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 LOSS MUTATED       22     12     14     28
  14Q LOSS WILD-TYPE    126    129     98     70
D65V12, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               22                126
  CLUS_2               12                129
  CLUS_3               14                 98
  CLUS_4               28                 70
[1] 4 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(66) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        1      2      1
  15Q LOSS WILD-TYPE      8      8      7
D66V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                  8
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      2      1      1
  15Q LOSS WILD-TYPE      7      5      6      5
D66V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                  5
  CLUS_3                1                  6
  CLUS_4                1                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       15      8     28
  15Q LOSS WILD-TYPE    153    110    198
D66V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               15                153
  CLUS_2                8                110
  CLUS_3               28                198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       19      3      1     28
  15Q LOSS WILD-TYPE    204     69     56    127
D66V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               19                204
  CLUS_2                3                 69
  CLUS_3                1                 56
  CLUS_4               28                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      9      6      4
  15Q LOSS WILD-TYPE     49     53     62     70
D66V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 49
  CLUS_2                9                 53
  CLUS_3                6                 62
  CLUS_4                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3     17      2
  15Q LOSS WILD-TYPE     64    114     56
D66V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2               17                114
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5     13     21      9      3
  15Q LOSS WILD-TYPE    130     99     87    118     25
D66V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                130
  CLUS_2               13                 99
  CLUS_3               21                 87
  CLUS_4                9                118
  CLUS_5                3                 25
[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        7     13     23      8
  15Q LOSS WILD-TYPE    128    100    102    129
D66V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                128
  CLUS_2               13                100
  CLUS_3               23                102
  CLUS_4                8                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15      9     14     10
  15Q LOSS WILD-TYPE    121     95    173     62
D66V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               15                121
  CLUS_2                9                 95
  CLUS_3               14                173
  CLUS_4               10                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15     15     11      7
  15Q LOSS WILD-TYPE    140     92    126     93
D66V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               15                140
  CLUS_2               15                 92
  CLUS_3               11                126
  CLUS_4                7                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5     14     11     11      4      1      2
  15Q LOSS WILD-TYPE    108     80     58    135     30     17     23
D66V11, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                108
  CLUS_2               14                 80
  CLUS_3               11                 58
  CLUS_4               11                135
  CLUS_5                4                 30
  CLUS_6                1                 17
  CLUS_7                2                 23
[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       13     22      7      6
  15Q LOSS WILD-TYPE    135    119    105     92
D66V12, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2               22                119
  CLUS_3                7                105
  CLUS_4                6                 92
[1] 4 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(67) Variable = 16P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED        0      0      2
  16P LOSS WILD-TYPE      9     10      6
D67V1, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED        0      1      0      1
  16P LOSS WILD-TYPE      7      6      7      5
D67V2, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED        6      7      1
  16P LOSS WILD-TYPE    162    111    225
D67V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                162
  CLUS_2                7                111
  CLUS_3                1                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
  16P LOSS MUTATED        6      5      1      2
  16P LOSS WILD-TYPE    217     67     56    153
D67V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                217
  CLUS_2                5                 67
  CLUS_3                1                 56
  CLUS_4                2                153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      3      2      2
  16P LOSS WILD-TYPE     51     59     66     72
D67V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                3                 59
  CLUS_3                2                 66
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED        0      6      2
  16P LOSS WILD-TYPE     67    125     56
D67V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                6                125
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        1      8      1      4      0
  16P LOSS WILD-TYPE    134    104    107    123     28
D67V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                8                104
  CLUS_3                1                107
  CLUS_4                4                123
  CLUS_5                0                 28
[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 LOSS MUTATED        1      6      2      5
  16P LOSS WILD-TYPE    134    107    123    132
D67V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                6                107
  CLUS_3                2                123
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        3      1      7      2
  16P LOSS WILD-TYPE    133    103    180     70
D67V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                133
  CLUS_2                1                103
  CLUS_3                7                180
  CLUS_4                2                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        3      3      3      4
  16P LOSS WILD-TYPE    152    104    134     96
D67V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                152
  CLUS_2                3                104
  CLUS_3                3                134
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        1      3      2      6      0      1      0
  16P LOSS WILD-TYPE    112     91     67    140     34     17     25
D67V11, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                112
  CLUS_2                3                 91
  CLUS_3                2                 67
  CLUS_4                6                140
  CLUS_5                0                 34
  CLUS_6                1                 17
  CLUS_7                0                 25
[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 LOSS MUTATED        4      3      2      4
  16P LOSS WILD-TYPE    144    138    110     94
D67V12, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                144
  CLUS_2                3                138
  CLUS_3                2                110
  CLUS_4                4                 94
[1] 4 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(68) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        0      0      2
  16Q LOSS WILD-TYPE      9     10      6
D68V1, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      1      0      1
  16Q LOSS WILD-TYPE      7      6      7      5
D68V2, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        9     10      3
  16Q LOSS WILD-TYPE    159    108    223
D68V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                9                159
  CLUS_2               10                108
  CLUS_3                3                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
  16Q LOSS MUTATED        9      9      1      3
  16Q LOSS WILD-TYPE    214     63     56    152
D68V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                9                214
  CLUS_2                9                 63
  CLUS_3                1                 56
  CLUS_4                3                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        1      5      4      2
  16Q LOSS WILD-TYPE     51     57     64     72
D68V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                5                 57
  CLUS_3                4                 64
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        0      9      3
  16Q LOSS WILD-TYPE     67    122     55
D68V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                9                122
  CLUS_3                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q LOSS MUTATED        4     12      2      4      0
  16Q LOSS WILD-TYPE    131    100    106    123     28
D68V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                131
  CLUS_2               12                100
  CLUS_3                2                106
  CLUS_4                4                123
  CLUS_5                0                 28
[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 LOSS MUTATED        4     10      3      5
  16Q LOSS WILD-TYPE    131    103    122    132
D68V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                131
  CLUS_2               10                103
  CLUS_3                3                122
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        7      2      8      3
  16Q LOSS WILD-TYPE    129    102    179     69
D68V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                129
  CLUS_2                2                102
  CLUS_3                8                179
  CLUS_4                3                 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 CLUS_4
  16Q LOSS MUTATED        5      4      3      8
  16Q LOSS WILD-TYPE    150    103    134     92
D68V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                150
  CLUS_2                4                103
  CLUS_3                3                134
  CLUS_4                8                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        4      5      3      6      0      2      0
  16Q LOSS WILD-TYPE    109     89     66    140     34     16     25
D68V11, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                109
  CLUS_2                5                 89
  CLUS_3                3                 66
  CLUS_4                6                140
  CLUS_5                0                 34
  CLUS_6                2                 16
  CLUS_7                0                 25
[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 LOSS MUTATED        5      4      2      9
  16Q LOSS WILD-TYPE    143    137    110     89
D68V12, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                143
  CLUS_2                4                137
  CLUS_3                2                110
  CLUS_4                9                 89
[1] 4 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(69) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        0      0      0
  17P LOSS WILD-TYPE      9     10      8
D69V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        0      0      0      0
  17P LOSS WILD-TYPE      7      7      7      6
D69V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        7      5      1
  17P LOSS WILD-TYPE    161    113    225
D69V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                161
  CLUS_2                5                113
  CLUS_3                1                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
  17P LOSS MUTATED        5      4      2      2
  17P LOSS WILD-TYPE    218     68     55    153
D69V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                218
  CLUS_2                4                 68
  CLUS_3                2                 55
  CLUS_4                2                153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      3      3      3
  17P LOSS WILD-TYPE     50     59     65     71
D69V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 50
  CLUS_2                3                 59
  CLUS_3                3                 65
  CLUS_4                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        2      7      2
  17P LOSS WILD-TYPE     65    124     56
D69V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                7                124
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      8      2      1      1
  17P LOSS WILD-TYPE    134    104    106    126     27
D69V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                8                104
  CLUS_3                2                106
  CLUS_4                1                126
  CLUS_5                1                 27
[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      7      2      1
  17P LOSS WILD-TYPE    132    106    123    136
D69V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                132
  CLUS_2                7                106
  CLUS_3                2                123
  CLUS_4                1                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      3      2      2
  17P LOSS WILD-TYPE    130    101    185     70
D69V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                130
  CLUS_2                3                101
  CLUS_3                2                185
  CLUS_4                2                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        4      2      0      7
  17P LOSS WILD-TYPE    151    105    137     93
D69V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                151
  CLUS_2                2                105
  CLUS_3                0                137
  CLUS_4                7                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      7      1      1      1      0      1
  17P LOSS WILD-TYPE    111     87     68    145     33     18     24
D69V11, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                111
  CLUS_2                7                 87
  CLUS_3                1                 68
  CLUS_4                1                145
  CLUS_5                1                 33
  CLUS_6                0                 18
  CLUS_7                1                 24
[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        5      2      0      6
  17P LOSS WILD-TYPE    143    139    112     92
D69V12, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                143
  CLUS_2                2                139
  CLUS_3                0                112
  CLUS_4                6                 92
[1] 4 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(70) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        0      0      0
  17Q LOSS WILD-TYPE      9     10      8
D70V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      0      0      0
  17Q LOSS WILD-TYPE      7      7      7      6
D70V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        5      2      1
  17Q LOSS WILD-TYPE    163    116    225
D70V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                163
  CLUS_2                2                116
  CLUS_3                1                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
  17Q LOSS MUTATED        3      2      2      1
  17Q LOSS WILD-TYPE    220     70     55    154
D70V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                220
  CLUS_2                2                 70
  CLUS_3                2                 55
  CLUS_4                1                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        2      1      3      2
  17Q LOSS WILD-TYPE     50     61     65     72
D70V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 50
  CLUS_2                1                 61
  CLUS_3                3                 65
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      6      1
  17Q LOSS WILD-TYPE     66    125     57
D70V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                6                125
  CLUS_3                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      4      1      1      1
  17Q LOSS WILD-TYPE    134    108    107    126     27
D70V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                4                108
  CLUS_3                1                107
  CLUS_4                1                126
  CLUS_5                1                 27
[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        3      3      1      1
  17Q LOSS WILD-TYPE    132    110    124    136
D70V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                132
  CLUS_2                3                110
  CLUS_3                1                124
  CLUS_4                1                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      1      1      1
  17Q LOSS WILD-TYPE    131    103    186     71
D70V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                131
  CLUS_2                1                103
  CLUS_3                1                186
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      1      0      3
  17Q LOSS WILD-TYPE    151    106    137     97
D70V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                151
  CLUS_2                1                106
  CLUS_3                0                137
  CLUS_4                3                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        1      4      0      1      1      0      1
  17Q LOSS WILD-TYPE    112     90     69    145     33     18     24
D70V11, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                112
  CLUS_2                4                 90
  CLUS_3                0                 69
  CLUS_4                1                145
  CLUS_5                1                 33
  CLUS_6                0                 18
  CLUS_7                1                 24
[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 LOSS MUTATED        4      1      0      3
  17Q LOSS WILD-TYPE    144    140    112     95
D70V12, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                144
  CLUS_2                1                140
  CLUS_3                0                112
  CLUS_4                3                 95
[1] 4 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(71) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        2      3      0
  18P LOSS WILD-TYPE      7      7      8
D71V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                3                  7
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      4      1      0
  18P LOSS WILD-TYPE      7      3      6      6
D71V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                4                  3
  CLUS_3                1                  6
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       19     15     34
  18P LOSS WILD-TYPE    149    103    192
D71V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               19                149
  CLUS_2               15                103
  CLUS_3               34                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
  18P LOSS MUTATED       23     10      4     31
  18P LOSS WILD-TYPE    200     62     53    124
D71V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               23                200
  CLUS_2               10                 62
  CLUS_3                4                 53
  CLUS_4               31                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5     11     11      9
  18P LOSS WILD-TYPE     47     51     57     65
D71V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 47
  CLUS_2               11                 51
  CLUS_3               11                 57
  CLUS_4                9                 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
  18P LOSS MUTATED        5     24      7
  18P LOSS WILD-TYPE     62    107     51
D71V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 62
  CLUS_2               24                107
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       12     20     19     15      2
  18P LOSS WILD-TYPE    123     92     89    112     26
D71V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                123
  CLUS_2               20                 92
  CLUS_3               19                 89
  CLUS_4               15                112
  CLUS_5                2                 26
[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       12     19     24     13
  18P LOSS WILD-TYPE    123     94    101    124
D71V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                123
  CLUS_2               19                 94
  CLUS_3               24                101
  CLUS_4               13                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       20     11     23     13
  18P LOSS WILD-TYPE    116     93    164     59
D71V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               20                116
  CLUS_2               11                 93
  CLUS_3               23                164
  CLUS_4               13                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       18     18     16     15
  18P LOSS WILD-TYPE    137     89    121     85
D71V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               18                137
  CLUS_2               18                 89
  CLUS_3               16                121
  CLUS_4               15                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       10     16     14     20      2      3      2
  18P LOSS WILD-TYPE    103     78     55    126     32     15     23
D71V11, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               10                103
  CLUS_2               16                 78
  CLUS_3               14                 55
  CLUS_4               20                126
  CLUS_5                2                 32
  CLUS_6                3                 15
  CLUS_7                2                 23
[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       19     22     12     14
  18P LOSS WILD-TYPE    129    119    100     84
D71V12, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               19                129
  CLUS_2               22                119
  CLUS_3               12                100
  CLUS_4               14                 84
[1] 4 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(72) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      3      0
  18Q LOSS WILD-TYPE      8      7      8
D72V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                3                  7
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      3      1      0
  18Q LOSS WILD-TYPE      7      4      6      6
D72V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                3                  4
  CLUS_3                1                  6
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       15     13     34
  18Q LOSS WILD-TYPE    153    105    192
D72V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               15                153
  CLUS_2               13                105
  CLUS_3               34                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
  18Q LOSS MUTATED       19      8      2     33
  18Q LOSS WILD-TYPE    204     64     55    122
D72V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               19                204
  CLUS_2                8                 64
  CLUS_3                2                 55
  CLUS_4               33                122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        3     10     11      9
  18Q LOSS WILD-TYPE     49     52     57     65
D72V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 49
  CLUS_2               10                 52
  CLUS_3               11                 57
  CLUS_4                9                 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
  18Q LOSS MUTATED        4     22      7
  18Q LOSS WILD-TYPE     63    109     51
D72V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2               22                109
  CLUS_3                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9     14     22     14      3
  18Q LOSS WILD-TYPE    126     98     86    113     25
D72V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                126
  CLUS_2               14                 98
  CLUS_3               22                 86
  CLUS_4               14                113
  CLUS_5                3                 25
[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        9     15     26     12
  18Q LOSS WILD-TYPE    126     98     99    125
D72V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                126
  CLUS_2               15                 98
  CLUS_3               26                 99
  CLUS_4               12                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       18      7     22     15
  18Q LOSS WILD-TYPE    118     97    165     57
D72V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               18                118
  CLUS_2                7                 97
  CLUS_3               22                165
  CLUS_4               15                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       17     19     15     11
  18Q LOSS WILD-TYPE    138     88    122     89
D72V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               17                138
  CLUS_2               19                 88
  CLUS_3               15                122
  CLUS_4               11                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9     11     16     19      2      2      3
  18Q LOSS WILD-TYPE    104     83     53    127     32     16     22
D72V11, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                104
  CLUS_2               11                 83
  CLUS_3               16                 53
  CLUS_4               19                127
  CLUS_5                2                 32
  CLUS_6                2                 16
  CLUS_7                3                 22
[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       17     23     11     11
  18Q LOSS WILD-TYPE    131    118    101     87
D72V12, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               17                131
  CLUS_2               23                118
  CLUS_3               11                101
  CLUS_4               11                 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"

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        2      3      1
  19P LOSS WILD-TYPE      7      7      7
D73V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                3                  7
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        1      3      2      0
  19P LOSS WILD-TYPE      6      4      5      6
D73V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                3                  4
  CLUS_3                2                  5
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       10      5      8
  19P LOSS WILD-TYPE    158    113    218
D73V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               10                158
  CLUS_2                5                113
  CLUS_3                8                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
  19P LOSS MUTATED       12      2      3      6
  19P LOSS WILD-TYPE    211     70     54    149
D73V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               12                211
  CLUS_2                2                 70
  CLUS_3                3                 54
  CLUS_4                6                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      6      1      2
  19P LOSS WILD-TYPE     48     56     67     72
D73V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 48
  CLUS_2                6                 56
  CLUS_3                1                 67
  CLUS_4                2                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      8      2
  19P LOSS WILD-TYPE     64    123     56
D73V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                8                123
  CLUS_3                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7      6      6      4      0
  19P LOSS WILD-TYPE    128    106    102    123     28
D73V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                7                128
  CLUS_2                6                106
  CLUS_3                6                102
  CLUS_4                4                123
  CLUS_5                0                 28
[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        6      7      6      4
  19P LOSS WILD-TYPE    129    106    119    133
D73V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                6                129
  CLUS_2                7                106
  CLUS_3                6                119
  CLUS_4                4                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      5      5      4
  19P LOSS WILD-TYPE    128     99    182     68
D73V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                8                128
  CLUS_2                5                 99
  CLUS_3                5                182
  CLUS_4                4                 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 CLUS_4
  19P LOSS MUTATED       10      6      2      4
  19P LOSS WILD-TYPE    145    101    135     96
D73V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               10                145
  CLUS_2                6                101
  CLUS_3                2                135
  CLUS_4                4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        6      5      4      4      0      1      2
  19P LOSS WILD-TYPE    107     89     65    142     34     17     23
D73V11, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                6                107
  CLUS_2                5                 89
  CLUS_3                4                 65
  CLUS_4                4                142
  CLUS_5                0                 34
  CLUS_6                1                 17
  CLUS_7                2                 23
[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       11      6      2      3
  19P LOSS WILD-TYPE    137    135    110     95
D73V12, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               11                137
  CLUS_2                6                135
  CLUS_3                2                110
  CLUS_4                3                 95
[1] 4 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(74) Variable = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        4      8      3
  19Q LOSS WILD-TYPE      5      2      5
D74V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                  5
  CLUS_2                8                  2
  CLUS_3                3                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        1      6      6      2
  19Q LOSS WILD-TYPE      6      1      1      4
D74V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                6                  1
  CLUS_3                6                  1
  CLUS_4                2                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       28     19    162
  19Q LOSS WILD-TYPE    140     99     64
D74V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               28                140
  CLUS_2               19                 99
  CLUS_3              162                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       30      4     18    154
  19Q LOSS WILD-TYPE    193     68     39      1
D74V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               30                193
  CLUS_2                4                 68
  CLUS_3               18                 39
  CLUS_4              154                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       13     22     25     37
  19Q LOSS WILD-TYPE     39     40     43     37
D74V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               13                 39
  CLUS_2               22                 40
  CLUS_3               25                 43
  CLUS_4               37                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED       29     44     24
  19Q LOSS WILD-TYPE     38     87     34
D74V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               29                 38
  CLUS_2               44                 87
  CLUS_3               24                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       18     15    106     59     10
  19Q LOSS WILD-TYPE    117     97      2     68     18
D74V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               18                117
  CLUS_2               15                 97
  CLUS_3              106                  2
  CLUS_4               59                 68
  CLUS_5               10                 18
[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 LOSS MUTATED       16     14    122     56
  19Q LOSS WILD-TYPE    119     99      3     81
D74V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                119
  CLUS_2               14                 99
  CLUS_3              122                  3
  CLUS_4               56                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       32     22     94     57
  19Q LOSS WILD-TYPE    104     82     93     15
D74V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               32                104
  CLUS_2               22                 82
  CLUS_3               94                 93
  CLUS_4               57                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED       45     85     65     10
  19Q LOSS WILD-TYPE    110     22     72     90
D74V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               45                110
  CLUS_2               85                 22
  CLUS_3               65                 72
  CLUS_4               10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       16     18     63     75     15      4     14
  19Q LOSS WILD-TYPE     97     76      6     71     19     14     11
D74V11, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                 97
  CLUS_2               18                 76
  CLUS_3               63                  6
  CLUS_4               75                 71
  CLUS_5               15                 19
  CLUS_6                4                 14
  CLUS_7               14                 11
[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 LOSS MUTATED       36    101     60      8
  19Q LOSS WILD-TYPE    112     40     52     90
D74V12, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               36                112
  CLUS_2              101                 40
  CLUS_3               60                 52
  CLUS_4                8                 90
[1] 4 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(75) Variable = 20P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        0      0      1
  20P LOSS WILD-TYPE      9     10      7
D75V1, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        0      1      0      0
  20P LOSS WILD-TYPE      7      6      7      6
D75V2, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        4      2      1
  20P LOSS WILD-TYPE    164    116    225
D75V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                164
  CLUS_2                2                116
  CLUS_3                1                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
  20P LOSS MUTATED        5      1      1      0
  20P LOSS WILD-TYPE    218     71     56    155
D75V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                218
  CLUS_2                1                 71
  CLUS_3                1                 56
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        1      1      0      1
  20P LOSS WILD-TYPE     51     61     68     73
D75V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                1                 61
  CLUS_3                0                 68
  CLUS_4                1                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        1      2      0
  20P LOSS WILD-TYPE     66    129     58
D75V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                2                129
  CLUS_3                0                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        2      3      0      1      1
  20P LOSS WILD-TYPE    133    109    108    126     27
D75V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                133
  CLUS_2                3                109
  CLUS_3                0                108
  CLUS_4                1                126
  CLUS_5                1                 27
[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 LOSS MUTATED        2      3      0      2
  20P LOSS WILD-TYPE    133    110    125    135
D75V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                133
  CLUS_2                3                110
  CLUS_3                0                125
  CLUS_4                2                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        2      1      2      1
  20P LOSS WILD-TYPE    134    103    185     71
D75V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                134
  CLUS_2                1                103
  CLUS_3                2                185
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        4      0      1      1
  20P LOSS WILD-TYPE    151    107    136     99
D75V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                151
  CLUS_2                0                107
  CLUS_3                1                136
  CLUS_4                1                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED        2      1      0      1      2      0      0
  20P LOSS WILD-TYPE    111     93     69    145     32     18     25
D75V11, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                111
  CLUS_2                1                 93
  CLUS_3                0                 69
  CLUS_4                1                145
  CLUS_5                2                 32
  CLUS_6                0                 18
  CLUS_7                0                 25
[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 LOSS MUTATED        4      0      1      1
  20P LOSS WILD-TYPE    144    141    111     97
D75V12, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                144
  CLUS_2                0                141
  CLUS_3                1                111
  CLUS_4                1                 97
[1] 4 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(76) Variable = 20Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        0      0      0
  20Q LOSS WILD-TYPE      9     10      8
D76V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        0      0      0      0
  20Q LOSS WILD-TYPE      7      7      7      6
D76V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        2      1      0
  20Q LOSS WILD-TYPE    166    117    226
D76V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                166
  CLUS_2                1                117
  CLUS_3                0                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
  20Q LOSS MUTATED        3      0      0      0
  20Q LOSS WILD-TYPE    220     72     57    155
D76V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                220
  CLUS_2                0                 72
  CLUS_3                0                 57
  CLUS_4                0                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        0      0      0      0
  20Q LOSS WILD-TYPE     52     62     68     74
D76V5, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        0      0      0
  20Q LOSS WILD-TYPE     67    131     58
D76V6, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q LOSS MUTATED        0      2      0      0      1
  20Q LOSS WILD-TYPE    135    110    108    127     27
D76V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                135
  CLUS_2                2                110
  CLUS_3                0                108
  CLUS_4                0                127
  CLUS_5                1                 27
[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 LOSS MUTATED        1      2      0      0
  20Q LOSS WILD-TYPE    134    111    125    137
D76V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                2                111
  CLUS_3                0                125
  CLUS_4                0                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        2      1      0      0
  20Q LOSS WILD-TYPE    134    103    187     72
D76V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                134
  CLUS_2                1                103
  CLUS_3                0                187
  CLUS_4                0                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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 LOSS MUTATED        2      0      1      0
  20Q LOSS WILD-TYPE    153    107    136    100
D76V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                153
  CLUS_2                0                107
  CLUS_3                1                136
  CLUS_4                0                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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q LOSS MUTATED        2      1      0      0      0      0      0
  20Q LOSS WILD-TYPE    111     93     69    146     34     18     25
D76V11, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                111
  CLUS_2                1                 93
  CLUS_3                0                 69
  CLUS_4                0                146
  CLUS_5                0                 34
  CLUS_6                0                 18
  CLUS_7                0                 25
[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 LOSS MUTATED        2      1      0      0
  20Q LOSS WILD-TYPE    146    140    112     98
D76V12, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                146
  CLUS_2                1                140
  CLUS_3                0                112
  CLUS_4                0                 98
[1] 4 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(77) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        2      1      0
  21Q LOSS WILD-TYPE      7      9      8
D77V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  9
  CLUS_3                0                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        0      3      0      0
  21Q LOSS WILD-TYPE      7      4      7      6
D77V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                3                  4
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       26      5      5
  21Q LOSS WILD-TYPE    142    113    221
D77V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               26                142
  CLUS_2                5                113
  CLUS_3                5                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
  21Q LOSS MUTATED       26      4      4      2
  21Q LOSS WILD-TYPE    197     68     53    153
D77V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               26                197
  CLUS_2                4                 68
  CLUS_3                4                 53
  CLUS_4                2                153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      7      4
  21Q LOSS WILD-TYPE     48     54     61     70
D77V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 48
  CLUS_2                8                 54
  CLUS_3                7                 61
  CLUS_4                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     13      6
  21Q LOSS WILD-TYPE     63    118     52
D77V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2               13                118
  CLUS_3                6                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       13     12      1      5      5
  21Q LOSS WILD-TYPE    122    100    107    122     23
D77V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               13                122
  CLUS_2               12                100
  CLUS_3                1                107
  CLUS_4                5                122
  CLUS_5                5                 23
[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       16     13      2      5
  21Q LOSS WILD-TYPE    119    100    123    132
D77V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               16                119
  CLUS_2               13                100
  CLUS_3                2                123
  CLUS_4                5                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11     10      9      4
  21Q LOSS WILD-TYPE    125     94    178     68
D77V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                125
  CLUS_2               10                 94
  CLUS_3                9                178
  CLUS_4                4                 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 CLUS_4
  21Q LOSS MUTATED       16      4      6      8
  21Q LOSS WILD-TYPE    139    103    131     92
D77V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               16                139
  CLUS_2                4                103
  CLUS_3                6                131
  CLUS_4                8                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       14     10      2      4      3      0      1
  21Q LOSS WILD-TYPE     99     84     67    142     31     18     24
D77V11, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               14                 99
  CLUS_2               10                 84
  CLUS_3                2                 67
  CLUS_4                4                142
  CLUS_5                3                 31
  CLUS_6                0                 18
  CLUS_7                1                 24
[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       18      3      5      8
  21Q LOSS WILD-TYPE    130    138    107     90
D77V12, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               18                130
  CLUS_2                3                138
  CLUS_3                5                107
  CLUS_4                8                 90
[1] 4 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(78) Variable = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        2      1      1
  22Q LOSS WILD-TYPE      7      9      7
D78V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  9
  CLUS_3                1                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        0      4      0      0
  22Q LOSS WILD-TYPE      7      3      7      6
D78V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                4                  3
  CLUS_3                0                  7
  CLUS_4                0                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       28     27      2
  22Q LOSS WILD-TYPE    140     91    224
D78V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               28                140
  CLUS_2               27                 91
  CLUS_3                2                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
  22Q LOSS MUTATED       24     21      8      4
  22Q LOSS WILD-TYPE    199     51     49    151
D78V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               24                199
  CLUS_2               21                 51
  CLUS_3                8                 49
  CLUS_4                4                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2     18      5      4
  22Q LOSS WILD-TYPE     50     44     63     70
D78V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 50
  CLUS_2               18                 44
  CLUS_3                5                 63
  CLUS_4                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3     21      5
  22Q LOSS WILD-TYPE     64    110     53
D78V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2               21                110
  CLUS_3                5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     31      2     10      4
  22Q LOSS WILD-TYPE    126     81    106    117     24
D78V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                9                126
  CLUS_2               31                 81
  CLUS_3                2                106
  CLUS_4               10                117
  CLUS_5                4                 24
[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       11     29      4     12
  22Q LOSS WILD-TYPE    124     84    121    125
D78V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                124
  CLUS_2               29                 84
  CLUS_3                4                121
  CLUS_4               12                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       19     12     17      6
  22Q LOSS WILD-TYPE    117     92    170     66
D78V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               19                117
  CLUS_2               12                 92
  CLUS_3               17                170
  CLUS_4                6                 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 CLUS_4
  22Q LOSS MUTATED       14      6     13     21
  22Q LOSS WILD-TYPE    141    101    124     79
D78V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               14                141
  CLUS_2                6                101
  CLUS_3               13                124
  CLUS_4               21                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7     23      6     12      2      2      2
  22Q LOSS WILD-TYPE    106     71     63    134     32     16     23
D78V11, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                106
  CLUS_2               23                 71
  CLUS_3                6                 63
  CLUS_4               12                134
  CLUS_5                2                 32
  CLUS_6                2                 16
  CLUS_7                2                 23
[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       13      9      8     24
  22Q LOSS WILD-TYPE    135    132    104     74
D78V12, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                9                132
  CLUS_3                8                104
  CLUS_4               24                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        1      2      2
  XQ LOSS WILD-TYPE      8      8      6
D79V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 8
  CLUS_3               2                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        1      3      0      1
  XQ LOSS WILD-TYPE      6      4      7      5
D79V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                 4
  CLUS_3               0                 7
  CLUS_4               1                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       24     13     32
  XQ LOSS WILD-TYPE    144    105    194
D79V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              24               144
  CLUS_2              13               105
  CLUS_3              32               194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       25     10      2     32
  XQ LOSS WILD-TYPE    198     62     55    123
D79V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              25               198
  CLUS_2              10                62
  CLUS_3               2                55
  CLUS_4              32               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5     15      8      6
  XQ LOSS WILD-TYPE     47     47     60     68
D79V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5                47
  CLUS_2              15                47
  CLUS_3               8                60
  CLUS_4               6                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        4     25      5
  XQ LOSS WILD-TYPE     63    106     53
D79V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                63
  CLUS_2              25               106
  CLUS_3               5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       11     23     25     10      0
  XQ LOSS WILD-TYPE    124     89     83    117     28
D79V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              11               124
  CLUS_2              23                89
  CLUS_3              25                83
  CLUS_4              10               117
  CLUS_5               0                28
[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       10     23     29      7
  XQ LOSS WILD-TYPE    125     90     96    130
D79V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2              23                90
  CLUS_3              29                96
  CLUS_4               7               130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12     14     19     21
  XQ LOSS WILD-TYPE    124     90    168     51
D79V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              12               124
  CLUS_2              14                90
  CLUS_3              19               168
  CLUS_4              21                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       19     23      7     17
  XQ LOSS WILD-TYPE    136     84    130     83
D79V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              19               136
  CLUS_2              23                84
  CLUS_3               7               130
  CLUS_4              17                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        8     16     19     11      7      4      1
  XQ LOSS WILD-TYPE    105     78     50    135     27     14     24
D79V11, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               8               105
  CLUS_2              16                78
  CLUS_3              19                50
  CLUS_4              11               135
  CLUS_5               7                27
  CLUS_6               4                14
  CLUS_7               1                24
[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       21     27      2     16
  XQ LOSS WILD-TYPE    127    114    110     82
D79V12, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              21               127
  CLUS_2              27               114
  CLUS_3               2               110
  CLUS_4              16                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
