[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/22553887/LGG-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/22533657/transformed.cor.cli.txt"

nPatients in clinical file=516, in cluster file=513, common to both=513
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 513
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               500 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               500 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               490 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               490 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               499 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               499 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               500 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               500 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               502 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               502 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               505 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               505 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               501 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               501 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               506 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               506 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               502 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               502 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               504 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               504 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               506 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               506 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120               393 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120               393 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               363 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               363 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               468 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               468 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               55               458 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               55               458 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               496 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               496 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               489 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               489 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                456 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                456 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                502 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                502 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                483 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                483 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                455 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                455 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                481 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                481 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                498 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                498 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                507 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                507 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                509 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                509 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                502 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                502 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                497 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                497 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                494 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                494 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                493 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                493 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                490 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                490 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                495 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                495 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                500 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                500 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                99                414 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                99                414 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                488 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                488 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                45                468 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                45                468 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                469 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                469 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                490 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                490 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                490 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                490 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               22               491 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               22               491 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               42               471 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               42               471 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              184               329 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              184               329 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               487 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               487 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               492 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               492 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               495 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               495 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               483 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               483 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               485 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               485 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               441 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               441 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               94               419 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               94               419 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               35               478 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               35               478 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               32               481 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               32               481 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               483 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               483 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               63               450 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               63               450 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               510 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               510 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               509 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               509 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               496 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               496 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               502 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               502 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              118               395 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              118               395 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               462 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               462 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                430 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                430 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                97                416 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                97                416 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                450 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                450 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                492 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                492 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                28                485 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                28                485 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                461 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                461 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                398 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                398 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                81                432 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                81                432 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                462 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                462 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                499 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                499 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                491 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                491 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                499 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                499 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                504 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                504 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                446 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                446 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                451 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                451 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                487 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                487 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                304 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                304 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                506 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                506 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                510 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                510 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                475 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                475 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                456 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                456 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               99               414 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               99               414 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               443 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               443 
[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 513 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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 513 columns, 0 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [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"
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=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, 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        2     10      1
  1P GAIN WILD-TYPE    225    101    174
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               225
  CLUS_2              10               101
  CLUS_3               1               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      0      2
  1P GAIN WILD-TYPE    206    126    157     11
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               206
  CLUS_2               8               126
  CLUS_3               0               157
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        2      5      1      0
  1P GAIN WILD-TYPE     89     90    124    115
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                89
  CLUS_2               5                90
  CLUS_3               1               124
  CLUS_4               0               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
  1P GAIN MUTATED        2      1      5
  1P GAIN WILD-TYPE     81    157    180
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                81
  CLUS_2               1               157
  CLUS_3               5               180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    130    102    105    133     30
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               130
  CLUS_2              13               102
  CLUS_3               0               105
  CLUS_4               0               133
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      8      0      0      0      5      0
  1P GAIN WILD-TYPE    135     63     36     68     90     36     72
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               8                63
  CLUS_3               0                36
  CLUS_4               0                68
  CLUS_5               0                90
  CLUS_6               5                36
  CLUS_7               0                72
[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        8      4      0      1
  1P GAIN WILD-TYPE    132    103     82    179
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               8               132
  CLUS_2               4               103
  CLUS_3               0                82
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        3      0     10
  1P GAIN WILD-TYPE    219    184     93
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               219
  CLUS_2               0               184
  CLUS_3              10                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      8      0      1
  1P GAIN WILD-TYPE    123    111    105    153
D1V11, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               4               123
  CLUS_2               8               111
  CLUS_3               0               105
  CLUS_4               1               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 CLUS_5 CLUS_6
  1P GAIN MUTATED        1      4      0      0      6      2
  1P GAIN WILD-TYPE     98     73    118     56     57     90
D1V12, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               4                73
  CLUS_3               0               118
  CLUS_4               0                56
  CLUS_5               6                57
  CLUS_6               2                90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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        4     15      4
  1Q GAIN WILD-TYPE    223     96    171
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4               223
  CLUS_2              15                96
  CLUS_3               4               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7     12      2      2
  1Q GAIN WILD-TYPE    202    122    155     11
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               7               202
  CLUS_2              12               122
  CLUS_3               2               155
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        3      5      2      5
  1Q GAIN WILD-TYPE     88     90    123    110
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                88
  CLUS_2               5                90
  CLUS_3               2               123
  CLUS_4               5               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      8
  1Q GAIN WILD-TYPE     81    153    177
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                81
  CLUS_2               5               153
  CLUS_3               8               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    128    101    105    128     28
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               128
  CLUS_2              14               101
  CLUS_3               0               105
  CLUS_4               5               128
  CLUS_5               2                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 CLUS_5 CLUS_6 CLUS_7
  1Q GAIN MUTATED        3      9      1      2      1      5      2
  1Q GAIN WILD-TYPE    132     62     35     66     89     36     70
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3               132
  CLUS_2               9                62
  CLUS_3               1                35
  CLUS_4               2                66
  CLUS_5               1                89
  CLUS_6               5                36
  CLUS_7               2                70
[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       12      4      0      7
  1Q GAIN WILD-TYPE    128    103     82    173
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              12               128
  CLUS_2               4               103
  CLUS_3               0                82
  CLUS_4               7               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7      6     10
  1Q GAIN WILD-TYPE    215    178     93
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               7               215
  CLUS_2               6               178
  CLUS_3              10                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5     10      0      8
  1Q GAIN WILD-TYPE    122    109    105    146
D2V11, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5               122
  CLUS_2              10               109
  CLUS_3               0               105
  CLUS_4               8               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 CLUS_5 CLUS_6
  1Q GAIN MUTATED        5      3      5      0      6      4
  1Q GAIN WILD-TYPE     94     74    113     56     57     88
D2V12, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                94
  CLUS_2               3                74
  CLUS_3               5               113
  CLUS_4               0                56
  CLUS_5               6                57
  CLUS_6               4                88
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 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        1     10      3
  2P GAIN WILD-TYPE    226    101    172
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1               226
  CLUS_2              10               101
  CLUS_3               3               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      6      4      1
  2P GAIN WILD-TYPE    206    128    153     12
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3               206
  CLUS_2               6               128
  CLUS_3               4               153
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED        1      4      1      1
  2P GAIN WILD-TYPE     90     91    124    114
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                90
  CLUS_2               4                91
  CLUS_3               1               124
  CLUS_4               1               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        2      1      4
  2P GAIN WILD-TYPE     81    157    181
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                81
  CLUS_2               1               157
  CLUS_3               4               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P GAIN MUTATED        1      9      2      2      0
  2P GAIN WILD-TYPE    129    106    103    131     30
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1               129
  CLUS_2               9               106
  CLUS_3               2               103
  CLUS_4               2               131
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      5      1      2      2      4      0
  2P GAIN WILD-TYPE    135     66     35     66     88     37     72
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5                66
  CLUS_3               1                35
  CLUS_4               2                66
  CLUS_5               2                88
  CLUS_6               4                37
  CLUS_7               0                72
[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        5      4      2      3
  2P GAIN WILD-TYPE    135    103     80    177
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5               135
  CLUS_2               4               103
  CLUS_3               2                80
  CLUS_4               3               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      7
  2P GAIN WILD-TYPE    217    182     96
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5               217
  CLUS_2               2               182
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      9      0      3
  2P GAIN WILD-TYPE    125    110    105    151
D3V11, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2               125
  CLUS_2               9               110
  CLUS_3               0               105
  CLUS_4               3               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 CLUS_5 CLUS_6
  2P GAIN MUTATED        2      4      1      1      5      1
  2P GAIN WILD-TYPE     97     73    117     55     58     91
D3V12, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                97
  CLUS_2               4                73
  CLUS_3               1               117
  CLUS_4               1                55
  CLUS_5               5                58
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 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        1      9      3
  2Q GAIN WILD-TYPE    226    102    172
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1               226
  CLUS_2               9               102
  CLUS_3               3               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      6      3      1
  2Q GAIN WILD-TYPE    206    128    154     12
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3               206
  CLUS_2               6               128
  CLUS_3               3               154
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED        1      4      1      1
  2Q GAIN WILD-TYPE     90     91    124    114
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                90
  CLUS_2               4                91
  CLUS_3               1               124
  CLUS_4               1               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        2      1      4
  2Q GAIN WILD-TYPE     81    157    181
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                81
  CLUS_2               1               157
  CLUS_3               4               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q GAIN MUTATED        1      8      2      2      0
  2Q GAIN WILD-TYPE    129    107    103    131     30
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1               129
  CLUS_2               8               107
  CLUS_3               2               103
  CLUS_4               2               131
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      5      1      2      1      4      0
  2Q GAIN WILD-TYPE    135     66     35     66     89     37     72
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5                66
  CLUS_3               1                35
  CLUS_4               2                66
  CLUS_5               1                89
  CLUS_6               4                37
  CLUS_7               0                72
[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        5      4      1      3
  2Q GAIN WILD-TYPE    135    103     81    177
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5               135
  CLUS_2               4               103
  CLUS_3               1                81
  CLUS_4               3               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      2      7
  2Q GAIN WILD-TYPE    218    182     96
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4               218
  CLUS_2               2               182
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      8      0      3
  2Q GAIN WILD-TYPE    125    111    105    151
D4V11, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2               125
  CLUS_2               8               111
  CLUS_3               0               105
  CLUS_4               3               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 CLUS_5 CLUS_6
  2Q GAIN MUTATED        2      4      1      0      5      1
  2Q GAIN WILD-TYPE     97     73    117     56     58     91
D4V12, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                97
  CLUS_2               4                73
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               5                58
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 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        2      8      1
  3P GAIN WILD-TYPE    225    103    174
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               225
  CLUS_2               8               103
  CLUS_3               1               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      4      3      1
  3P GAIN WILD-TYPE    206    130    154     12
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3               206
  CLUS_2               4               130
  CLUS_3               3               154
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        1      5      1      1
  3P GAIN WILD-TYPE     90     90    124    114
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                90
  CLUS_2               5                90
  CLUS_3               1               124
  CLUS_4               1               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        1      1      6
  3P GAIN WILD-TYPE     82    157    179
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                82
  CLUS_2               1               157
  CLUS_3               6               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED        1      6      3      1      0
  3P GAIN WILD-TYPE    129    109    102    132     30
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               129
  CLUS_2               6               109
  CLUS_3               3               102
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      2      0      0      2      1
  3P GAIN WILD-TYPE    133     67     34     68     90     39     71
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               4                67
  CLUS_3               2                34
  CLUS_4               0                68
  CLUS_5               0                90
  CLUS_6               2                39
  CLUS_7               1                71
[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        6      2      2      1
  3P GAIN WILD-TYPE    134    105     80    179
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               6               134
  CLUS_2               2               105
  CLUS_3               2                80
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      4
  3P GAIN WILD-TYPE    217    182     99
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5               217
  CLUS_2               2               182
  CLUS_3               4                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      2      2
  3P GAIN WILD-TYPE    125    114    103    152
D5V11, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               125
  CLUS_2               5               114
  CLUS_3               2               103
  CLUS_4               2               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 CLUS_5 CLUS_6
  3P GAIN MUTATED        3      1      1      1      4      1
  3P GAIN WILD-TYPE     96     76    117     55     59     91
D5V12, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                96
  CLUS_2               1                76
  CLUS_3               1               117
  CLUS_4               1                55
  CLUS_5               4                59
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 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        1      7      0
  3Q GAIN WILD-TYPE    226    104    175
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1               226
  CLUS_2               7               104
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      0
  3Q GAIN WILD-TYPE    207    130    155     13
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               207
  CLUS_2               4               130
  CLUS_3               2               155
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      1
  3Q GAIN WILD-TYPE     91     90    125    114
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                91
  CLUS_2               5                90
  CLUS_3               0               125
  CLUS_4               1               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        0      1      5
  3Q GAIN WILD-TYPE     83    157    180
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                83
  CLUS_2               1               157
  CLUS_3               5               180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    130    110    103    132     30
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0               130
  CLUS_2               5               110
  CLUS_3               2               103
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      4      1      0      0      2      1
  3Q GAIN WILD-TYPE    135     67     35     68     90     39     71
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               4                67
  CLUS_3               1                35
  CLUS_4               0                68
  CLUS_5               0                90
  CLUS_6               2                39
  CLUS_7               1                71
[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        4      2      1      1
  3Q GAIN WILD-TYPE    136    105     81    179
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4               136
  CLUS_2               2               105
  CLUS_3               1                81
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        2      2      4
  3Q GAIN WILD-TYPE    220    182     99
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               220
  CLUS_2               2               182
  CLUS_3               4                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      3      1      2
  3Q GAIN WILD-TYPE    125    116    104    152
D6V11, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2               125
  CLUS_2               3               116
  CLUS_3               1               104
  CLUS_4               2               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 CLUS_5 CLUS_6
  3Q GAIN MUTATED        1      1      1      0      4      1
  3Q GAIN WILD-TYPE     98     76    117     56     59     91
D6V12, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               1                76
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               4                59
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 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        5      7      0
  4P GAIN WILD-TYPE    222    104    175
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               222
  CLUS_2               7               104
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      1
  4P GAIN WILD-TYPE    203    129    157     12
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               203
  CLUS_2               5               129
  CLUS_3               0               157
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        2      5      2      2
  4P GAIN WILD-TYPE     89     90    123    113
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                89
  CLUS_2               5                90
  CLUS_3               2               123
  CLUS_4               2               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
  4P GAIN MUTATED        1      3      7
  4P GAIN WILD-TYPE     82    155    178
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                82
  CLUS_2               3               155
  CLUS_3               7               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 CLUS_5
  4P GAIN MUTATED        3      8      0      1      0
  4P GAIN WILD-TYPE    127    107    105    132     30
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               127
  CLUS_2               8               107
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      0      0      0      3      1
  4P GAIN WILD-TYPE    132     66     36     68     90     38     71
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               132
  CLUS_2               5                66
  CLUS_3               0                36
  CLUS_4               0                68
  CLUS_5               0                90
  CLUS_6               3                38
  CLUS_7               1                71
[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        5      4      1      2
  4P GAIN WILD-TYPE    135    103     81    178
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               135
  CLUS_2               4               103
  CLUS_3               1                81
  CLUS_4               2               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      3      6
  4P GAIN WILD-TYPE    219    181     97
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               219
  CLUS_2               3               181
  CLUS_3               6                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      8      0      1
  4P GAIN WILD-TYPE    124    111    105    153
D7V11, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               124
  CLUS_2               8               111
  CLUS_3               0               105
  CLUS_4               1               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 CLUS_5 CLUS_6
  4P GAIN MUTATED        2      4      1      0      4      1
  4P GAIN WILD-TYPE     97     73    117     56     59     91
D7V12, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                97
  CLUS_2               4                73
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               4                59
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 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        2      5      0
  4Q GAIN WILD-TYPE    225    106    175
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               225
  CLUS_2               5               106
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      0
  4Q GAIN WILD-TYPE    207    129    157     13
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               207
  CLUS_2               5               129
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2
  4Q GAIN WILD-TYPE     91     92    125    113
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                91
  CLUS_2               3                92
  CLUS_3               0               125
  CLUS_4               2               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
  4Q GAIN MUTATED        0      2      3
  4Q GAIN WILD-TYPE     83    156    182
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                83
  CLUS_2               2               156
  CLUS_3               3               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        0      6      0      1      0
  4Q GAIN WILD-TYPE    130    109    105    132     30
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               130
  CLUS_2               6               109
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      0      0      1      1
  4Q GAIN WILD-TYPE    135     66     36     68     90     40     71
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               135
  CLUS_2               5                66
  CLUS_3               0                36
  CLUS_4               0                68
  CLUS_5               0                90
  CLUS_6               1                40
  CLUS_7               1                71
[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        3      3      0      1
  4Q GAIN WILD-TYPE    137    104     82    179
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               137
  CLUS_2               3               104
  CLUS_3               0                82
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        1      2      4
  4Q GAIN WILD-TYPE    221    182     99
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               221
  CLUS_2               2               182
  CLUS_3               4                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      0      1
  4Q GAIN WILD-TYPE    126    114    105    153
D8V11, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               126
  CLUS_2               5               114
  CLUS_3               0               105
  CLUS_4               1               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 CLUS_5 CLUS_6
  4Q GAIN MUTATED        1      1      1      0      4      0
  4Q GAIN WILD-TYPE     98     76    117     56     59     92
D8V12, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               1                76
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               4                59
  CLUS_6               0                92
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 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      7      0
  5P GAIN WILD-TYPE    223    104    175
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               223
  CLUS_2               7               104
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      0      0
  5P GAIN WILD-TYPE    205    127    157     13
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4               205
  CLUS_2               7               127
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      4      2      0
  5P GAIN WILD-TYPE     89     91    123    115
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                89
  CLUS_2               4                91
  CLUS_3               2               123
  CLUS_4               0               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
  5P GAIN MUTATED        3      0      5
  5P GAIN WILD-TYPE     80    158    180
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                80
  CLUS_2               0               158
  CLUS_3               5               180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    130    106    105    132     29
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0               130
  CLUS_2               9               106
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      7      0      1      0      2      0
  5P GAIN WILD-TYPE    134     64     36     67     90     39     72
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               7                64
  CLUS_3               0                36
  CLUS_4               1                67
  CLUS_5               0                90
  CLUS_6               2                39
  CLUS_7               0                72
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        5      5      0      1
  5P GAIN WILD-TYPE    135    102     82    179
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5               135
  CLUS_2               5               102
  CLUS_3               0                82
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      2      6
  5P GAIN WILD-TYPE    219    182     97
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3               219
  CLUS_2               2               182
  CLUS_3               6                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     10      0      1
  5P GAIN WILD-TYPE    127    109    105    153
D9V11, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0               127
  CLUS_2              10               109
  CLUS_3               0               105
  CLUS_4               1               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 CLUS_5 CLUS_6
  5P GAIN MUTATED        1      3      0      0      6      1
  5P GAIN WILD-TYPE     98     74    118     56     57     91
D9V12, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               3                74
  CLUS_3               0               118
  CLUS_4               0                56
  CLUS_5               6                57
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 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        3      6      0
  5Q GAIN WILD-TYPE    224    105    175
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3               224
  CLUS_2               6               105
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      0      0
  5Q GAIN WILD-TYPE    207    127    157     13
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               207
  CLUS_2               7               127
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      2      0
  5Q GAIN WILD-TYPE     89     93    123    115
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                89
  CLUS_2               2                93
  CLUS_3               2               123
  CLUS_4               0               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
  5Q GAIN MUTATED        3      0      3
  5Q GAIN WILD-TYPE     80    158    182
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                80
  CLUS_2               0               158
  CLUS_3               3               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED        0      7      0      1      1
  5Q GAIN WILD-TYPE    130    108    105    132     29
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0               130
  CLUS_2               7               108
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      7      0      1      0      0      0
  5Q GAIN WILD-TYPE    134     64     36     67     90     41     72
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1               134
  CLUS_2               7                64
  CLUS_3               0                36
  CLUS_4               1                67
  CLUS_5               0                90
  CLUS_6               0                41
  CLUS_7               0                72
[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        5      3      0      1
  5Q GAIN WILD-TYPE    135    104     82    179
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5               135
  CLUS_2               3               104
  CLUS_3               0                82
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        2      1      6
  5Q GAIN WILD-TYPE    220    183     97
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2               220
  CLUS_2               1               183
  CLUS_3               6                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      0      1
  5Q GAIN WILD-TYPE    127    111    105    153
D10V11, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0               127
  CLUS_2               8               111
  CLUS_3               0               105
  CLUS_4               1               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 CLUS_5 CLUS_6
  5Q GAIN MUTATED        1      1      0      0      6      1
  5Q GAIN WILD-TYPE     98     76    118     56     57     91
D10V12, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               1                76
  CLUS_3               0               118
  CLUS_4               0                56
  CLUS_5               6                57
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 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        5      2      0
  6P GAIN WILD-TYPE    222    109    175
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               5               222
  CLUS_2               2               109
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      1      0      3
  6P GAIN WILD-TYPE    206    133    157     10
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3               206
  CLUS_2               1               133
  CLUS_3               0               157
  CLUS_4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        2      4      0      0
  6P GAIN WILD-TYPE     89     91    125    115
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                89
  CLUS_2               4                91
  CLUS_3               0               125
  CLUS_4               0               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
  6P GAIN MUTATED        2      1      3
  6P GAIN WILD-TYPE     81    157    182
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                81
  CLUS_2               1               157
  CLUS_3               3               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P GAIN MUTATED        1      4      1      1      0
  6P GAIN WILD-TYPE    129    111    104    132     30
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1               129
  CLUS_2               4               111
  CLUS_3               1               104
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      0      0      1      0      4      0
  6P GAIN WILD-TYPE    133     71     36     67     90     37     72
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               0                71
  CLUS_3               0                36
  CLUS_4               1                67
  CLUS_5               0                90
  CLUS_6               4                37
  CLUS_7               0                72
[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        4      3      0      0
  6P GAIN WILD-TYPE    136    104     82    180
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               136
  CLUS_2               3               104
  CLUS_3               0                82
  CLUS_4               0               180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      0      3
  6P GAIN WILD-TYPE    218    184    100
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               218
  CLUS_2               0               184
  CLUS_3               3               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      1      0
  6P GAIN WILD-TYPE    123    117    104    154
D11V11, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               123
  CLUS_2               2               117
  CLUS_3               1               104
  CLUS_4               0               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 CLUS_5 CLUS_6
  6P GAIN MUTATED        4      1      0      0      0      2
  6P GAIN WILD-TYPE     95     76    118     56     63     90
D11V12, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                95
  CLUS_2               1                76
  CLUS_3               0               118
  CLUS_4               0                56
  CLUS_5               0                63
  CLUS_6               2                90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2      2      2
  7P GAIN WILD-TYPE      7      8      6
D12V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 7
  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
  7P GAIN MUTATED        2      2      1      1
  7P GAIN WILD-TYPE      5      5      6      5
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 5
  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
  7P GAIN MUTATED       42     66     12
  7P GAIN WILD-TYPE    185     45    163
D12V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              42               185
  CLUS_2              66                45
  CLUS_3              12               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       40     64     15      1
  7P GAIN WILD-TYPE    169     70    142     12
D12V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              40               169
  CLUS_2              64                70
  CLUS_3              15               142
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       22     32     20     20
  7P GAIN WILD-TYPE     69     63    105     95
D12V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22                69
  CLUS_2              32                63
  CLUS_3              20               105
  CLUS_4              20                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
  7P GAIN MUTATED       13     28     53
  7P GAIN WILD-TYPE     70    130    132
D12V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13                70
  CLUS_2              28               130
  CLUS_3              53               132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     24      6
  7P GAIN WILD-TYPE    108     56     96    109     24
D12V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22               108
  CLUS_2              59                56
  CLUS_3               9                96
  CLUS_4              24               109
  CLUS_5               6                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 CLUS_5 CLUS_6 CLUS_7
  7P GAIN MUTATED       19     51      3     26      8      8      5
  7P GAIN WILD-TYPE    116     20     33     42     82     33     67
D12V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              19               116
  CLUS_2              51                20
  CLUS_3               3                33
  CLUS_4              26                42
  CLUS_5               8                82
  CLUS_6               8                33
  CLUS_7               5                67
[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       43     33     12     30
  7P GAIN WILD-TYPE     97     74     70    150
D12V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              43                97
  CLUS_2              33                74
  CLUS_3              12                70
  CLUS_4              30               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
  7P GAIN MUTATED       37     26     55
  7P GAIN WILD-TYPE    185    158     48
D12V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              37               185
  CLUS_2              26               158
  CLUS_3              55                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
  7P GAIN MUTATED       31     45     11     30
  7P GAIN WILD-TYPE     96     74     94    124
D12V11, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              31                96
  CLUS_2              45                74
  CLUS_3              11                94
  CLUS_4              30               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 CLUS_5 CLUS_6
  7P GAIN MUTATED       15     11     17      7     47     20
  7P GAIN WILD-TYPE     84     66    101     49     16     72
D12V12, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              15                84
  CLUS_2              11                66
  CLUS_3              17               101
  CLUS_4               7                49
  CLUS_5              47                16
  CLUS_6              20                72
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        3      2      2
  7Q GAIN WILD-TYPE      6      8      6
D13V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 6
  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
  7Q GAIN MUTATED        3      2      1      1
  7Q GAIN WILD-TYPE      4      5      6      5
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 4
  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
  7Q GAIN MUTATED       57     73     20
  7Q GAIN WILD-TYPE    170     38    155
D13V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              57               170
  CLUS_2              73                38
  CLUS_3              20               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       57     68     23      2
  7Q GAIN WILD-TYPE    152     66    134     11
D13V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              57               152
  CLUS_2              68                66
  CLUS_3              23               134
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       27     35     27     29
  7Q GAIN WILD-TYPE     64     60     98     86
D13V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              27                64
  CLUS_2              35                60
  CLUS_3              27                98
  CLUS_4              29                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
  7Q GAIN MUTATED       17     40     61
  7Q GAIN WILD-TYPE     66    118    124
D13V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              17                66
  CLUS_2              40               118
  CLUS_3              61               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       35     63     12     32      8
  7Q GAIN WILD-TYPE     95     52     93    101     22
D13V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              35                95
  CLUS_2              63                52
  CLUS_3              12                93
  CLUS_4              32               101
  CLUS_5               8                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 CLUS_5 CLUS_6 CLUS_7
  7Q GAIN MUTATED       32     54      4     29     12      7     12
  7Q GAIN WILD-TYPE    103     17     32     39     78     34     60
D13V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32               103
  CLUS_2              54                17
  CLUS_3               4                32
  CLUS_4              29                39
  CLUS_5              12                78
  CLUS_6               7                34
  CLUS_7              12                60
[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       49     41     15     43
  7Q GAIN WILD-TYPE     91     66     67    137
D13V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              49                91
  CLUS_2              41                66
  CLUS_3              15                67
  CLUS_4              43               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
  7Q GAIN MUTATED       50     39     59
  7Q GAIN WILD-TYPE    172    145     44
D13V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              50               172
  CLUS_2              39               145
  CLUS_3              59                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
  7Q GAIN MUTATED       38     53     14     42
  7Q GAIN WILD-TYPE     89     66     91    112
D13V11, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              38                89
  CLUS_2              53                66
  CLUS_3              14                91
  CLUS_4              42               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q GAIN MUTATED       21     15     25      7     50     29
  7Q GAIN WILD-TYPE     78     62     93     49     13     63
D13V12, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              21                78
  CLUS_2              15                62
  CLUS_3              25                93
  CLUS_4               7                49
  CLUS_5              50                13
  CLUS_6              29                63
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 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       24     16      5
  8P GAIN WILD-TYPE    203     95    170
D14V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              24               203
  CLUS_2              16                95
  CLUS_3               5               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       29      6      8      2
  8P GAIN WILD-TYPE    180    128    149     11
D14V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              29               180
  CLUS_2               6               128
  CLUS_3               8               149
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       12     11     10      3
  8P GAIN WILD-TYPE     79     84    115    112
D14V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              12                79
  CLUS_2              11                84
  CLUS_3              10               115
  CLUS_4               3               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
  8P GAIN MUTATED        9      7     20
  8P GAIN WILD-TYPE     74    151    165
D14V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               9                74
  CLUS_2               7               151
  CLUS_3              20               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       20      8      4      9      4
  8P GAIN WILD-TYPE    110    107    101    124     26
D14V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              20               110
  CLUS_2               8               107
  CLUS_3               4               101
  CLUS_4               9               124
  CLUS_5               4                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 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED       22      3      2      6      3      5      4
  8P GAIN WILD-TYPE    113     68     34     62     87     36     68
D14V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              22               113
  CLUS_2               3                68
  CLUS_3               2                34
  CLUS_4               6                62
  CLUS_5               3                87
  CLUS_6               5                36
  CLUS_7               4                68
[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       17     10      4     13
  8P GAIN WILD-TYPE    123     97     78    167
D14V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              17               123
  CLUS_2              10                97
  CLUS_3               4                78
  CLUS_4              13               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       24     13      7
  8P GAIN WILD-TYPE    198    171     96
D14V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              24               198
  CLUS_2              13               171
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       17     11      8      8
  8P GAIN WILD-TYPE    110    108     97    146
D14V11, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              17               110
  CLUS_2              11               108
  CLUS_3               8                97
  CLUS_4               8               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 CLUS_5 CLUS_6
  8P GAIN MUTATED       18      6      5      2      3     10
  8P GAIN WILD-TYPE     81     71    113     54     60     82
D14V12, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              18                81
  CLUS_2               6                71
  CLUS_3               5               113
  CLUS_4               2                54
  CLUS_5               3                60
  CLUS_6              10                82
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 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       32     17      6
  8Q GAIN WILD-TYPE    195     94    169
D15V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              32               195
  CLUS_2              17                94
  CLUS_3               6               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
  8Q GAIN MUTATED       38      7      8      2
  8Q GAIN WILD-TYPE    171    127    149     11
D15V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              38               171
  CLUS_2               7               127
  CLUS_3               8               149
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED       14     14     11      4
  8Q GAIN WILD-TYPE     77     81    114    111
D15V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                77
  CLUS_2              14                81
  CLUS_3              11               114
  CLUS_4               4               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
  8Q GAIN MUTATED       12      9     22
  8Q GAIN WILD-TYPE     71    149    163
D15V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12                71
  CLUS_2               9               149
  CLUS_3              22               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED       26      9      4     12      4
  8Q GAIN WILD-TYPE    104    106    101    121     26
D15V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              26               104
  CLUS_2               9               106
  CLUS_3               4               101
  CLUS_4              12               121
  CLUS_5               4                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 CLUS_5 CLUS_6 CLUS_7
  8Q GAIN MUTATED       27      3      2      9      3      6      5
  8Q GAIN WILD-TYPE    108     68     34     59     87     35     67
D15V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27               108
  CLUS_2               3                68
  CLUS_3               2                34
  CLUS_4               9                59
  CLUS_5               3                87
  CLUS_6               6                35
  CLUS_7               5                67
[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       22     10      5     17
  8Q GAIN WILD-TYPE    118     97     77    163
D15V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              22               118
  CLUS_2              10                97
  CLUS_3               5                77
  CLUS_4              17               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       31     16      7
  8Q GAIN WILD-TYPE    191    168     96
D15V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              31               191
  CLUS_2              16               168
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       21     12     11     10
  8Q GAIN WILD-TYPE    106    107     94    144
D15V11, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              21               106
  CLUS_2              12               107
  CLUS_3              11                94
  CLUS_4              10               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 CLUS_5 CLUS_6
  8Q GAIN MUTATED       21      8      6      2      3     14
  8Q GAIN WILD-TYPE     78     69    112     54     60     78
D15V12, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              21                78
  CLUS_2               8                69
  CLUS_3               6               112
  CLUS_4               2                54
  CLUS_5               3                60
  CLUS_6              14                78
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 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        8      8      1
  9P GAIN WILD-TYPE    219    103    174
D16V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8               219
  CLUS_2               8               103
  CLUS_3               1               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      2      2
  9P GAIN WILD-TYPE    203    127    155     11
D16V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6               203
  CLUS_2               7               127
  CLUS_3               2               155
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        4      7      1      2
  9P GAIN WILD-TYPE     87     88    124    113
D16V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                87
  CLUS_2               7                88
  CLUS_3               1               124
  CLUS_4               2               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
  9P GAIN MUTATED        3      4      7
  9P GAIN WILD-TYPE     80    154    178
D16V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                80
  CLUS_2               4               154
  CLUS_3               7               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 CLUS_5
  9P GAIN MUTATED        2      9      2      4      0
  9P GAIN WILD-TYPE    128    106    103    129     30
D16V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               128
  CLUS_2               9               106
  CLUS_3               2               103
  CLUS_4               4               129
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      5      1      2      1      4      2
  9P GAIN WILD-TYPE    133     66     35     66     89     37     70
D16V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               133
  CLUS_2               5                66
  CLUS_3               1                35
  CLUS_4               2                66
  CLUS_5               1                89
  CLUS_6               4                37
  CLUS_7               2                70
[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        6      4      2      5
  9P GAIN WILD-TYPE    134    103     80    175
D16V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6               134
  CLUS_2               4               103
  CLUS_3               2                80
  CLUS_4               5               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      8
  9P GAIN WILD-TYPE    218    179     95
D16V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               218
  CLUS_2               5               179
  CLUS_3               8                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      4      3      6
  9P GAIN WILD-TYPE    123    115    102    148
D16V11, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               123
  CLUS_2               4               115
  CLUS_3               3               102
  CLUS_4               6               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 CLUS_5 CLUS_6
  9P GAIN MUTATED        1      2      3      1      5      5
  9P GAIN WILD-TYPE     98     75    115     55     58     87
D16V12, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               2                75
  CLUS_3               3               115
  CLUS_4               1                55
  CLUS_5               5                58
  CLUS_6               5                87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 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       10     11      3
  9Q GAIN WILD-TYPE    217    100    172
D17V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              10               217
  CLUS_2              11               100
  CLUS_3               3               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10      7      3      4
  9Q GAIN WILD-TYPE    199    127    154      9
D17V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              10               199
  CLUS_2               7               127
  CLUS_3               3               154
  CLUS_4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        5     10      2      2
  9Q GAIN WILD-TYPE     86     85    123    113
D17V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5                86
  CLUS_2              10                85
  CLUS_3               2               123
  CLUS_4               2               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
  9Q GAIN MUTATED        4      6      9
  9Q GAIN WILD-TYPE     79    152    176
D17V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                79
  CLUS_2               6               152
  CLUS_3               9               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3     12      3      5      1
  9Q GAIN WILD-TYPE    127    103    102    128     29
D17V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               127
  CLUS_2              12               103
  CLUS_3               3               102
  CLUS_4               5               128
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3      5      1      5      2      7      1
  9Q GAIN WILD-TYPE    132     66     35     63     88     34     71
D17V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               132
  CLUS_2               5                66
  CLUS_3               1                35
  CLUS_4               5                63
  CLUS_5               2                88
  CLUS_6               7                34
  CLUS_7               1                71
[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        7      8      3      6
  9Q GAIN WILD-TYPE    133     99     79    174
D17V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               133
  CLUS_2               8                99
  CLUS_3               3                79
  CLUS_4               6               174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     11
  9Q GAIN WILD-TYPE    216    177     92
D17V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6               216
  CLUS_2               7               177
  CLUS_3              11                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      9      4      7
  9Q GAIN WILD-TYPE    123    110    101    147
D17V11, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               123
  CLUS_2               9               110
  CLUS_3               4               101
  CLUS_4               7               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 CLUS_5 CLUS_6
  9Q GAIN MUTATED        1      6      3      2      5      7
  9Q GAIN WILD-TYPE     98     71    115     54     58     85
D17V12, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                98
  CLUS_2               6                71
  CLUS_3               3               115
  CLUS_4               2                54
  CLUS_5               5                58
  CLUS_6               7                85
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 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      9      0
  10P GAIN WILD-TYPE    179    102    175
D18V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               48                179
  CLUS_2                9                102
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       47      3      0      7
  10P GAIN WILD-TYPE    162    131    157      6
D18V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               47                162
  CLUS_2                3                131
  CLUS_3                0                157
  CLUS_4                7                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       16     10     14      4
  10P GAIN WILD-TYPE     75     85    111    111
D18V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               16                 75
  CLUS_2               10                 85
  CLUS_3               14                111
  CLUS_4                4                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
  10P GAIN MUTATED       15      7     22
  10P GAIN WILD-TYPE     68    151    163
D18V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               15                 68
  CLUS_2                7                151
  CLUS_3               22                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P GAIN MUTATED       25     16      0     13      3
  10P GAIN WILD-TYPE    105     99    105    120     27
D18V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               25                105
  CLUS_2               16                 99
  CLUS_3                0                105
  CLUS_4               13                120
  CLUS_5                3                 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 CLUS_5 CLUS_6 CLUS_7
  10P GAIN MUTATED       29      0      0     11      0     14      3
  10P GAIN WILD-TYPE    106     71     36     57     90     27     69
D18V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               29                106
  CLUS_2                0                 71
  CLUS_3                0                 36
  CLUS_4               11                 57
  CLUS_5                0                 90
  CLUS_6               14                 27
  CLUS_7                3                 69
[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       16     20      5     15
  10P GAIN WILD-TYPE    124     87     77    165
D18V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               16                124
  CLUS_2               20                 87
  CLUS_3                5                 77
  CLUS_4               15                165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       28     15     13
  10P GAIN WILD-TYPE    194    169     90
D18V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               28                194
  CLUS_2               15                169
  CLUS_3               13                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       18     20      6     12
  10P GAIN WILD-TYPE    109     99     99    142
D18V11, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               18                109
  CLUS_2               20                 99
  CLUS_3                6                 99
  CLUS_4               12                142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  10P GAIN MUTATED       21     17      7      0      0     11
  10P GAIN WILD-TYPE     78     60    111     56     63     81
D18V12, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               21                 78
  CLUS_2               17                 60
  CLUS_3                7                111
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6               11                 81
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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        9      2      0
  10Q GAIN WILD-TYPE    218    109    175
D19V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                9                218
  CLUS_2                2                109
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      1      0      2
  10Q GAIN WILD-TYPE    201    133    157     11
D19V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                8                201
  CLUS_2                1                133
  CLUS_3                0                157
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        2      5      4      0
  10Q GAIN WILD-TYPE     89     90    121    115
D19V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                5                 90
  CLUS_3                4                121
  CLUS_4                0                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
  10Q GAIN MUTATED        1      1      9
  10Q GAIN WILD-TYPE     82    157    176
D19V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                1                157
  CLUS_3                9                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      5      0      4      0
  10Q GAIN WILD-TYPE    128    110    105    129     30
D19V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                128
  CLUS_2                5                110
  CLUS_3                0                105
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      0      0      4      0      5      0
  10Q GAIN WILD-TYPE    133     71     36     64     90     36     72
D19V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                0                 71
  CLUS_3                0                 36
  CLUS_4                4                 64
  CLUS_5                0                 90
  CLUS_6                5                 36
  CLUS_7                0                 72
[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        0      3      3      5
  10Q GAIN WILD-TYPE    140    104     79    175
D19V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                140
  CLUS_2                3                104
  CLUS_3                3                 79
  CLUS_4                5                175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        2      4      5
  10Q GAIN WILD-TYPE    220    180     98
D19V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                220
  CLUS_2                4                180
  CLUS_3                5                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      4      2      2
  10Q GAIN WILD-TYPE    124    115    103    152
D19V11, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                124
  CLUS_2                4                115
  CLUS_3                2                103
  CLUS_4                2                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 CLUS_5 CLUS_6
  10Q GAIN MUTATED        0      7      2      0      0      2
  10Q GAIN WILD-TYPE     99     70    116     56     63     90
D19V12, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 99
  CLUS_2                7                 70
  CLUS_3                2                116
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                2                 90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 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     10     15
  11P GAIN WILD-TYPE    222    101    160
D20V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                222
  CLUS_2               10                101
  CLUS_3               15                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        8      2     20      0
  11P GAIN WILD-TYPE    201    132    137     13
D20V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                201
  CLUS_2                2                132
  CLUS_3               20                137
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      8      9      7
  11P GAIN WILD-TYPE     88     87    116    108
D20V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                8                 87
  CLUS_3                9                116
  CLUS_4                7                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
  11P GAIN MUTATED        2      9     16
  11P GAIN WILD-TYPE     81    149    169
D20V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                9                149
  CLUS_3               16                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 CLUS_5
  11P GAIN MUTATED        7      1     13      7      2
  11P GAIN WILD-TYPE    123    114     92    126     28
D20V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                123
  CLUS_2                1                114
  CLUS_3               13                 92
  CLUS_4                7                126
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  11P GAIN MUTATED        6      0      6      3      9      1      5
  11P GAIN WILD-TYPE    129     71     30     65     81     40     67
D20V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                129
  CLUS_2                0                 71
  CLUS_3                6                 30
  CLUS_4                3                 65
  CLUS_5                9                 81
  CLUS_6                1                 40
  CLUS_7                5                 67
[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        6      4     11      9
  11P GAIN WILD-TYPE    134    103     71    171
D20V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                134
  CLUS_2                4                103
  CLUS_3               11                 71
  CLUS_4                9                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       14     15      1
  11P GAIN WILD-TYPE    208    169    102
D20V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               14                208
  CLUS_2               15                169
  CLUS_3                1                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6      3     10     11
  11P GAIN WILD-TYPE    121    116     95    143
D20V11, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                121
  CLUS_2                3                116
  CLUS_3               10                 95
  CLUS_4               11                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  11P GAIN MUTATED        4      2      7      8      0      9
  11P GAIN WILD-TYPE     95     75    111     48     63     83
D20V12, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 95
  CLUS_2                2                 75
  CLUS_3                7                111
  CLUS_4                8                 48
  CLUS_5                0                 63
  CLUS_6                9                 83
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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       26     12     20
  11Q GAIN WILD-TYPE    201     99    155
D21V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               26                201
  CLUS_2               12                 99
  CLUS_3               20                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED       28      5     24      1
  11Q GAIN WILD-TYPE    181    129    133     12
D21V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               28                181
  CLUS_2                5                129
  CLUS_3               24                133
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        8     11     21     10
  11Q GAIN WILD-TYPE     83     84    104    105
D21V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                 83
  CLUS_2               11                 84
  CLUS_3               21                104
  CLUS_4               10                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
  11Q GAIN MUTATED        9     12     29
  11Q GAIN WILD-TYPE     74    146    156
D21V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                9                 74
  CLUS_2               12                146
  CLUS_3               29                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED       16      5     17     16      4
  11Q GAIN WILD-TYPE    114    110     88    117     26
D21V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               16                114
  CLUS_2                5                110
  CLUS_3               17                 88
  CLUS_4               16                117
  CLUS_5                4                 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 CLUS_5 CLUS_6 CLUS_7
  11Q GAIN MUTATED       17      1      5      8     14      4      9
  11Q GAIN WILD-TYPE    118     70     31     60     76     37     63
D21V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               17                118
  CLUS_2                1                 70
  CLUS_3                5                 31
  CLUS_4                8                 60
  CLUS_5               14                 76
  CLUS_6                4                 37
  CLUS_7                9                 63
[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       14     11     14     19
  11Q GAIN WILD-TYPE    126     96     68    161
D21V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               14                126
  CLUS_2               11                 96
  CLUS_3               14                 68
  CLUS_4               19                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       30     23      5
  11Q GAIN WILD-TYPE    192    161     98
D21V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               30                192
  CLUS_2               23                161
  CLUS_3                5                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       16      8     13     21
  11Q GAIN WILD-TYPE    111    111     92    133
D21V11, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               16                111
  CLUS_2                8                111
  CLUS_3               13                 92
  CLUS_4               21                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 CLUS_5 CLUS_6
  11Q GAIN MUTATED       12      8     12     10      1     15
  11Q GAIN WILD-TYPE     87     69    106     46     62     77
D21V12, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               12                 87
  CLUS_2                8                 69
  CLUS_3               12                106
  CLUS_4               10                 46
  CLUS_5                1                 62
  CLUS_6               15                 77
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 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       15     15      2
  12P GAIN WILD-TYPE    212     96    173
D22V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               15                212
  CLUS_2               15                 96
  CLUS_3                2                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       21      7      4      0
  12P GAIN WILD-TYPE    188    127    153     13
D22V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               21                188
  CLUS_2                7                127
  CLUS_3                4                153
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7     10      5      5
  12P GAIN WILD-TYPE     84     85    120    110
D22V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 84
  CLUS_2               10                 85
  CLUS_3                5                120
  CLUS_4                5                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      9     15
  12P GAIN WILD-TYPE     80    149    170
D22V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                9                149
  CLUS_3               15                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED       11     12      3      4      2
  12P GAIN WILD-TYPE    119    103    102    129     28
D22V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                119
  CLUS_2               12                103
  CLUS_3                3                102
  CLUS_4                4                129
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  12P GAIN MUTATED       12      6      1      6      3      4      0
  12P GAIN WILD-TYPE    123     65     35     62     87     37     72
D22V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                123
  CLUS_2                6                 65
  CLUS_3                1                 35
  CLUS_4                6                 62
  CLUS_5                3                 87
  CLUS_6                4                 37
  CLUS_7                0                 72
[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     11      5      5
  12P GAIN WILD-TYPE    129     96     77    175
D22V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                129
  CLUS_2               11                 96
  CLUS_3                5                 77
  CLUS_4                5                175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       17      5     10
  12P GAIN WILD-TYPE    205    179     93
D22V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               17                205
  CLUS_2                5                179
  CLUS_3               10                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     11      3      7
  12P GAIN WILD-TYPE    116    108    102    147
D22V11, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                116
  CLUS_2               11                108
  CLUS_3                3                102
  CLUS_4                7                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 CLUS_5 CLUS_6
  12P GAIN MUTATED        6      7      1      3      5     10
  12P GAIN WILD-TYPE     93     70    117     53     58     82
D22V12, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                 93
  CLUS_2                7                 70
  CLUS_3                1                117
  CLUS_4                3                 53
  CLUS_5                5                 58
  CLUS_6               10                 82
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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        4     11      0
  12Q GAIN WILD-TYPE    223    100    175
D23V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                223
  CLUS_2               11                100
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      3      0
  12Q GAIN WILD-TYPE    203    128    154     13
D23V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                203
  CLUS_2                6                128
  CLUS_3                3                154
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      1
  12Q GAIN WILD-TYPE     88     87    124    114
D23V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                8                 87
  CLUS_3                1                124
  CLUS_4                1                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        1      3      9
  12Q GAIN WILD-TYPE     82    155    176
D23V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                3                155
  CLUS_3                9                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      0
  12Q GAIN WILD-TYPE    126    106    103    133     30
D23V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                126
  CLUS_2                9                106
  CLUS_3                2                103
  CLUS_4                0                133
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      6      1      1      2      2      0
  12Q GAIN WILD-TYPE    132     65     35     67     88     39     72
D23V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                6                 65
  CLUS_3                1                 35
  CLUS_4                1                 67
  CLUS_5                2                 88
  CLUS_6                2                 39
  CLUS_7                0                 72
[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        6      4      4      1
  12Q GAIN WILD-TYPE    134    103     78    179
D23V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                134
  CLUS_2                4                103
  CLUS_3                4                 78
  CLUS_4                1                179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        6      2      7
  12Q GAIN WILD-TYPE    216    182     96
D23V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                216
  CLUS_2                2                182
  CLUS_3                7                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      1      2
  12Q GAIN WILD-TYPE    122    112    104    152
D23V11, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                122
  CLUS_2                7                112
  CLUS_3                1                104
  CLUS_4                2                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 CLUS_5 CLUS_6
  12Q GAIN MUTATED        2      2      0      2      6      3
  12Q GAIN WILD-TYPE     97     75    118     54     57     89
D23V12, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                2                 75
  CLUS_3                0                118
  CLUS_4                2                 54
  CLUS_5                6                 57
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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    224    109    174
D24V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                224
  CLUS_2                2                109
  CLUS_3                1                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      1
  13Q GAIN WILD-TYPE    206    133    156     12
D24V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                206
  CLUS_2                1                133
  CLUS_3                1                156
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        3      1      0      2
  13Q GAIN WILD-TYPE     88     94    125    113
D24V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                1                 94
  CLUS_3                0                125
  CLUS_4                2                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
  13Q GAIN MUTATED        3      2      1
  13Q GAIN WILD-TYPE     80    156    184
D24V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                2                156
  CLUS_3                1                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q GAIN MUTATED        1      1      0      3      1
  13Q GAIN WILD-TYPE    129    114    105    130     29
D24V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                129
  CLUS_2                1                114
  CLUS_3                0                105
  CLUS_4                3                130
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      0      0      2      0      1      1
  13Q GAIN WILD-TYPE    133     71     36     66     90     40     71
D24V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                0                 71
  CLUS_3                0                 36
  CLUS_4                2                 66
  CLUS_5                0                 90
  CLUS_6                1                 40
  CLUS_7                1                 71
[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      0      0      3
  13Q GAIN WILD-TYPE    137    107     82    177
D24V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                137
  CLUS_2                0                107
  CLUS_3                0                 82
  CLUS_4                3                177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3      3      0
  13Q GAIN WILD-TYPE    219    181    103
D24V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                219
  CLUS_2                3                181
  CLUS_3                0                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        1      2      0      3
  13Q GAIN WILD-TYPE    126    117    105    151
D24V11, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                126
  CLUS_2                2                117
  CLUS_3                0                105
  CLUS_4                3                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 CLUS_5 CLUS_6
  13Q GAIN MUTATED        2      1      2      0      0      1
  13Q GAIN WILD-TYPE     97     76    116     56     63     91
D24V12, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                1                 76
  CLUS_3                2                116
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                1                 91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 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        2      2      0
  14Q GAIN WILD-TYPE    225    109    175
D25V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                225
  CLUS_2                2                109
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      1      1
  14Q GAIN WILD-TYPE    207    134    156     12
D25V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                207
  CLUS_2                0                134
  CLUS_3                1                156
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        1      1      1      0
  14Q GAIN WILD-TYPE     90     94    124    115
D25V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 90
  CLUS_2                1                 94
  CLUS_3                1                124
  CLUS_4                0                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
  14Q GAIN MUTATED        1      0      2
  14Q GAIN WILD-TYPE     82    158    183
D25V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                0                158
  CLUS_3                2                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q GAIN MUTATED        1      2      0      1      0
  14Q GAIN WILD-TYPE    129    113    105    132     30
D25V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                129
  CLUS_2                2                113
  CLUS_3                0                105
  CLUS_4                1                132
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2      0      0      0      1      1      0
  14Q GAIN WILD-TYPE    133     71     36     68     89     40     72
D25V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                0                 71
  CLUS_3                0                 36
  CLUS_4                0                 68
  CLUS_5                1                 89
  CLUS_6                1                 40
  CLUS_7                0                 72
[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      1      2      1
  14Q GAIN WILD-TYPE    140    106     80    179
D25V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                140
  CLUS_2                1                106
  CLUS_3                2                 80
  CLUS_4                1                179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      2      1
  14Q GAIN WILD-TYPE    221    182    102
D25V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                221
  CLUS_2                2                182
  CLUS_3                1                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      1      1
  14Q GAIN WILD-TYPE    126    118    104    153
D25V11, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                126
  CLUS_2                1                118
  CLUS_3                1                104
  CLUS_4                1                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 CLUS_5 CLUS_6
  14Q GAIN MUTATED        0      0      0      2      0      2
  14Q GAIN WILD-TYPE     99     77    118     54     63     90
D25V12, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 99
  CLUS_2                0                 77
  CLUS_3                0                118
  CLUS_4                2                 54
  CLUS_5                0                 63
  CLUS_6                2                 90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 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        6      5      0
  15Q GAIN WILD-TYPE    221    106    175
D26V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                221
  CLUS_2                5                106
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      3      0      1
  15Q GAIN WILD-TYPE    202    131    157     12
D26V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                7                202
  CLUS_2                3                131
  CLUS_3                0                157
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        0      4      6      0
  15Q GAIN WILD-TYPE     91     91    119    115
D26V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 91
  CLUS_2                4                 91
  CLUS_3                6                119
  CLUS_4                0                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
  15Q GAIN MUTATED        0      1      9
  15Q GAIN WILD-TYPE     83    157    176
D26V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                1                157
  CLUS_3                9                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    126    109    105    132     30
D26V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                126
  CLUS_2                6                109
  CLUS_3                0                105
  CLUS_4                1                132
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      3      0      1      0      3      0
  15Q GAIN WILD-TYPE    131     68     36     67     90     38     72
D26V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                3                 68
  CLUS_3                0                 36
  CLUS_4                1                 67
  CLUS_5                0                 90
  CLUS_6                3                 38
  CLUS_7                0                 72
[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        3      5      0      3
  15Q GAIN WILD-TYPE    137    102     82    177
D26V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                137
  CLUS_2                5                102
  CLUS_3                0                 82
  CLUS_4                3                177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      4
  15Q GAIN WILD-TYPE    217    182     99
D26V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                217
  CLUS_2                2                182
  CLUS_3                4                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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    123    113    105    153
D26V11, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                123
  CLUS_2                6                113
  CLUS_3                0                105
  CLUS_4                1                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 CLUS_5 CLUS_6
  15Q GAIN MUTATED        2      4      0      0      3      2
  15Q GAIN WILD-TYPE     97     73    118     56     60     90
D26V12, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                4                 73
  CLUS_3                0                118
  CLUS_4                0                 56
  CLUS_5                3                 60
  CLUS_6                2                 90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 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        5      7      4
  16P GAIN WILD-TYPE    222    104    171
D27V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                222
  CLUS_2                7                104
  CLUS_3                4                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      4      5      2
  16P GAIN WILD-TYPE    204    130    152     11
D27V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                204
  CLUS_2                4                130
  CLUS_3                5                152
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        3      5      4      2
  16P GAIN WILD-TYPE     88     90    121    113
D27V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                5                 90
  CLUS_3                4                121
  CLUS_4                2                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
  16P GAIN MUTATED        2      5      7
  16P GAIN WILD-TYPE     81    153    178
D27V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                5                153
  CLUS_3                7                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 CLUS_5
  16P GAIN MUTATED        2      8      2      4      0
  16P GAIN WILD-TYPE    128    107    103    129     30
D27V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                128
  CLUS_2                8                107
  CLUS_3                2                103
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      1      2      3      1      6      2
  16P GAIN WILD-TYPE    134     70     34     65     89     35     70
D27V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                134
  CLUS_2                1                 70
  CLUS_3                2                 34
  CLUS_4                3                 65
  CLUS_5                1                 89
  CLUS_6                6                 35
  CLUS_7                2                 70
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        1      5      2      8
  16P GAIN WILD-TYPE    139    102     80    172
D27V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                139
  CLUS_2                5                102
  CLUS_3                2                 80
  CLUS_4                8                172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     10      3
  16P GAIN WILD-TYPE    219    174    100
D27V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                219
  CLUS_2               10                174
  CLUS_3                3                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      8
  16P GAIN WILD-TYPE    126    114    103    146
D27V11, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                126
  CLUS_2                5                114
  CLUS_3                2                103
  CLUS_4                8                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 CLUS_5 CLUS_6
  16P GAIN MUTATED        1      5      4      0      0      6
  16P GAIN WILD-TYPE     98     72    114     56     63     86
D27V12, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                5                 72
  CLUS_3                4                114
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                6                 86
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 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        6     10      3
  16Q GAIN WILD-TYPE    221    101    172
D28V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                221
  CLUS_2               10                101
  CLUS_3                3                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9      4      4      2
  16Q GAIN WILD-TYPE    200    130    153     11
D28V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                9                200
  CLUS_2                4                130
  CLUS_3                4                153
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        4      5      3      3
  16Q GAIN WILD-TYPE     87     90    122    112
D28V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 87
  CLUS_2                5                 90
  CLUS_3                3                122
  CLUS_4                3                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
  16Q GAIN MUTATED        3      6      6
  16Q GAIN WILD-TYPE     80    152    179
D28V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                6                152
  CLUS_3                6                179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        4      9      1      5      0
  16Q GAIN WILD-TYPE    126    106    104    128     30
D28V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                126
  CLUS_2                9                106
  CLUS_3                1                104
  CLUS_4                5                128
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        2      1      1      3      1      8      3
  16Q GAIN WILD-TYPE    133     70     35     65     89     33     69
D28V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                1                 70
  CLUS_3                1                 35
  CLUS_4                3                 65
  CLUS_5                1                 89
  CLUS_6                8                 33
  CLUS_7                3                 69
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        1      7      2      9
  16Q GAIN WILD-TYPE    139    100     80    171
D28V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                139
  CLUS_2                7                100
  CLUS_3                2                 80
  CLUS_4                9                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     10      5
  16Q GAIN WILD-TYPE    218    174     98
D28V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                218
  CLUS_2               10                174
  CLUS_3                5                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      1      9
  16Q GAIN WILD-TYPE    124    113    104    145
D28V11, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                124
  CLUS_2                6                113
  CLUS_3                1                104
  CLUS_4                9                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  16Q GAIN MUTATED        2      7      5      0      0      5
  16Q GAIN WILD-TYPE     97     70    113     56     63     87
D28V12, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                7                 70
  CLUS_3                5                113
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 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        5     10      5
  17P GAIN WILD-TYPE    222    101    170
D29V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                222
  CLUS_2               10                101
  CLUS_3                5                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        6      4      8      2
  17P GAIN WILD-TYPE    203    130    149     11
D29V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                203
  CLUS_2                4                130
  CLUS_3                8                149
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        3      8      2      1
  17P GAIN WILD-TYPE     88     87    123    114
D29V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                8                 87
  CLUS_3                2                123
  CLUS_4                1                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        4      3      7
  17P GAIN WILD-TYPE     79    155    178
D29V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                 79
  CLUS_2                3                155
  CLUS_3                7                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 CLUS_5
  17P GAIN MUTATED        3      9      4      4      0
  17P GAIN WILD-TYPE    127    106    101    129     30
D29V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                127
  CLUS_2                9                106
  CLUS_3                4                101
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      1      2      5      5      1
  17P GAIN WILD-TYPE    133     67     35     66     85     36     71
D29V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                4                 67
  CLUS_3                1                 35
  CLUS_4                2                 66
  CLUS_5                5                 85
  CLUS_6                5                 36
  CLUS_7                1                 71
[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        5      8      3      4
  17P GAIN WILD-TYPE    135     99     79    176
D29V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                135
  CLUS_2                8                 99
  CLUS_3                3                 79
  CLUS_4                4                176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7      7      6
  17P GAIN WILD-TYPE    215    177     97
D29V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                215
  CLUS_2                7                177
  CLUS_3                6                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      4      4
  17P GAIN WILD-TYPE    122    112    101    150
D29V11, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                122
  CLUS_2                7                112
  CLUS_3                4                101
  CLUS_4                4                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P GAIN MUTATED        4      3      2      5      3      3
  17P GAIN WILD-TYPE     95     74    116     51     60     89
D29V12, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                 95
  CLUS_2                3                 74
  CLUS_3                2                116
  CLUS_4                5                 51
  CLUS_5                3                 60
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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      9      6
  17Q GAIN WILD-TYPE    219    102    169
D30V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                219
  CLUS_2                9                102
  CLUS_3                6                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
  17Q GAIN MUTATED        8      5      9      1
  17Q GAIN WILD-TYPE    201    129    148     12
D30V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                201
  CLUS_2                5                129
  CLUS_3                9                148
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        5      8      2      1
  17Q GAIN WILD-TYPE     86     87    123    114
D30V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                 86
  CLUS_2                8                 87
  CLUS_3                2                123
  CLUS_4                1                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        7      2      7
  17Q GAIN WILD-TYPE     76    156    178
D30V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                7                 76
  CLUS_2                2                156
  CLUS_3                7                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 CLUS_5
  17Q GAIN MUTATED        5      9      5      4      0
  17Q GAIN WILD-TYPE    125    106    100    129     30
D30V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                125
  CLUS_2                9                106
  CLUS_3                5                100
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      5      1      2      6      4      1
  17Q GAIN WILD-TYPE    131     66     35     66     84     37     71
D30V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                5                 66
  CLUS_3                1                 35
  CLUS_4                2                 66
  CLUS_5                6                 84
  CLUS_6                4                 37
  CLUS_7                1                 71
[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        6      9      4      4
  17Q GAIN WILD-TYPE    134     98     78    176
D30V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                134
  CLUS_2                9                 98
  CLUS_3                4                 78
  CLUS_4                4                176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       10      7      6
  17Q GAIN WILD-TYPE    212    177     97
D30V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               10                212
  CLUS_2                7                177
  CLUS_3                6                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      5      4
  17Q GAIN WILD-TYPE    121    111    100    150
D30V11, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                121
  CLUS_2                8                111
  CLUS_3                5                100
  CLUS_4                4                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q GAIN MUTATED        6      2      2      6      4      3
  17Q GAIN WILD-TYPE     93     75    116     50     59     89
D30V12, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                 93
  CLUS_2                2                 75
  CLUS_3                2                116
  CLUS_4                6                 50
  CLUS_5                4                 59
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 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        9      8      1
  18P GAIN WILD-TYPE    218    103    174
D31V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                218
  CLUS_2                8                103
  CLUS_3                1                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      5      1      4
  18P GAIN WILD-TYPE    201    129    156      9
D31V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                201
  CLUS_2                5                129
  CLUS_3                1                156
  CLUS_4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        3      5      3      3
  18P GAIN WILD-TYPE     88     90    122    112
D31V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                5                 90
  CLUS_3                3                122
  CLUS_4                3                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
  18P GAIN MUTATED        2      5      7
  18P GAIN WILD-TYPE     81    153    178
D31V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                5                153
  CLUS_3                7                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 CLUS_5
  18P GAIN MUTATED        2      8      0      5      3
  18P GAIN WILD-TYPE    128    107    105    128     27
D31V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                128
  CLUS_2                8                107
  CLUS_3                0                105
  CLUS_4                5                128
  CLUS_5                3                 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 CLUS_5 CLUS_6 CLUS_7
  18P GAIN MUTATED        4      4      0      3      0      5      2
  18P GAIN WILD-TYPE    131     67     36     65     90     36     70
D31V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2                4                 67
  CLUS_3                0                 36
  CLUS_4                3                 65
  CLUS_5                0                 90
  CLUS_6                5                 36
  CLUS_7                2                 70
[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        6      4      2      6
  18P GAIN WILD-TYPE    134    103     80    174
D31V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                134
  CLUS_2                4                103
  CLUS_3                2                 80
  CLUS_4                6                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7      4      7
  18P GAIN WILD-TYPE    215    180     96
D31V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                215
  CLUS_2                4                180
  CLUS_3                7                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      2      5
  18P GAIN WILD-TYPE    124    111    103    149
D31V11, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                124
  CLUS_2                8                111
  CLUS_3                2                103
  CLUS_4                5                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 CLUS_5 CLUS_6
  18P GAIN MUTATED        2      8      2      0      3      3
  18P GAIN WILD-TYPE     97     69    116     56     60     89
D31V12, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                8                 69
  CLUS_3                2                116
  CLUS_4                0                 56
  CLUS_5                3                 60
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 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        6      7      0
  18Q GAIN WILD-TYPE    221    104    175
D32V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                221
  CLUS_2                7                104
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      0      4
  18Q GAIN WILD-TYPE    206    128    157      9
D32V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                206
  CLUS_2                6                128
  CLUS_3                0                157
  CLUS_4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        2      4      4      1
  18Q GAIN WILD-TYPE     89     91    121    114
D32V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                4                 91
  CLUS_3                4                121
  CLUS_4                1                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        1      3      7
  18Q GAIN WILD-TYPE     82    155    178
D32V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                3                155
  CLUS_3                7                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 CLUS_5
  18Q GAIN MUTATED        1      9      0      1      2
  18Q GAIN WILD-TYPE    129    106    105    132     28
D32V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                129
  CLUS_2                9                106
  CLUS_3                0                105
  CLUS_4                1                132
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  18Q GAIN MUTATED        2      5      0      0      0      5      1
  18Q GAIN WILD-TYPE    133     66     36     68     90     36     71
D32V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2                5                 66
  CLUS_3                0                 36
  CLUS_4                0                 68
  CLUS_5                0                 90
  CLUS_6                5                 36
  CLUS_7                1                 71
[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        5      4      1      3
  18Q GAIN WILD-TYPE    135    103     81    177
D32V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                135
  CLUS_2                4                103
  CLUS_3                1                 81
  CLUS_4                3                177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        4      2      7
  18Q GAIN WILD-TYPE    218    182     96
D32V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                218
  CLUS_2                2                182
  CLUS_3                7                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      1      2
  18Q GAIN WILD-TYPE    125    111    104    152
D32V11, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                125
  CLUS_2                8                111
  CLUS_3                1                104
  CLUS_4                2                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 CLUS_5 CLUS_6
  18Q GAIN MUTATED        1      6      1      0      4      1
  18Q GAIN WILD-TYPE     98     71    117     56     59     91
D32V12, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                6                 71
  CLUS_3                1                117
  CLUS_4                0                 56
  CLUS_5                4                 59
  CLUS_6                1                 91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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       20     25     54
  19P GAIN WILD-TYPE    207     86    121
D33V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               20                207
  CLUS_2               25                 86
  CLUS_3               54                121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     30     59      0
  19P GAIN WILD-TYPE    199    104     98     13
D33V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                199
  CLUS_2               30                104
  CLUS_3               59                 98
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       16     23     28     17
  19P GAIN WILD-TYPE     75     72     97     98
D33V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                 75
  CLUS_2               23                 72
  CLUS_3               28                 97
  CLUS_4               17                 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
  19P GAIN MUTATED       10     24     50
  19P GAIN WILD-TYPE     73    134    135
D33V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                 73
  CLUS_2               24                134
  CLUS_3               50                135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     42     21      1
  19P GAIN WILD-TYPE    125     85     63    112     29
D33V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                5                125
  CLUS_2               30                 85
  CLUS_3               42                 63
  CLUS_4               21                112
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        6     25     14      7     30      3     14
  19P GAIN WILD-TYPE    129     46     22     61     60     38     58
D33V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                129
  CLUS_2               25                 46
  CLUS_3               14                 22
  CLUS_4                7                 61
  CLUS_5               30                 60
  CLUS_6                3                 38
  CLUS_7               14                 58
[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       21     18     29     31
  19P GAIN WILD-TYPE    119     89     53    149
D33V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               21                119
  CLUS_2               18                 89
  CLUS_3               29                 53
  CLUS_4               31                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
  19P GAIN MUTATED       35     36     28
  19P GAIN WILD-TYPE    187    148     75
D33V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               35                187
  CLUS_2               36                148
  CLUS_3               28                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED       14     24     36     25
  19P GAIN WILD-TYPE    113     95     69    129
D33V11, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               14                113
  CLUS_2               24                 95
  CLUS_3               36                 69
  CLUS_4               25                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 CLUS_5 CLUS_6
  19P GAIN MUTATED        8      9     21     24     23     14
  19P GAIN WILD-TYPE     91     68     97     32     40     78
D33V12, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 91
  CLUS_2                9                 68
  CLUS_3               21                 97
  CLUS_4               24                 32
  CLUS_5               23                 40
  CLUS_6               14                 78
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 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       11     14      0
  19Q GAIN WILD-TYPE    216     97    175
D34V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               11                216
  CLUS_2               14                 97
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     23      0      0
  19Q GAIN WILD-TYPE    207    111    157     13
D34V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                207
  CLUS_2               23                111
  CLUS_3                0                157
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      5      2
  19Q GAIN WILD-TYPE     88     87    120    113
D34V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                8                 87
  CLUS_3                5                120
  CLUS_4                2                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
  19Q GAIN MUTATED        1      3     14
  19Q GAIN WILD-TYPE     82    155    171
D34V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                3                155
  CLUS_3               14                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    129     96    105    129     29
D34V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                129
  CLUS_2               19                 96
  CLUS_3                0                105
  CLUS_4                4                129
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        2     19      0      4      0      0      0
  19Q GAIN WILD-TYPE    133     52     36     64     90     41     72
D34V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                133
  CLUS_2               19                 52
  CLUS_3                0                 36
  CLUS_4                4                 64
  CLUS_5                0                 90
  CLUS_6                0                 41
  CLUS_7                0                 72
[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        7     12      0      6
  19Q GAIN WILD-TYPE    133     95     82    174
D34V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                133
  CLUS_2               12                 95
  CLUS_3                0                 82
  CLUS_4                6                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        3      2     20
  19Q GAIN WILD-TYPE    219    182     83
D34V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                219
  CLUS_2                2                182
  CLUS_3               20                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     14      0      4
  19Q GAIN WILD-TYPE    120    105    105    150
D34V11, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                120
  CLUS_2               14                105
  CLUS_3                0                105
  CLUS_4                4                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q GAIN MUTATED        2      0      3      0     19      1
  19Q GAIN WILD-TYPE     97     77    115     56     44     91
D34V12, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                0                 77
  CLUS_3                3                115
  CLUS_4                0                 56
  CLUS_5               19                 44
  CLUS_6                1                 91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 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       15     28      2
  20P GAIN WILD-TYPE    212     83    173
D35V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                212
  CLUS_2               28                 83
  CLUS_3                2                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6     31      6      2
  20P GAIN WILD-TYPE    203    103    151     11
D35V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                203
  CLUS_2               31                103
  CLUS_3                6                151
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        9     17      7      5
  20P GAIN WILD-TYPE     82     78    118    110
D35V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                 82
  CLUS_2               17                 78
  CLUS_3                7                118
  CLUS_4                5                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      8     25
  20P GAIN WILD-TYPE     78    150    160
D35V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                 78
  CLUS_2                8                150
  CLUS_3               25                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P GAIN MUTATED        3     30      3      8      1
  20P GAIN WILD-TYPE    127     85    102    125     29
D35V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                127
  CLUS_2               30                 85
  CLUS_3                3                102
  CLUS_4                8                125
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        3     23      2      8      2      5      2
  20P GAIN WILD-TYPE    132     48     34     60     88     36     70
D35V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2               23                 48
  CLUS_3                2                 34
  CLUS_4                8                 60
  CLUS_5                2                 88
  CLUS_6                5                 36
  CLUS_7                2                 70
[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       16     13      3     13
  20P GAIN WILD-TYPE    124     94     79    167
D35V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               16                124
  CLUS_2               13                 94
  CLUS_3                3                 79
  CLUS_4               13                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        9     10     26
  20P GAIN WILD-TYPE    213    174     77
D35V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                213
  CLUS_2               10                174
  CLUS_3               26                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       14     19      1     11
  20P GAIN WILD-TYPE    113    100    104    143
D35V11, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               14                113
  CLUS_2               19                100
  CLUS_3                1                104
  CLUS_4               11                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  20P GAIN MUTATED        4      4      9      2     21      5
  20P GAIN WILD-TYPE     95     73    109     54     42     87
D35V12, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 95
  CLUS_2                4                 73
  CLUS_3                9                109
  CLUS_4                2                 54
  CLUS_5               21                 42
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 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       16     26      2
  20Q GAIN WILD-TYPE    211     85    173
D36V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               16                211
  CLUS_2               26                 85
  CLUS_3                2                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6     30      6      2
  20Q GAIN WILD-TYPE    203    104    151     11
D36V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                203
  CLUS_2               30                104
  CLUS_3                6                151
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        9     17      7      3
  20Q GAIN WILD-TYPE     82     78    118    112
D36V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                 82
  CLUS_2               17                 78
  CLUS_3                7                118
  CLUS_4                3                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
  20Q GAIN MUTATED        5      6     25
  20Q GAIN WILD-TYPE     78    152    160
D36V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                 78
  CLUS_2                6                152
  CLUS_3               25                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q GAIN MUTATED        4     30      3      6      1
  20Q GAIN WILD-TYPE    126     85    102    127     29
D36V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                126
  CLUS_2               30                 85
  CLUS_3                3                102
  CLUS_4                6                127
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4     23      2      7      2      5      1
  20Q GAIN WILD-TYPE    131     48     34     61     88     36     71
D36V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                131
  CLUS_2               23                 48
  CLUS_3                2                 34
  CLUS_4                7                 61
  CLUS_5                2                 88
  CLUS_6                5                 36
  CLUS_7                1                 71
[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       17     13      3     11
  20Q GAIN WILD-TYPE    123     94     79    169
D36V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               17                123
  CLUS_2               13                 94
  CLUS_3                3                 79
  CLUS_4               11                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       10      8     26
  20Q GAIN WILD-TYPE    212    176     77
D36V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                212
  CLUS_2                8                176
  CLUS_3               26                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       16     18      1      9
  20Q GAIN WILD-TYPE    111    101    104    145
D36V11, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               16                111
  CLUS_2               18                101
  CLUS_3                1                104
  CLUS_4                9                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  20Q GAIN MUTATED        6      3      7      2     21      5
  20Q GAIN WILD-TYPE     93     74    111     54     42     87
D36V12, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                 93
  CLUS_2                3                 74
  CLUS_3                7                111
  CLUS_4                2                 54
  CLUS_5               21                 42
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        0      0      1
  21Q GAIN WILD-TYPE      9     10      7
D37V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 26 
        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-E1-5304         TCGA-E1-5311 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        0      1      0      0
  21Q GAIN WILD-TYPE      7      6      7      6
D37V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 26 
        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-E1-5304         TCGA-E1-5311 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        4     13      6
  21Q GAIN WILD-TYPE    223     98    169
D37V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                223
  CLUS_2               13                 98
  CLUS_3                6                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
  21Q GAIN MUTATED        5      9      9      0
  21Q GAIN WILD-TYPE    204    125    148     13
D37V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                204
  CLUS_2                9                125
  CLUS_3                9                148
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      8      4      5
  21Q GAIN WILD-TYPE     89     87    121    110
D37V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                8                 87
  CLUS_3                4                121
  CLUS_4                5                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      6     12
  21Q GAIN WILD-TYPE     82    152    173
D37V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                6                152
  CLUS_3               12                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      7      5      7      1
  21Q GAIN WILD-TYPE    127    108    100    126     29
D37V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                127
  CLUS_2                7                108
  CLUS_3                5                100
  CLUS_4                7                126
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      7      3      3      3      1      3
  21Q GAIN WILD-TYPE    132     64     33     65     87     40     69
D37V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                132
  CLUS_2                7                 64
  CLUS_3                3                 33
  CLUS_4                3                 65
  CLUS_5                3                 87
  CLUS_6                1                 40
  CLUS_7                3                 69
[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        8      2      6      7
  21Q GAIN WILD-TYPE    132    105     76    173
D37V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                8                132
  CLUS_2                2                105
  CLUS_3                6                 76
  CLUS_4                7                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        6      8      9
  21Q GAIN WILD-TYPE    216    176     94
D37V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                6                216
  CLUS_2                8                176
  CLUS_3                9                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      5      5      9
  21Q GAIN WILD-TYPE    123    114    100    145
D37V11, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                123
  CLUS_2                5                114
  CLUS_3                5                100
  CLUS_4                9                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  21Q GAIN MUTATED        2      1      7      2      6      5
  21Q GAIN WILD-TYPE     97     76    111     54     57     87
D37V12, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                1                 76
  CLUS_3                7                111
  CLUS_4                2                 54
  CLUS_5                6                 57
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 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      4     16
  22Q GAIN WILD-TYPE    224    107    159
D38V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                224
  CLUS_2                4                107
  CLUS_3               16                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        1      3     18      1
  22Q GAIN WILD-TYPE    208    131    139     12
D38V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                208
  CLUS_2                3                131
  CLUS_3               18                139
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        3      6      5      4
  22Q GAIN WILD-TYPE     88     89    120    111
D38V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 88
  CLUS_2                6                 89
  CLUS_3                5                120
  CLUS_4                4                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
  22Q GAIN MUTATED        6      3      9
  22Q GAIN WILD-TYPE     77    155    176
D38V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                 77
  CLUS_2                3                155
  CLUS_3                9                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    129    111     92    128     30
D38V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                129
  CLUS_2                4                111
  CLUS_3               13                 92
  CLUS_4                5                128
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      2      6      2      7      2      4
  22Q GAIN WILD-TYPE    135     69     30     66     83     39     68
D38V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                135
  CLUS_2                2                 69
  CLUS_3                6                 30
  CLUS_4                2                 66
  CLUS_5                7                 83
  CLUS_6                2                 39
  CLUS_7                4                 68
[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        4      3      9      7
  22Q GAIN WILD-TYPE    136    104     73    173
D38V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                136
  CLUS_2                3                104
  CLUS_3                9                 73
  CLUS_4                7                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8     11      4
  22Q GAIN WILD-TYPE    214    173     99
D38V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                214
  CLUS_2               11                173
  CLUS_3                4                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     12      8
  22Q GAIN WILD-TYPE    126    117     93    146
D38V11, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                126
  CLUS_2                2                117
  CLUS_3               12                 93
  CLUS_4                8                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 CLUS_5 CLUS_6
  22Q GAIN MUTATED        1      1      3      7      2      9
  22Q GAIN WILD-TYPE     98     76    115     49     61     83
D38V12, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                1                 76
  CLUS_3                3                115
  CLUS_4                7                 49
  CLUS_5                2                 61
  CLUS_6                9                 83
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED        1      0      1
  XP GAIN WILD-TYPE      8     10      7
D39V1, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-E1-5322 
"XP GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        1      1      0      0
  XP GAIN WILD-TYPE      6      6      7      6
D39V2, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-E1-5322 
"XP GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       13      8      1
  XP GAIN WILD-TYPE    214    103    174
D39V3, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              13               214
  CLUS_2               8               103
  CLUS_3               1               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED       18      2      0      2
  XP GAIN WILD-TYPE    191    132    157     11
D39V4, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              18               191
  CLUS_2               2               132
  CLUS_3               0               157
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        5      5      4      2
  XP GAIN WILD-TYPE     86     90    121    113
D39V5, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               5                86
  CLUS_2               5                90
  CLUS_3               4               121
  CLUS_4               2               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
  XP GAIN MUTATED        4      4      8
  XP GAIN WILD-TYPE     79    154    177
D39V6, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               4                79
  CLUS_2               4               154
  CLUS_3               8               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP GAIN MUTATED       10      4      0      7      1
  XP GAIN WILD-TYPE    120    111    105    126     29
D39V7, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              10               120
  CLUS_2               4               111
  CLUS_3               0               105
  CLUS_4               7               126
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XP GAIN MUTATED        9      2      0      7      0      2      2
  XP GAIN WILD-TYPE    126     69     36     61     90     39     70
D39V8, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               9               126
  CLUS_2               2                69
  CLUS_3               0                36
  CLUS_4               7                61
  CLUS_5               0                90
  CLUS_6               2                39
  CLUS_7               2                70
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        8      6      2      5
  XP GAIN WILD-TYPE    132    101     80    175
D39V9, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               8               132
  CLUS_2               6               101
  CLUS_3               2                80
  CLUS_4               5               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       10      6      5
  XP GAIN WILD-TYPE    212    178     98
D39V10, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              10               212
  CLUS_2               6               178
  CLUS_3               5                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        5      6      5      5
  XP GAIN WILD-TYPE    122    113    100    149
D39V11, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               5               122
  CLUS_2               6               113
  CLUS_3               5               100
  CLUS_4               5               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 CLUS_5 CLUS_6
  XP GAIN MUTATED        8      3      3      0      2      5
  XP GAIN WILD-TYPE     91     74    115     56     61     87
D39V12, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               8                91
  CLUS_2               3                74
  CLUS_3               3               115
  CLUS_4               0                56
  CLUS_5               2                61
  CLUS_6               5                87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 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
D40V1, 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
D40V2, 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       29     12      1
  XQ GAIN WILD-TYPE    198     99    174
D40V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              29               198
  CLUS_2              12                99
  CLUS_3               1               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      0      2
  XQ GAIN WILD-TYPE    175    128    157     11
D40V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              34               175
  CLUS_2               6               128
  CLUS_3               0               157
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED       10      7     15      3
  XQ GAIN WILD-TYPE     81     88    110    112
D40V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              10                81
  CLUS_2               7                88
  CLUS_3              15               110
  CLUS_4               3               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
  XQ GAIN MUTATED       10      6     19
  XQ GAIN WILD-TYPE     73    152    166
D40V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              10                73
  CLUS_2               6               152
  CLUS_3              19               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED       18      9      0     10      5
  XQ GAIN WILD-TYPE    112    106    105    123     25
D40V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              18               112
  CLUS_2               9               106
  CLUS_3               0               105
  CLUS_4              10               123
  CLUS_5               5                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 CLUS_5 CLUS_6 CLUS_7
  XQ GAIN MUTATED       24      3      0      8      0      4      3
  XQ GAIN WILD-TYPE    111     68     36     60     90     37     69
D40V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              24               111
  CLUS_2               3                68
  CLUS_3               0                36
  CLUS_4               8                60
  CLUS_5               0                90
  CLUS_6               4                37
  CLUS_7               3                69
[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       18     10      1     12
  XQ GAIN WILD-TYPE    122     97     81    168
D40V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              18               122
  CLUS_2              10                97
  CLUS_3               1                81
  CLUS_4              12               168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       22     12      7
  XQ GAIN WILD-TYPE    200    172     96
D40V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              22               200
  CLUS_2              12               172
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     13      3     10
  XQ GAIN WILD-TYPE    112    106    102    144
D40V11, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              15               112
  CLUS_2              13               106
  CLUS_3               3               102
  CLUS_4              10               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 CLUS_5 CLUS_6
  XQ GAIN MUTATED       16      7      5      0      3     10
  XQ GAIN WILD-TYPE     83     70    113     56     60     82
D40V12, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              16                83
  CLUS_2               7                70
  CLUS_3               5               113
  CLUS_4               0                56
  CLUS_5               3                60
  CLUS_6              10                82
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 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
D41V1, 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
D41V2, 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        7     12    165
  1P LOSS WILD-TYPE    220     99     10
D41V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7               220
  CLUS_2              12                99
  CLUS_3             165                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        5     23    156      0
  1P LOSS WILD-TYPE    204    111      1     13
D41V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5               204
  CLUS_2              23               111
  CLUS_3             156                 1
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       24     31     47     58
  1P LOSS WILD-TYPE     67     64     78     57
D41V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              24                67
  CLUS_2              31                64
  CLUS_3              47                78
  CLUS_4              58                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
  1P LOSS MUTATED       23     77     60
  1P LOSS WILD-TYPE     60     81    125
D41V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              23                60
  CLUS_2              77                81
  CLUS_3              60               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     10    104     58      9
  1P LOSS WILD-TYPE    127    105      1     75     21
D41V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               127
  CLUS_2              10               105
  CLUS_3             104                 1
  CLUS_4              58                75
  CLUS_5               9                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 CLUS_5 CLUS_6 CLUS_7
  1P LOSS MUTATED        3      6     36      1     87      1     50
  1P LOSS WILD-TYPE    132     65      0     67      3     40     22
D41V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               132
  CLUS_2               6                65
  CLUS_3              36                 0
  CLUS_4               1                67
  CLUS_5              87                 3
  CLUS_6               1                40
  CLUS_7              50                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
  1P LOSS MUTATED       27      8     68     81
  1P LOSS WILD-TYPE    113     99     14     99
D41V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              27               113
  CLUS_2               8                99
  CLUS_3              68                14
  CLUS_4              81                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
  1P LOSS MUTATED       80     97      7
  1P LOSS WILD-TYPE    142     87     96
D41V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              80               142
  CLUS_2              97                87
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       16     17     83     68
  1P LOSS WILD-TYPE    111    102     22     86
D41V11, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              16               111
  CLUS_2              17               102
  CLUS_3              83                22
  CLUS_4              68                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 CLUS_5 CLUS_6
  1P LOSS MUTATED        6     25     59     55      4     35
  1P LOSS WILD-TYPE     93     52     59      1     59     57
D41V12, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6                93
  CLUS_2              25                52
  CLUS_3              59                59
  CLUS_4              55                 1
  CLUS_5               4                59
  CLUS_6              35                57
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) 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
D42V1, 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
D42V2, 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      8     11
  1Q LOSS WILD-TYPE    220    103    164
D42V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               220
  CLUS_2               8               103
  CLUS_3              11               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        6      7     13      0
  1Q LOSS WILD-TYPE    203    127    144     13
D42V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6               203
  CLUS_2               7               127
  CLUS_3              13               144
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        3      7      6      8
  1Q LOSS WILD-TYPE     88     88    119    107
D42V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                88
  CLUS_2               7                88
  CLUS_3               6               119
  CLUS_4               8               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
  1Q LOSS MUTATED        1     10     13
  1Q LOSS WILD-TYPE     82    148    172
D42V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                82
  CLUS_2              10               148
  CLUS_3              13               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      5      7     10      1
  1Q LOSS WILD-TYPE    127    110     98    123     29
D42V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               127
  CLUS_2               5               110
  CLUS_3               7                98
  CLUS_4              10               123
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        4      3      5      0      5      1      8
  1Q LOSS WILD-TYPE    131     68     31     68     85     40     64
D42V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               131
  CLUS_2               3                68
  CLUS_3               5                31
  CLUS_4               0                68
  CLUS_5               5                85
  CLUS_6               1                40
  CLUS_7               8                64
[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      4      9      9
  1Q LOSS WILD-TYPE    136    103     73    171
D42V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               136
  CLUS_2               4               103
  CLUS_3               9                73
  CLUS_4               9               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       10     13      3
  1Q LOSS WILD-TYPE    212    171    100
D42V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              10               212
  CLUS_2              13               171
  CLUS_3               3               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      7      6      9
  1Q LOSS WILD-TYPE    123    112     99    145
D42V11, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               123
  CLUS_2               7               112
  CLUS_3               6                99
  CLUS_4               9               145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  1Q LOSS MUTATED        1      5      8      4      3      5
  1Q LOSS WILD-TYPE     98     72    110     52     60     87
D42V12, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                98
  CLUS_2               5                72
  CLUS_3               8               110
  CLUS_4               4                52
  CLUS_5               3                60
  CLUS_6               5                87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 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
D43V1, 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
D43V2, 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       14      5      2
  2P LOSS WILD-TYPE    213    106    173
D43V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              14               213
  CLUS_2               5               106
  CLUS_3               2               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      6      2      2
  2P LOSS WILD-TYPE    198    128    155     11
D43V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              11               198
  CLUS_2               6               128
  CLUS_3               2               155
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        2      9      4      4
  2P LOSS WILD-TYPE     89     86    121    111
D43V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                89
  CLUS_2               9                86
  CLUS_3               4               121
  CLUS_4               4               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
  2P LOSS MUTATED        3      7      9
  2P LOSS WILD-TYPE     80    151    176
D43V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               7               151
  CLUS_3               9               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    124    106    103    130     29
D43V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               124
  CLUS_2               9               106
  CLUS_3               2               103
  CLUS_4               3               130
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      0      2      2      6      1
  2P LOSS WILD-TYPE    129     67     36     66     88     35     71
D43V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               129
  CLUS_2               4                67
  CLUS_3               0                36
  CLUS_4               2                66
  CLUS_5               2                88
  CLUS_6               6                35
  CLUS_7               1                71
[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        5      9      1      5
  2P LOSS WILD-TYPE    135     98     81    175
D43V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5               135
  CLUS_2               9                98
  CLUS_3               1                81
  CLUS_4               5               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9      5      6
  2P LOSS WILD-TYPE    213    179     97
D43V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9               213
  CLUS_2               5               179
  CLUS_3               6                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      6      1      5
  2P LOSS WILD-TYPE    120    113    104    149
D43V11, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               7               120
  CLUS_2               6               113
  CLUS_3               1               104
  CLUS_4               5               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 CLUS_5 CLUS_6
  2P LOSS MUTATED        4      7      4      1      0      3
  2P LOSS WILD-TYPE     95     70    114     55     63     89
D43V12, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4                95
  CLUS_2               7                70
  CLUS_3               4               114
  CLUS_4               1                55
  CLUS_5               0                63
  CLUS_6               3                89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 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
D44V1, 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
D44V2, 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       14      2      2
  2Q LOSS WILD-TYPE    213    109    173
D44V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              14               213
  CLUS_2               2               109
  CLUS_3               2               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12      2      2      2
  2Q LOSS WILD-TYPE    197    132    155     11
D44V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              12               197
  CLUS_2               2               132
  CLUS_3               2               155
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        2      9      3      3
  2Q LOSS WILD-TYPE     89     86    122    112
D44V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                89
  CLUS_2               9                86
  CLUS_3               3               122
  CLUS_4               3               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
  2Q LOSS MUTATED        3      5      9
  2Q LOSS WILD-TYPE     80    153    176
D44V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               5               153
  CLUS_3               9               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    125    108    103    130     29
D44V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               125
  CLUS_2               7               108
  CLUS_3               2               103
  CLUS_4               3               130
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        5      1      0      3      2      7      0
  2Q LOSS WILD-TYPE    130     70     36     65     88     34     72
D44V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               130
  CLUS_2               1                70
  CLUS_3               0                36
  CLUS_4               3                65
  CLUS_5               2                88
  CLUS_6               7                34
  CLUS_7               0                72
[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        3      9      2      3
  2Q LOSS WILD-TYPE    137     98     80    177
D44V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               137
  CLUS_2               9                98
  CLUS_3               2                80
  CLUS_4               3               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9      5      3
  2Q LOSS WILD-TYPE    213    179    100
D44V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9               213
  CLUS_2               5               179
  CLUS_3               3               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      2      3
  2Q LOSS WILD-TYPE    124    111    103    151
D44V11, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               124
  CLUS_2               8               111
  CLUS_3               2               103
  CLUS_4               3               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 CLUS_5 CLUS_6
  2Q LOSS MUTATED        1      9      2      1      0      3
  2Q LOSS WILD-TYPE     98     68    116     55     63     89
D44V12, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                98
  CLUS_2               9                68
  CLUS_3               2               116
  CLUS_4               1                55
  CLUS_5               0                63
  CLUS_6               3                89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 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
D45V1, 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
D45V2, 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       13     12      5
  3P LOSS WILD-TYPE    214     99    170
D45V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              13               214
  CLUS_2              12                99
  CLUS_3               5               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED       14      9      5      2
  3P LOSS WILD-TYPE    195    125    152     11
D45V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              14               195
  CLUS_2               9               125
  CLUS_3               5               152
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        4     13      6      3
  3P LOSS WILD-TYPE     87     82    119    112
D45V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                87
  CLUS_2              13                82
  CLUS_3               6               119
  CLUS_4               3               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
  3P LOSS MUTATED        3      6     17
  3P LOSS WILD-TYPE     80    152    168
D45V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               6               152
  CLUS_3              17               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P LOSS MUTATED        8     13      3      5      1
  3P LOSS WILD-TYPE    122    102    102    128     29
D45V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               8               122
  CLUS_2              13               102
  CLUS_3               3               102
  CLUS_4               5               128
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9      7      1      3      3      6      1
  3P LOSS WILD-TYPE    126     64     35     65     87     35     71
D45V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2               7                64
  CLUS_3               1                35
  CLUS_4               3                65
  CLUS_5               3                87
  CLUS_6               6                35
  CLUS_7               1                71
[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        9     14      4      3
  3P LOSS WILD-TYPE    131     93     78    177
D45V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               131
  CLUS_2              14                93
  CLUS_3               4                78
  CLUS_4               3               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       18      2     10
  3P LOSS WILD-TYPE    204    182     93
D45V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              18               204
  CLUS_2               2               182
  CLUS_3              10                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      9      8      3
  3P LOSS WILD-TYPE    118    110     97    151
D45V11, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9               118
  CLUS_2               9               110
  CLUS_3               8                97
  CLUS_4               3               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 CLUS_5 CLUS_6
  3P LOSS MUTATED        9      7      2      2      4      5
  3P LOSS WILD-TYPE     90     70    116     54     59     87
D45V12, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9                90
  CLUS_2               7                70
  CLUS_3               2               116
  CLUS_4               2                54
  CLUS_5               4                59
  CLUS_6               5                87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 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
D46V1, 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
D46V2, 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       16      7      5
  3Q LOSS WILD-TYPE    211    104    170
D46V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              16               211
  CLUS_2               7               104
  CLUS_3               5               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED       16      7      4      1
  3Q LOSS WILD-TYPE    193    127    153     12
D46V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              16               193
  CLUS_2               7               127
  CLUS_3               4               153
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        3      9     10      4
  3Q LOSS WILD-TYPE     88     86    115    111
D46V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                88
  CLUS_2               9                86
  CLUS_3              10               115
  CLUS_4               4               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
  3Q LOSS MUTATED        3      6     17
  3Q LOSS WILD-TYPE     80    152    168
D46V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               6               152
  CLUS_3              17               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q LOSS MUTATED        8     11      2      6      1
  3Q LOSS WILD-TYPE    122    104    103    127     29
D46V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8               122
  CLUS_2              11               104
  CLUS_3               2               103
  CLUS_4               6               127
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9      4      1      4      2      7      1
  3Q LOSS WILD-TYPE    126     67     35     64     88     34     71
D46V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2               4                67
  CLUS_3               1                35
  CLUS_4               4                64
  CLUS_5               2                88
  CLUS_6               7                34
  CLUS_7               1                71
[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        8     11      3      6
  3Q LOSS WILD-TYPE    132     96     79    174
D46V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8               132
  CLUS_2              11                96
  CLUS_3               3                79
  CLUS_4               6               174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       14      4     10
  3Q LOSS WILD-TYPE    208    180     93
D46V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              14               208
  CLUS_2               4               180
  CLUS_3              10                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      8      4      4
  3Q LOSS WILD-TYPE    116    111    101    150
D46V11, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              11               116
  CLUS_2               8               111
  CLUS_3               4               101
  CLUS_4               4               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q LOSS MUTATED        8     10      2      2      2      3
  3Q LOSS WILD-TYPE     91     67    116     54     61     89
D46V12, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8                91
  CLUS_2              10                67
  CLUS_3               2               116
  CLUS_4               2                54
  CLUS_5               2                61
  CLUS_6               3                89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 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
D47V1, 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
D47V2, 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       12     16     44
  4P LOSS WILD-TYPE    215     95    131
D47V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              12               215
  CLUS_2              16                95
  CLUS_3              44               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       24      3     44      1
  4P LOSS WILD-TYPE    185    131    113     12
D47V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              24               185
  CLUS_2               3               131
  CLUS_3              44               113
  CLUS_4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        6     21     20     12
  4P LOSS WILD-TYPE     85     74    105    103
D47V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                85
  CLUS_2              21                74
  CLUS_3              20               105
  CLUS_4              12               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       11     21     27
  4P LOSS WILD-TYPE     72    137    158
D47V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11                72
  CLUS_2              21               137
  CLUS_3              27               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P LOSS MUTATED       16      6     29     18      3
  4P LOSS WILD-TYPE    114    109     76    115     27
D47V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              16               114
  CLUS_2               6               109
  CLUS_3              29                76
  CLUS_4              18               115
  CLUS_5               3                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 CLUS_5 CLUS_6 CLUS_7
  4P LOSS MUTATED       14      2     14      7     23      3      9
  4P LOSS WILD-TYPE    121     69     22     61     67     38     63
D47V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              14               121
  CLUS_2               2                69
  CLUS_3              14                22
  CLUS_4               7                61
  CLUS_5              23                67
  CLUS_6               3                38
  CLUS_7               9                63
[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       13     12     26     21
  4P LOSS WILD-TYPE    127     95     56    159
D47V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13               127
  CLUS_2              12                95
  CLUS_3              26                56
  CLUS_4              21               159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       39     29      4
  4P LOSS WILD-TYPE    183    155     99
D47V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              39               183
  CLUS_2              29               155
  CLUS_3               4                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11     11     28     22
  4P LOSS WILD-TYPE    116    108     77    132
D47V11, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11               116
  CLUS_2              11               108
  CLUS_3              28                77
  CLUS_4              22               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 CLUS_5 CLUS_6
  4P LOSS MUTATED        7     13     13     18      1     20
  4P LOSS WILD-TYPE     92     64    105     38     62     72
D47V12, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                92
  CLUS_2              13                64
  CLUS_3              13               105
  CLUS_4              18                38
  CLUS_5               1                62
  CLUS_6              20                72
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) 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
D48V1, 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
D48V2, 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       24     21     49
  4Q LOSS WILD-TYPE    203     90    126
D48V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              24               203
  CLUS_2              21                90
  CLUS_3              49               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       37      8     47      2
  4Q LOSS WILD-TYPE    172    126    110     11
D48V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              37               172
  CLUS_2               8               126
  CLUS_3              47               110
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        8     25     23     21
  4Q LOSS WILD-TYPE     83     70    102     94
D48V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                83
  CLUS_2              25                70
  CLUS_3              23               102
  CLUS_4              21                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
  4Q LOSS MUTATED       11     32     34
  4Q LOSS WILD-TYPE     72    126    151
D48V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11                72
  CLUS_2              32               126
  CLUS_3              34               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       22     11     31     28      2
  4Q LOSS WILD-TYPE    108    104     74    105     28
D48V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              22               108
  CLUS_2              11               104
  CLUS_3              31                74
  CLUS_4              28               105
  CLUS_5               2                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 CLUS_5 CLUS_6 CLUS_7
  4Q LOSS MUTATED       19      2     15     11     24      8     15
  4Q LOSS WILD-TYPE    116     69     21     57     66     33     57
D48V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              19               116
  CLUS_2               2                69
  CLUS_3              15                21
  CLUS_4              11                57
  CLUS_5              24                66
  CLUS_6               8                33
  CLUS_7              15                57
[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       14     18     27     35
  4Q LOSS WILD-TYPE    126     89     55    145
D48V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              14               126
  CLUS_2              18                89
  CLUS_3              27                55
  CLUS_4              35               145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       45     41      8
  4Q LOSS WILD-TYPE    177    143     95
D48V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              45               177
  CLUS_2              41               143
  CLUS_3               8                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       16     16     30     32
  4Q LOSS WILD-TYPE    111    103     75    122
D48V11, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              16               111
  CLUS_2              16               103
  CLUS_3              30                75
  CLUS_4              32               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 CLUS_5 CLUS_6
  4Q LOSS MUTATED        9     18     20     18      2     27
  4Q LOSS WILD-TYPE     90     59     98     38     61     65
D48V12, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                90
  CLUS_2              18                59
  CLUS_3              20                98
  CLUS_4              18                38
  CLUS_5               2                61
  CLUS_6              27                65
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 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
D49V1, 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
D49V2, 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       18     14      3
  5P LOSS WILD-TYPE    209     97    172
D49V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              18               209
  CLUS_2              14                97
  CLUS_3               3               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       24      7      2      2
  5P LOSS WILD-TYPE    185    127    155     11
D49V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              24               185
  CLUS_2               7               127
  CLUS_3               2               155
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED        3     12      7      8
  5P LOSS WILD-TYPE     88     83    118    107
D49V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                88
  CLUS_2              12                83
  CLUS_3               7               118
  CLUS_4               8               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
  5P LOSS MUTATED        5     11     14
  5P LOSS WILD-TYPE     78    147    171
D49V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                78
  CLUS_2              11               147
  CLUS_3              14               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     11      1     11      2
  5P LOSS WILD-TYPE    120    104    104    122     28
D49V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               120
  CLUS_2              11               104
  CLUS_3               1               104
  CLUS_4              11               122
  CLUS_5               2                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 CLUS_5 CLUS_6 CLUS_7
  5P LOSS MUTATED       10      2      0      8      2      9      4
  5P LOSS WILD-TYPE    125     69     36     60     88     32     68
D49V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               125
  CLUS_2               2                69
  CLUS_3               0                36
  CLUS_4               8                60
  CLUS_5               2                88
  CLUS_6               9                32
  CLUS_7               4                68
[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        6     13      4     12
  5P LOSS WILD-TYPE    134     94     78    168
D49V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6               134
  CLUS_2              13                94
  CLUS_3               4                78
  CLUS_4              12               168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       13     11     11
  5P LOSS WILD-TYPE    209    173     92
D49V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              13               209
  CLUS_2              11               173
  CLUS_3              11                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9     12      3     11
  5P LOSS WILD-TYPE    118    107    102    143
D49V11, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               9               118
  CLUS_2              12               107
  CLUS_3               3               102
  CLUS_4              11               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  5P LOSS MUTATED        3     15      6      0      2      9
  5P LOSS WILD-TYPE     96     62    112     56     61     83
D49V12, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                96
  CLUS_2              15                62
  CLUS_3               6               112
  CLUS_4               0                56
  CLUS_5               2                61
  CLUS_6               9                83
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) 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
D50V1, 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
D50V2, 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       20     10      2
  5Q LOSS WILD-TYPE    207    101    173
D50V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              20               207
  CLUS_2              10               101
  CLUS_3               2               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       21      5      2      4
  5Q LOSS WILD-TYPE    188    129    155      9
D50V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              21               188
  CLUS_2               5               129
  CLUS_3               2               155
  CLUS_4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        6     14      6      2
  5Q LOSS WILD-TYPE     85     81    119    113
D50V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                85
  CLUS_2              14                81
  CLUS_3               6               119
  CLUS_4               2               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
  5Q LOSS MUTATED        7      6     15
  5Q LOSS WILD-TYPE     76    152    170
D50V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7                76
  CLUS_2               6               152
  CLUS_3              15               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q LOSS MUTATED       10     13      1      6      2
  5Q LOSS WILD-TYPE    120    102    104    127     28
D50V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              10               120
  CLUS_2              13               102
  CLUS_3               1               104
  CLUS_4               6               127
  CLUS_5               2                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 CLUS_5 CLUS_6 CLUS_7
  5Q LOSS MUTATED        9      2      0      6      2     12      1
  5Q LOSS WILD-TYPE    126     69     36     62     88     29     71
D50V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2               2                69
  CLUS_3               0                36
  CLUS_4               6                62
  CLUS_5               2                88
  CLUS_6              12                29
  CLUS_7               1                71
[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        5     18      2      7
  5Q LOSS WILD-TYPE    135     89     80    173
D50V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               5               135
  CLUS_2              18                89
  CLUS_3               2                80
  CLUS_4               7               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       13      8     11
  5Q LOSS WILD-TYPE    209    176     92
D50V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              13               209
  CLUS_2               8               176
  CLUS_3              11                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     12      2      6
  5Q LOSS WILD-TYPE    115    107    103    148
D50V11, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              12               115
  CLUS_2              12               107
  CLUS_3               2               103
  CLUS_4               6               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 CLUS_5 CLUS_6
  5Q LOSS MUTATED        4     14      2      0      2     10
  5Q LOSS WILD-TYPE     95     63    116     56     61     82
D50V12, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                95
  CLUS_2              14                63
  CLUS_3               2               116
  CLUS_4               0                56
  CLUS_5               2                61
  CLUS_6              10                82
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 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
D51V1, 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
D51V2, 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       10     16      4
  6P LOSS WILD-TYPE    217     95    171
D51V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              10               217
  CLUS_2              16                95
  CLUS_3               4               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     13      6      0
  6P LOSS WILD-TYPE    198    121    151     13
D51V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               198
  CLUS_2              13               121
  CLUS_3               6               151
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      6      9      7
  6P LOSS WILD-TYPE     87     89    116    108
D51V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                87
  CLUS_2               6                89
  CLUS_3               9               116
  CLUS_4               7               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
  6P LOSS MUTATED        3      8     15
  6P LOSS WILD-TYPE     80    150    170
D51V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               8               150
  CLUS_3              15               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P LOSS MUTATED        7     11      4      7      1
  6P LOSS WILD-TYPE    123    104    101    126     29
D51V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               123
  CLUS_2              11               104
  CLUS_3               4               101
  CLUS_4               7               126
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        7     10      1      4      5      1      2
  6P LOSS WILD-TYPE    128     61     35     64     85     40     70
D51V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               128
  CLUS_2              10                61
  CLUS_3               1                35
  CLUS_4               4                64
  CLUS_5               5                85
  CLUS_6               1                40
  CLUS_7               2                70
[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       12      5      5      8
  6P LOSS WILD-TYPE    128    102     77    172
D51V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              12               128
  CLUS_2               5               102
  CLUS_3               5                77
  CLUS_4               8               172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       12      9      9
  6P LOSS WILD-TYPE    210    175     94
D51V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              12               210
  CLUS_2               9               175
  CLUS_3               9                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10      8      3      8
  6P LOSS WILD-TYPE    117    111    102    146
D51V11, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              10               117
  CLUS_2               8               111
  CLUS_3               3               102
  CLUS_4               8               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 CLUS_5 CLUS_6
  6P LOSS MUTATED        6      2      4      3     10      4
  6P LOSS WILD-TYPE     93     75    114     53     53     88
D51V12, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6                93
  CLUS_2               2                75
  CLUS_3               4               114
  CLUS_4               3                53
  CLUS_5              10                53
  CLUS_6               4                88
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 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
D52V1, 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
D52V2, 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       23     35      5
  6Q LOSS WILD-TYPE    204     76    170
D52V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              23               204
  CLUS_2              35                76
  CLUS_3               5               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED       32     21      7      3
  6Q LOSS WILD-TYPE    177    113    150     10
D52V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              32               177
  CLUS_2              21               113
  CLUS_3               7               150
  CLUS_4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        9     15     19     12
  6Q LOSS WILD-TYPE     82     80    106    103
D52V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               9                82
  CLUS_2              15                80
  CLUS_3              19               106
  CLUS_4              12               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        8     14     33
  6Q LOSS WILD-TYPE     75    144    152
D52V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8                75
  CLUS_2              14               144
  CLUS_3              33               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      6     15      3
  6Q LOSS WILD-TYPE    112     94     99    118     27
D52V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              18               112
  CLUS_2              21                94
  CLUS_3               6                99
  CLUS_4              15               118
  CLUS_5               3                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 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED       20     14      1      9      6      7      6
  6Q LOSS WILD-TYPE    115     57     35     59     84     34     66
D52V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              20               115
  CLUS_2              14                57
  CLUS_3               1                35
  CLUS_4               9                59
  CLUS_5               6                84
  CLUS_6               7                34
  CLUS_7               6                66
[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       29     14      4     16
  6Q LOSS WILD-TYPE    111     93     78    164
D52V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              29               111
  CLUS_2              14                93
  CLUS_3               4                78
  CLUS_4              16               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       29     17     17
  6Q LOSS WILD-TYPE    193    167     86
D52V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              29               193
  CLUS_2              17               167
  CLUS_3              17                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22     18      5     16
  6Q LOSS WILD-TYPE    105    101    100    138
D52V11, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              22               105
  CLUS_2              18               101
  CLUS_3               5               100
  CLUS_4              16               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  6Q LOSS MUTATED       20      5     11      4     14      7
  6Q LOSS WILD-TYPE     79     72    107     52     49     85
D52V12, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              20                79
  CLUS_2               5                72
  CLUS_3              11               107
  CLUS_4               4                52
  CLUS_5              14                49
  CLUS_6               7                85
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) 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
D53V1, 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
D53V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        3      0      0
  7P LOSS WILD-TYPE    224    111    175
D53V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3               224
  CLUS_2               0               111
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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    207    133    157     13
D53V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               207
  CLUS_2               1               133
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      0      2      0
  7P LOSS WILD-TYPE     91     95    123    115
D53V5, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               424 
       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-DB-A64L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64O        TCGA-DB-A64P        TCGA-DB-A64Q        TCGA-DB-A64R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64S        TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64X        TCGA-DB-A75K        TCGA-DB-A75L        TCGA-DB-A75M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75O        TCGA-DB-A75P        TCGA-DH-5140        TCGA-DH-5141 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66D        TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7US 
"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-DU-A6S2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S3        TCGA-DU-A6S8        TCGA-DU-A76K        TCGA-DU-A76L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A76O        TCGA-DU-A76R        TCGA-DU-A7T6        TCGA-DU-A7TA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TB        TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-DU-A7TI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TJ        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YH        TCGA-E1-A7YI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YJ        TCGA-E1-A7YL        TCGA-E1-A7YM        TCGA-E1-A7YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YQ        TCGA-E1-A7YS        TCGA-E1-A7YV        TCGA-E1-A7YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YY        TCGA-E1-A7Z2        TCGA-E1-A7Z3        TCGA-E1-A7Z6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-F6-A8O3        TCGA-F6-A8O4        TCGA-FG-5962 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A70Y        TCGA-FG-A70Z        TCGA-FG-A710 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A713        TCGA-FG-A87N        TCGA-FG-A87Q        TCGA-HT-7467 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HT-A614 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A615        TCGA-HT-A616        TCGA-HT-A617        TCGA-HT-A618 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A619        TCGA-HT-A61B        TCGA-HT-A74H        TCGA-HT-A74J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A74L        TCGA-HT-A74O        TCGA-HW-7486        TCGA-HW-7487 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-KT-A74X        TCGA-P5-A5ET 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A72U        TCGA-P5-A72W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A72X        TCGA-P5-A72Z        TCGA-P5-A730        TCGA-P5-A731 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A733        TCGA-P5-A735        TCGA-P5-A736        TCGA-P5-A737 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A77W        TCGA-P5-A77X        TCGA-P5-A780        TCGA-P5-A781 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X        TCGA-QH-A65Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV        TCGA-QH-A6CW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870        TCGA-R8-A6MK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A6ML        TCGA-R8-A6MO        TCGA-R8-A6YH        TCGA-RY-A83X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RY-A83Y        TCGA-RY-A83Z        TCGA-RY-A843        TCGA-RY-A845 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TX        TCGA-S9-A6TY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U5        TCGA-S9-A6U6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U9        TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WH        TCGA-S9-A6WN        TCGA-S9-A6WP        TCGA-S9-A6WQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7QX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R4        TCGA-S9-A7R8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C5        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TQ-A7RF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RG        TCGA-TQ-A7RH        TCGA-TQ-A7RK        TCGA-TQ-A7RN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RQ        TCGA-TQ-A7RR        TCGA-TQ-A7RS        TCGA-TQ-A7RV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-TQ-A8XE        TCGA-VM-A8C8        TCGA-VM-A8C9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CA        TCGA-VM-A8CB        TCGA-VM-A8CD        TCGA-VM-A8CE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-VV-A829        TCGA-VV-A86M        TCGA-VW-A7QS 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-W9-A837        TCGA-WY-A85B        TCGA-WY-A85C        TCGA-WY-A85D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        1      0      1
  7P LOSS WILD-TYPE     82    158    184
D53V6, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               424 
       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-DB-A64L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64O        TCGA-DB-A64P        TCGA-DB-A64Q        TCGA-DB-A64R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64S        TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64X        TCGA-DB-A75K        TCGA-DB-A75L        TCGA-DB-A75M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75O        TCGA-DB-A75P        TCGA-DH-5140        TCGA-DH-5141 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66D        TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7US 
"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-DU-A6S2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S3        TCGA-DU-A6S8        TCGA-DU-A76K        TCGA-DU-A76L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A76O        TCGA-DU-A76R        TCGA-DU-A7T6        TCGA-DU-A7TA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TB        TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-DU-A7TI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TJ        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YH        TCGA-E1-A7YI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YJ        TCGA-E1-A7YL        TCGA-E1-A7YM        TCGA-E1-A7YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YQ        TCGA-E1-A7YS        TCGA-E1-A7YV        TCGA-E1-A7YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YY        TCGA-E1-A7Z2        TCGA-E1-A7Z3        TCGA-E1-A7Z6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EZ-7264        TCGA-F6-A8O3        TCGA-F6-A8O4        TCGA-FG-5962 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A70Y        TCGA-FG-A70Z        TCGA-FG-A710 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A713        TCGA-FG-A87N        TCGA-FG-A87Q        TCGA-HT-7467 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7472        TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7476        TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7480        TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7604        TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7608        TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7616        TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7680        TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7687        TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7691        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7695        TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7857        TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7874        TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7880        TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7902        TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8013        TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8104        TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8109        TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8114        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HT-A614 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A615        TCGA-HT-A616        TCGA-HT-A617        TCGA-HT-A618 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A619        TCGA-HT-A61B        TCGA-HT-A74H        TCGA-HT-A74J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A74L        TCGA-HT-A74O        TCGA-HW-7486        TCGA-HW-7487 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-KT-A74X        TCGA-P5-A5ET 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EY        TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A72U        TCGA-P5-A72W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A72X        TCGA-P5-A72Z        TCGA-P5-A730        TCGA-P5-A731 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A733        TCGA-P5-A735        TCGA-P5-A736        TCGA-P5-A737 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A77W        TCGA-P5-A77X        TCGA-P5-A780        TCGA-P5-A781 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X        TCGA-QH-A65Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV        TCGA-QH-A6CW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870        TCGA-R8-A6MK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A6ML        TCGA-R8-A6MO        TCGA-R8-A6YH        TCGA-RY-A83X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RY-A83Y        TCGA-RY-A83Z        TCGA-RY-A843        TCGA-RY-A845 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TX        TCGA-S9-A6TY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U5        TCGA-S9-A6U6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U9        TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WH        TCGA-S9-A6WN        TCGA-S9-A6WP        TCGA-S9-A6WQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7QX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R4        TCGA-S9-A7R8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C5        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TQ-A7RF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RG        TCGA-TQ-A7RH        TCGA-TQ-A7RK        TCGA-TQ-A7RN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RQ        TCGA-TQ-A7RR        TCGA-TQ-A7RS        TCGA-TQ-A7RV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-TQ-A8XE        TCGA-VM-A8C8        TCGA-VM-A8C9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CA        TCGA-VM-A8CB        TCGA-VM-A8CD        TCGA-VM-A8CE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-VV-A829        TCGA-VV-A86M        TCGA-VW-A7QS 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-W9-A837        TCGA-WY-A85B        TCGA-WY-A85C        TCGA-WY-A85D 
"7P LOSS WILD-TYPE" "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    129    114    105    132     30
D53V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               129
  CLUS_2               1               114
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    134     70     36     67     90     41     72
D53V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               1                70
  CLUS_3               0                36
  CLUS_4               1                67
  CLUS_5               0                90
  CLUS_6               0                41
  CLUS_7               0                72
[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        1      1      0      1
  7P LOSS WILD-TYPE    139    106     82    179
D53V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               139
  CLUS_2               1               106
  CLUS_3               0                82
  CLUS_4               1               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED        2      1      0
  7P LOSS WILD-TYPE    220    183    103
D53V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               220
  CLUS_2               1               183
  CLUS_3               0               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        0      1      0      1
  7P LOSS WILD-TYPE    127    118    105    153
D53V11, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               503 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6188        TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6667        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-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DB-A64L        TCGA-DB-A64O 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64P        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75K        TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DB-A75P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5144        TCGA-DH-A669        TCGA-DH-A66B        TCGA-DH-A66D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7US 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A7UT        TCGA-DH-A7UU        TCGA-DH-A7UV        TCGA-DU-5847 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7012        TCGA-DU-7013        TCGA-DU-7014 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7290 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-DU-A6S2        TCGA-DU-A6S3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A76L        TCGA-DU-A76O        TCGA-DU-A76R        TCGA-DU-A7T6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-DU-A7TI        TCGA-DU-A7TJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5322        TCGA-E1-A7YD        TCGA-E1-A7YE        TCGA-E1-A7YH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YI        TCGA-E1-A7YJ        TCGA-E1-A7YK        TCGA-E1-A7YL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YM        TCGA-E1-A7YN        TCGA-E1-A7YO        TCGA-E1-A7YQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YS        TCGA-E1-A7YU        TCGA-E1-A7YV        TCGA-E1-A7YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YY        TCGA-E1-A7Z2        TCGA-E1-A7Z3        TCGA-E1-A7Z4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7Z6        TCGA-EZ-7264        TCGA-F6-A8O3        TCGA-F6-A8O4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6692        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-FG-A60K        TCGA-FG-A60L        TCGA-FG-A6IZ        TCGA-FG-A6J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A70Y        TCGA-FG-A70Z        TCGA-FG-A710 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87N        TCGA-FG-A87Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FN-7833        TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8108        TCGA-HT-8109 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8563        TCGA-HT-8564        TCGA-HT-A4DS        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-A5RA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5RB        TCGA-HT-A5RC        TCGA-HT-A614        TCGA-HT-A615 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A616        TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A619 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A61B        TCGA-HT-A61C        TCGA-HT-A74H        TCGA-HT-A74K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A74L        TCGA-HT-A74O        TCGA-HW-7486        TCGA-HW-7487 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-KT-A74X        TCGA-KT-A7W1 
"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        TCGA-P5-A72U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A72W        TCGA-P5-A72X        TCGA-P5-A72Z        TCGA-P5-A730 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A731        TCGA-P5-A733        TCGA-P5-A735        TCGA-P5-A737 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A77W        TCGA-P5-A77X        TCGA-P5-A780        TCGA-P5-A781 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A6MK        TCGA-R8-A6ML        TCGA-R8-A6MO        TCGA-R8-A6YH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A73M        TCGA-RY-A83X        TCGA-RY-A83Y        TCGA-RY-A83Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RY-A840        TCGA-RY-A843        TCGA-RY-A845        TCGA-RY-A847 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6        TCGA-S9-A6U8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A89V        TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C5        TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84C        TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84I        TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84O        TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84T        TCGA-TQ-A7RF        TCGA-TQ-A7RG        TCGA-TQ-A7RH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RI        TCGA-TQ-A7RJ        TCGA-TQ-A7RK        TCGA-TQ-A7RM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RN        TCGA-TQ-A7RO        TCGA-TQ-A7RP        TCGA-TQ-A7RQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RR        TCGA-TQ-A7RS        TCGA-TQ-A7RU        TCGA-TQ-A7RV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-TQ-A8XE        TCGA-VM-A8C8        TCGA-VM-A8C9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CA        TCGA-VM-A8CB        TCGA-VM-A8CD        TCGA-VM-A8CE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CF        TCGA-VM-A8CH        TCGA-VV-A829        TCGA-VV-A86M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VW-A7QS        TCGA-VW-A8FI        TCGA-W9-A837        TCGA-WH-A86K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-WY-A858        TCGA-WY-A859        TCGA-WY-A85A        TCGA-WY-A85B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-WY-A85C        TCGA-WY-A85D        TCGA-WY-A85E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P LOSS MUTATED        1      0      0      0      0      1
  7P LOSS WILD-TYPE     98     77    118     56     63     91
D53V12, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               503 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6188        TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6667        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-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DB-A64L        TCGA-DB-A64O 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64P        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75K        TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DB-A75P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5144        TCGA-DH-A669        TCGA-DH-A66B        TCGA-DH-A66D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7US 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A7UT        TCGA-DH-A7UU        TCGA-DH-A7UV        TCGA-DU-5847 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7012        TCGA-DU-7013        TCGA-DU-7014 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7290 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-DU-A6S2        TCGA-DU-A6S3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A76L        TCGA-DU-A76O        TCGA-DU-A76R        TCGA-DU-A7T6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-DU-A7TI        TCGA-DU-A7TJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5322        TCGA-E1-A7YD        TCGA-E1-A7YE        TCGA-E1-A7YH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YI        TCGA-E1-A7YJ        TCGA-E1-A7YK        TCGA-E1-A7YL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YM        TCGA-E1-A7YN        TCGA-E1-A7YO        TCGA-E1-A7YQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YS        TCGA-E1-A7YU        TCGA-E1-A7YV        TCGA-E1-A7YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YY        TCGA-E1-A7Z2        TCGA-E1-A7Z3        TCGA-E1-A7Z4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7Z6        TCGA-EZ-7264        TCGA-F6-A8O3        TCGA-F6-A8O4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5962        TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6692        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-FG-A60K        TCGA-FG-A60L        TCGA-FG-A6IZ        TCGA-FG-A6J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A70Y        TCGA-FG-A70Z        TCGA-FG-A710 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87N        TCGA-FG-A87Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FN-7833        TCGA-HT-7467        TCGA-HT-7468        TCGA-HT-7469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472        TCGA-HT-7473 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476        TCGA-HT-7477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480        TCGA-HT-7481 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485        TCGA-HT-7601 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604        TCGA-HT-7605 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608        TCGA-HT-7609 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616        TCGA-HT-7620 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680        TCGA-HT-7681 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687        TCGA-HT-7688 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691        TCGA-HT-7692 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695        TCGA-HT-7854 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857        TCGA-HT-7858 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874        TCGA-HT-7875 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880        TCGA-HT-7881 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902        TCGA-HT-8010 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013        TCGA-HT-8015 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104        TCGA-HT-8105 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8108        TCGA-HT-8109 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8563        TCGA-HT-8564        TCGA-HT-A4DS        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-A5RA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5RB        TCGA-HT-A5RC        TCGA-HT-A614        TCGA-HT-A615 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A616        TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A619 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A61B        TCGA-HT-A61C        TCGA-HT-A74H        TCGA-HT-A74K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A74L        TCGA-HT-A74O        TCGA-HW-7486        TCGA-HW-7487 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-KT-A74X        TCGA-KT-A7W1 
"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        TCGA-P5-A72U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A72W        TCGA-P5-A72X        TCGA-P5-A72Z        TCGA-P5-A730 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A731        TCGA-P5-A733        TCGA-P5-A735        TCGA-P5-A737 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A77W        TCGA-P5-A77X        TCGA-P5-A780        TCGA-P5-A781 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A6MK        TCGA-R8-A6ML        TCGA-R8-A6MO        TCGA-R8-A6YH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-R8-A73M        TCGA-RY-A83X        TCGA-RY-A83Y        TCGA-RY-A83Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RY-A840        TCGA-RY-A843        TCGA-RY-A845        TCGA-RY-A847 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6        TCGA-S9-A6U8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A89V        TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C5        TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84C        TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84I        TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84O        TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84T        TCGA-TQ-A7RF        TCGA-TQ-A7RG        TCGA-TQ-A7RH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RI        TCGA-TQ-A7RJ        TCGA-TQ-A7RK        TCGA-TQ-A7RM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RN        TCGA-TQ-A7RO        TCGA-TQ-A7RP        TCGA-TQ-A7RQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RR        TCGA-TQ-A7RS        TCGA-TQ-A7RU        TCGA-TQ-A7RV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-TQ-A8XE        TCGA-VM-A8C8        TCGA-VM-A8C9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CA        TCGA-VM-A8CB        TCGA-VM-A8CD        TCGA-VM-A8CE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CF        TCGA-VM-A8CH        TCGA-VV-A829        TCGA-VV-A86M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VW-A7QS        TCGA-VW-A8FI        TCGA-W9-A837        TCGA-WH-A86K 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-WY-A858        TCGA-WY-A859        TCGA-WY-A85A        TCGA-WY-A85B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-WY-A85C        TCGA-WY-A85D        TCGA-WY-A85E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 

Clustering(54) 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
D54V1, 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
D54V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        4      0      0
  7Q LOSS WILD-TYPE    223    111    175
D54V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4               223
  CLUS_2               0               111
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      1      0      0
  7Q LOSS WILD-TYPE    206    133    157     13
D54V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3               206
  CLUS_2               1               133
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      4      0
  7Q LOSS WILD-TYPE     91     95    121    115
D54V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                91
  CLUS_2               0                95
  CLUS_3               4               121
  CLUS_4               0               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
  7Q LOSS MUTATED        1      0      3
  7Q LOSS WILD-TYPE     82    158    182
D54V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                82
  CLUS_2               0               158
  CLUS_3               3               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED        0      2      0      2      0
  7Q LOSS WILD-TYPE    130    113    105    131     30
D54V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               130
  CLUS_2               2               113
  CLUS_3               0               105
  CLUS_4               2               131
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      1      0      2      0      1      0
  7Q LOSS WILD-TYPE    135     70     36     66     90     40     72
D54V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               135
  CLUS_2               1                70
  CLUS_3               0                36
  CLUS_4               2                66
  CLUS_5               0                90
  CLUS_6               1                40
  CLUS_7               0                72
[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        1      1      0      2
  7Q LOSS WILD-TYPE    139    106     82    178
D54V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               139
  CLUS_2               1               106
  CLUS_3               0                82
  CLUS_4               2               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED        2      2      0
  7Q LOSS WILD-TYPE    220    182    103
D54V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2               220
  CLUS_2               2               182
  CLUS_3               0               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      1      0      2
  7Q LOSS WILD-TYPE    127    118    105    152
D54V11, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               127
  CLUS_2               1               118
  CLUS_3               0               105
  CLUS_4               2               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 CLUS_5 CLUS_6
  7Q LOSS MUTATED        0      1      1      0      0      1
  7Q LOSS WILD-TYPE     99     76    117     56     63     91
D54V12, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                99
  CLUS_2               1                76
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               0                63
  CLUS_6               1                91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) 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
D55V1, 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
D55V2, 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        5     12      0
  8P LOSS WILD-TYPE    222     99    175
D55V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5               222
  CLUS_2              12                99
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     10      0      2
  8P LOSS WILD-TYPE    204    124    157     11
D55V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5               204
  CLUS_2              10               124
  CLUS_3               0               157
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        0      8      4      3
  8P LOSS WILD-TYPE     91     87    121    112
D55V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                91
  CLUS_2               8                87
  CLUS_3               4               121
  CLUS_4               3               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
  8P LOSS MUTATED        0      3     12
  8P LOSS WILD-TYPE     83    155    173
D55V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                83
  CLUS_2               3               155
  CLUS_3              12               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    130    102    105    130     29
D55V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0               130
  CLUS_2              13               102
  CLUS_3               0               105
  CLUS_4               3               130
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      8      0      2      0      5      1
  8P LOSS WILD-TYPE    134     63     36     66     90     36     71
D55V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               8                63
  CLUS_3               0                36
  CLUS_4               2                66
  CLUS_5               0                90
  CLUS_6               5                36
  CLUS_7               1                71
[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        7      5      2      3
  8P LOSS WILD-TYPE    133    102     80    177
D55V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7               133
  CLUS_2               5               102
  CLUS_3               2                80
  CLUS_4               3               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      1      9
  8P LOSS WILD-TYPE    215    183     94
D55V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7               215
  CLUS_2               1               183
  CLUS_3               9                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        2     10      1      3
  8P LOSS WILD-TYPE    125    109    104    151
D55V11, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2               125
  CLUS_2              10               109
  CLUS_3               1               104
  CLUS_4               3               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 CLUS_5 CLUS_6
  8P LOSS MUTATED        1      6      1      0      8      0
  8P LOSS WILD-TYPE     98     71    117     56     55     92
D55V12, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                98
  CLUS_2               6                71
  CLUS_3               1               117
  CLUS_4               0                56
  CLUS_5               8                55
  CLUS_6               0                92
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) 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
D56V1, 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
D56V2, 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        2      9      0
  8Q LOSS WILD-TYPE    225    102    175
D56V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2               225
  CLUS_2               9               102
  CLUS_3               0               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      9      0      0
  8Q LOSS WILD-TYPE    207    125    157     13
D56V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2               207
  CLUS_2               9               125
  CLUS_3               0               157
  CLUS_4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        0      5      2      2
  8Q LOSS WILD-TYPE     91     90    123    113
D56V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                91
  CLUS_2               5                90
  CLUS_3               2               123
  CLUS_4               2               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
  8Q LOSS MUTATED        0      2      7
  8Q LOSS WILD-TYPE     83    156    178
D56V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                83
  CLUS_2               2               156
  CLUS_3               7               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 CLUS_5
  8Q LOSS MUTATED        0      9      0      1      1
  8Q LOSS WILD-TYPE    130    106    105    132     29
D56V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0               130
  CLUS_2               9               106
  CLUS_3               0               105
  CLUS_4               1               132
  CLUS_5               1                29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      7      0      1      0      2      0
  8Q LOSS WILD-TYPE    134     64     36     67     90     39     72
D56V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1               134
  CLUS_2               7                64
  CLUS_3               0                36
  CLUS_4               1                67
  CLUS_5               0                90
  CLUS_6               2                39
  CLUS_7               0                72
[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        6      2      1      2
  8Q LOSS WILD-TYPE    134    105     81    178
D56V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6               134
  CLUS_2               2               105
  CLUS_3               1                81
  CLUS_4               2               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        4      0      7
  8Q LOSS WILD-TYPE    218    184     96
D56V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               218
  CLUS_2               0               184
  CLUS_3               7                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      0      2
  8Q LOSS WILD-TYPE    125    113    105    152
D56V11, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2               125
  CLUS_2               6               113
  CLUS_3               0               105
  CLUS_4               2               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 CLUS_5 CLUS_6
  8Q LOSS MUTATED        0      3      0      0      7      0
  8Q LOSS WILD-TYPE     99     74    118     56     56     92
D56V12, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                99
  CLUS_2               3                74
  CLUS_3               0               118
  CLUS_4               0                56
  CLUS_5               7                56
  CLUS_6               0                92
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) 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
D57V1, 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
D57V2, 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       49     47     22
  9P LOSS WILD-TYPE    178     64    153
D57V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              49               178
  CLUS_2              47                64
  CLUS_3              22               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       58     35     21      4
  9P LOSS WILD-TYPE    151     99    136      9
D57V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              58               151
  CLUS_2              35                99
  CLUS_3              21               136
  CLUS_4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       13     37     29     22
  9P LOSS WILD-TYPE     78     58     96     93
D57V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              13                78
  CLUS_2              37                58
  CLUS_3              29                96
  CLUS_4              22                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
  9P LOSS MUTATED        9     27     65
  9P LOSS WILD-TYPE     74    131    120
D57V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                74
  CLUS_2              27               131
  CLUS_3              65               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     15     32      7
  9P LOSS WILD-TYPE    100     81     90    101     23
D57V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              30               100
  CLUS_2              34                81
  CLUS_3              15                90
  CLUS_4              32               101
  CLUS_5               7                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 CLUS_5 CLUS_6 CLUS_7
  9P LOSS MUTATED       33     21      9     25     10     13      7
  9P LOSS WILD-TYPE    102     50     27     43     80     28     65
D57V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              33               102
  CLUS_2              21                50
  CLUS_3               9                27
  CLUS_4              25                43
  CLUS_5              10                80
  CLUS_6              13                28
  CLUS_7               7                65
[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       31     24     20     43
  9P LOSS WILD-TYPE    109     83     62    137
D57V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              31               109
  CLUS_2              24                83
  CLUS_3              20                62
  CLUS_4              43               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
  9P LOSS MUTATED       44     45     29
  9P LOSS WILD-TYPE    178    139     74
D57V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              44               178
  CLUS_2              45               139
  CLUS_3              29                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       31     33     19     34
  9P LOSS WILD-TYPE     96     86     86    120
D57V11, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              31                96
  CLUS_2              33                86
  CLUS_3              19                86
  CLUS_4              34               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  9P LOSS MUTATED       24     17     25      6     21     24
  9P LOSS WILD-TYPE     75     60     93     50     42     68
D57V12, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              24                75
  CLUS_2              17                60
  CLUS_3              25                93
  CLUS_4               6                50
  CLUS_5              21                42
  CLUS_6              24                68
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) 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
D58V1, 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
D58V2, 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       22     14     15
  9Q LOSS WILD-TYPE    205     97    160
D58V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              22               205
  CLUS_2              14                97
  CLUS_3              15               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       19     15     15      2
  9Q LOSS WILD-TYPE    190    119    142     11
D58V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              19               190
  CLUS_2              15               119
  CLUS_3              15               142
  CLUS_4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED        5     16     11     12
  9Q LOSS WILD-TYPE     86     79    114    103
D58V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                86
  CLUS_2              16                79
  CLUS_3              11               114
  CLUS_4              12               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        3     12     29
  9Q LOSS WILD-TYPE     80    146    156
D58V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2              12               146
  CLUS_3              29               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q LOSS MUTATED       10     16     10     12      3
  9Q LOSS WILD-TYPE    120     99     95    121     27
D58V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10               120
  CLUS_2              16                99
  CLUS_3              10                95
  CLUS_4              12               121
  CLUS_5               3                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 CLUS_5 CLUS_6 CLUS_7
  9Q LOSS MUTATED       11     11      7      7      7      6      2
  9Q LOSS WILD-TYPE    124     60     29     61     83     35     70
D58V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               124
  CLUS_2              11                60
  CLUS_3               7                29
  CLUS_4               7                61
  CLUS_5               7                83
  CLUS_6               6                35
  CLUS_7               2                70
[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       15      9     12     15
  9Q LOSS WILD-TYPE    125     98     70    165
D58V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              15               125
  CLUS_2               9                98
  CLUS_3              12                70
  CLUS_4              15               165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       21     18     12
  9Q LOSS WILD-TYPE    201    166     91
D58V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              21               201
  CLUS_2              18               166
  CLUS_3              12                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     12     12     14
  9Q LOSS WILD-TYPE    116    107     93    140
D58V11, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11               116
  CLUS_2              12               107
  CLUS_3              12                93
  CLUS_4              14               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 CLUS_5 CLUS_6
  9Q LOSS MUTATED       11      6     11      3      9      9
  9Q LOSS WILD-TYPE     88     71    107     53     54     83
D58V12, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11                88
  CLUS_2               6                71
  CLUS_3              11               107
  CLUS_4               3                53
  CLUS_5               9                54
  CLUS_6               9                83
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) 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
D59V1, 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
D59V2, 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       23     54      6
  10P LOSS WILD-TYPE    204     57    169
D59V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               23                204
  CLUS_2               54                 57
  CLUS_3                6                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
  10P LOSS MUTATED        4     73      6      0
  10P LOSS WILD-TYPE    205     61    151     13
D59V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                205
  CLUS_2               73                 61
  CLUS_3                6                151
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10     24     11     16
  10P LOSS WILD-TYPE     81     71    114     99
D59V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                 81
  CLUS_2               24                 71
  CLUS_3               11                114
  CLUS_4               16                 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
  10P LOSS MUTATED        4     17     40
  10P LOSS WILD-TYPE     79    141    145
D59V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 79
  CLUS_2               17                141
  CLUS_3               40                145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     13      4
  10P LOSS WILD-TYPE    129     51    104    120     26
D59V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                129
  CLUS_2               64                 51
  CLUS_3                1                104
  CLUS_4               13                120
  CLUS_5                4                 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 CLUS_5 CLUS_6 CLUS_7
  10P LOSS MUTATED        1     60      3     12      3      4      0
  10P LOSS WILD-TYPE    134     11     33     56     87     37     72
D59V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2               60                 11
  CLUS_3                3                 33
  CLUS_4               12                 56
  CLUS_5                3                 87
  CLUS_6                4                 37
  CLUS_7                0                 72
[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       32     26      5     20
  10P LOSS WILD-TYPE    108     81     77    160
D59V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               32                108
  CLUS_2               26                 81
  CLUS_3                5                 77
  CLUS_4               20                160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       11     12     60
  10P LOSS WILD-TYPE    211    172     43
D59V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               11                211
  CLUS_2               12                172
  CLUS_3               60                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       26     37      3     17
  10P LOSS WILD-TYPE    101     82    102    137
D59V11, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               26                101
  CLUS_2               37                 82
  CLUS_3                3                102
  CLUS_4               17                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 CLUS_5 CLUS_6
  10P LOSS MUTATED        4      6     12      1     55      5
  10P LOSS WILD-TYPE     95     71    106     55      8     87
D59V12, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 95
  CLUS_2                6                 71
  CLUS_3               12                106
  CLUS_4                1                 55
  CLUS_5               55                  8
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) 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
D60V1, 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
D60V2, 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       32     59      6
  10Q LOSS WILD-TYPE    195     52    169
D60V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               32                195
  CLUS_2               59                 52
  CLUS_3                6                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
  10Q LOSS MUTATED       11     74      6      6
  10Q LOSS WILD-TYPE    198     60    151      7
D60V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               11                198
  CLUS_2               74                 60
  CLUS_3                6                151
  CLUS_4                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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     28     17     17
  10Q LOSS WILD-TYPE     79     67    108     98
D60V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                 79
  CLUS_2               28                 67
  CLUS_3               17                108
  CLUS_4               17                 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
  10Q LOSS MUTATED        6     20     48
  10Q LOSS WILD-TYPE     77    138    137
D60V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 77
  CLUS_2               20                138
  CLUS_3               48                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     71      1     16      4
  10Q LOSS WILD-TYPE    125     44    104    117     26
D60V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                125
  CLUS_2               71                 44
  CLUS_3                1                104
  CLUS_4               16                117
  CLUS_5                4                 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 CLUS_5 CLUS_6 CLUS_7
  10Q LOSS MUTATED        6     60      3     14      3     10      1
  10Q LOSS WILD-TYPE    129     11     33     54     87     31     71
D60V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                129
  CLUS_2               60                 11
  CLUS_3                3                 33
  CLUS_4               14                 54
  CLUS_5                3                 87
  CLUS_6               10                 31
  CLUS_7                1                 71
[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       35     32      6     24
  10Q LOSS WILD-TYPE    105     75     76    156
D60V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               35                105
  CLUS_2               32                 75
  CLUS_3                6                 76
  CLUS_4               24                156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       15     15     67
  10Q LOSS WILD-TYPE    207    169     36
D60V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               15                207
  CLUS_2               15                169
  CLUS_3               67                 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
  10Q LOSS MUTATED       31     42      5     19
  10Q LOSS WILD-TYPE     96     77    100    135
D60V11, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               31                 96
  CLUS_2               42                 77
  CLUS_3                5                100
  CLUS_4               19                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 CLUS_5 CLUS_6
  10Q LOSS MUTATED        8      9     12      1     56     11
  10Q LOSS WILD-TYPE     91     68    106     55      7     81
D60V12, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                 91
  CLUS_2                9                 68
  CLUS_3               12                106
  CLUS_4                1                 55
  CLUS_5               56                  7
  CLUS_6               11                 81
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) 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
D61V1, 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
D61V2, 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       46     17      0
  11P LOSS WILD-TYPE    181     94    175
D61V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               46                181
  CLUS_2               17                 94
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       38     17      0      8
  11P LOSS WILD-TYPE    171    117    157      5
D61V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               38                171
  CLUS_2               17                117
  CLUS_3                0                157
  CLUS_4                8                  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 CLUS_4
  11P LOSS MUTATED       14     18      8      9
  11P LOSS WILD-TYPE     77     77    117    106
D61V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               14                 77
  CLUS_2               18                 77
  CLUS_3                8                117
  CLUS_4                9                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9     14     26
  11P LOSS WILD-TYPE     74    144    159
D61V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                9                 74
  CLUS_2               14                144
  CLUS_3               26                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P LOSS MUTATED       13     31      0     12      7
  11P LOSS WILD-TYPE    117     84    105    121     23
D61V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                117
  CLUS_2               31                 84
  CLUS_3                0                105
  CLUS_4               12                121
  CLUS_5                7                 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 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED       17      9      0      6      0     25      6
  11P LOSS WILD-TYPE    118     62     36     62     90     16     66
D61V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               17                118
  CLUS_2                9                 62
  CLUS_3                0                 36
  CLUS_4                6                 62
  CLUS_5                0                 90
  CLUS_6               25                 16
  CLUS_7                6                 66
[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       13     29      4     17
  11P LOSS WILD-TYPE    127     78     78    163
D61V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                127
  CLUS_2               29                 78
  CLUS_3                4                 78
  CLUS_4               17                163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       22     14     27
  11P LOSS WILD-TYPE    200    170     76
D61V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               22                200
  CLUS_2               14                170
  CLUS_3               27                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED       19     24      4     15
  11P LOSS WILD-TYPE    108     95    101    139
D61V11, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               19                108
  CLUS_2               24                 95
  CLUS_3                4                101
  CLUS_4               15                139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  11P LOSS MUTATED       10     27     10      0      8      7
  11P LOSS WILD-TYPE     89     50    108     56     55     85
D61V12, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 89
  CLUS_2               27                 50
  CLUS_3               10                108
  CLUS_4                0                 56
  CLUS_5                8                 55
  CLUS_6                7                 85
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) 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
D62V1, 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
D62V2, 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        9     12      0
  11Q LOSS WILD-TYPE    218     99    175
D62V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                9                218
  CLUS_2               12                 99
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        7     13      0      1
  11Q LOSS WILD-TYPE    202    121    157     12
D62V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                202
  CLUS_2               13                121
  CLUS_3                0                157
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        2      8      3      4
  11Q LOSS WILD-TYPE     89     87    122    111
D62V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                8                 87
  CLUS_3                3                122
  CLUS_4                4                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
  11Q LOSS MUTATED        1      5     11
  11Q LOSS WILD-TYPE     82    153    174
D62V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                5                153
  CLUS_3               11                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0     16      0      3      2
  11Q LOSS WILD-TYPE    130     99    105    130     28
D62V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                130
  CLUS_2               16                 99
  CLUS_3                0                105
  CLUS_4                3                130
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED        2      9      0      2      0      7      1
  11Q LOSS WILD-TYPE    133     62     36     66     90     34     71
D62V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                133
  CLUS_2                9                 62
  CLUS_3                0                 36
  CLUS_4                2                 66
  CLUS_5                0                 90
  CLUS_6                7                 34
  CLUS_7                1                 71
[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      9      1      6
  11Q LOSS WILD-TYPE    135     98     81    174
D62V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                135
  CLUS_2                9                 98
  CLUS_3                1                 81
  CLUS_4                6                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      3     13
  11Q LOSS WILD-TYPE    217    181     90
D62V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                217
  CLUS_2                3                181
  CLUS_3               13                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     10      0      4
  11Q LOSS WILD-TYPE    121    109    105    150
D62V11, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                121
  CLUS_2               10                109
  CLUS_3                0                105
  CLUS_4                4                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q LOSS MUTATED        1      6      3      0      8      2
  11Q LOSS WILD-TYPE     98     71    115     56     55     90
D62V12, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                6                 71
  CLUS_3                3                115
  CLUS_4                0                 56
  CLUS_5                8                 55
  CLUS_6                2                 90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) 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
D63V1, 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
D63V2, 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       20      3      5
  12P LOSS WILD-TYPE    207    108    170
D63V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               20                207
  CLUS_2                3                108
  CLUS_3                5                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED       14      4      5      5
  12P LOSS WILD-TYPE    195    130    152      8
D63V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               14                195
  CLUS_2                4                130
  CLUS_3                5                152
  CLUS_4                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        4      6      8      7
  12P LOSS WILD-TYPE     87     89    117    108
D63V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 87
  CLUS_2                6                 89
  CLUS_3                8                117
  CLUS_4                7                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
  12P LOSS MUTATED        5      9     11
  12P LOSS WILD-TYPE     78    149    174
D63V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                5                 78
  CLUS_2                9                149
  CLUS_3               11                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      1      8      3
  12P LOSS WILD-TYPE    122    107    104    125     27
D63V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                122
  CLUS_2                8                107
  CLUS_3                1                104
  CLUS_4                8                125
  CLUS_5                3                 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 CLUS_5 CLUS_6 CLUS_7
  12P LOSS MUTATED       10      1      1      1      3      8      4
  12P LOSS WILD-TYPE    125     70     35     67     87     33     68
D63V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               10                125
  CLUS_2                1                 70
  CLUS_3                1                 35
  CLUS_4                1                 67
  CLUS_5                3                 87
  CLUS_6                8                 33
  CLUS_7                4                 68
[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        4     12      3      9
  12P LOSS WILD-TYPE    136     95     79    171
D63V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                136
  CLUS_2               12                 95
  CLUS_3                3                 79
  CLUS_4                9                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9     10      9
  12P LOSS WILD-TYPE    213    174     94
D63V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                9                213
  CLUS_2               10                174
  CLUS_3                9                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      9      3      9
  12P LOSS WILD-TYPE    120    110    102    145
D63V11, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                120
  CLUS_2                9                110
  CLUS_3                3                102
  CLUS_4                9                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  12P LOSS MUTATED        6      9      7      1      0      5
  12P LOSS WILD-TYPE     93     68    111     55     63     87
D63V12, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                6                 93
  CLUS_2                9                 68
  CLUS_3                7                111
  CLUS_4                1                 55
  CLUS_5                0                 63
  CLUS_6                5                 87
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) 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
D64V1, 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
D64V2, 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      6      6
  12Q LOSS WILD-TYPE    187    105    169
D64V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               40                187
  CLUS_2                6                105
  CLUS_3                6                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
  12Q LOSS MUTATED       33      8      5      6
  12Q LOSS WILD-TYPE    176    126    152      7
D64V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               33                176
  CLUS_2                8                126
  CLUS_3                5                152
  CLUS_4                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      8     16     13
  12Q LOSS WILD-TYPE     84     87    109    102
D64V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                 84
  CLUS_2                8                 87
  CLUS_3               16                109
  CLUS_4               13                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED        8     16     20
  12Q LOSS WILD-TYPE     75    142    165
D64V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 75
  CLUS_2               16                142
  CLUS_3               20                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      1     14      5
  12Q LOSS WILD-TYPE    113    100    104    119     25
D64V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               17                113
  CLUS_2               15                100
  CLUS_3                1                104
  CLUS_4               14                119
  CLUS_5                5                 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 CLUS_5 CLUS_6 CLUS_7
  12Q LOSS MUTATED       21      1      1      6      3     14      6
  12Q LOSS WILD-TYPE    114     70     35     62     87     27     66
D64V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               21                114
  CLUS_2                1                 70
  CLUS_3                1                 35
  CLUS_4                6                 62
  CLUS_5                3                 87
  CLUS_6               14                 27
  CLUS_7                6                 66
[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       10     22      5     15
  12Q LOSS WILD-TYPE    130     85     77    165
D64V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               10                130
  CLUS_2               22                 85
  CLUS_3                5                 77
  CLUS_4               15                165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       22     16     14
  12Q LOSS WILD-TYPE    200    168     89
D64V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               22                200
  CLUS_2               16                168
  CLUS_3               14                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15     16      6     15
  12Q LOSS WILD-TYPE    112    103     99    139
D64V11, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               15                112
  CLUS_2               16                103
  CLUS_3                6                 99
  CLUS_4               15                139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  12Q LOSS MUTATED       13     18     11      1      0      9
  12Q LOSS WILD-TYPE     86     59    107     55     63     83
D64V12, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               13                 86
  CLUS_2               18                 59
  CLUS_3               11                107
  CLUS_4                1                 55
  CLUS_5                0                 63
  CLUS_6                9                 83
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) 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
D65V1, 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
D65V2, 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       42     46     27
  13Q LOSS WILD-TYPE    185     65    148
D65V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               42                185
  CLUS_2               46                 65
  CLUS_3               27                148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       52     31     26      6
  13Q LOSS WILD-TYPE    157    103    131      7
D65V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               52                157
  CLUS_2               31                103
  CLUS_3               26                131
  CLUS_4                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       13     32     24     25
  13Q LOSS WILD-TYPE     78     63    101     90
D65V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               13                 78
  CLUS_2               32                 63
  CLUS_3               24                101
  CLUS_4               25                 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
  13Q LOSS MUTATED       14     37     43
  13Q LOSS WILD-TYPE     69    121    142
D65V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               14                 69
  CLUS_2               37                121
  CLUS_3               43                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q LOSS MUTATED       31     38     16     25      5
  13Q LOSS WILD-TYPE     99     77     89    108     25
D65V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               31                 99
  CLUS_2               38                 77
  CLUS_3               16                 89
  CLUS_4               25                108
  CLUS_5                5                 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 CLUS_5 CLUS_6 CLUS_7
  13Q LOSS MUTATED       33     19      2     11     17     19     14
  13Q LOSS WILD-TYPE    102     52     34     57     73     22     58
D65V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               33                102
  CLUS_2               19                 52
  CLUS_3                2                 34
  CLUS_4               11                 57
  CLUS_5               17                 73
  CLUS_6               19                 22
  CLUS_7               14                 58
[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       29     33     21     31
  13Q LOSS WILD-TYPE    111     74     61    149
D65V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               29                111
  CLUS_2               33                 74
  CLUS_3               21                 61
  CLUS_4               31                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
  13Q LOSS MUTATED       53     30     31
  13Q LOSS WILD-TYPE    169    154     72
D65V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               53                169
  CLUS_2               30                154
  CLUS_3               31                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       28     32     25     29
  13Q LOSS WILD-TYPE     99     87     80    125
D65V11, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               28                 99
  CLUS_2               32                 87
  CLUS_3               25                 80
  CLUS_4               29                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 CLUS_5 CLUS_6
  13Q LOSS MUTATED       17     24     20      9     18     26
  13Q LOSS WILD-TYPE     82     53     98     47     45     66
D65V12, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               17                 82
  CLUS_2               24                 53
  CLUS_3               20                 98
  CLUS_4                9                 47
  CLUS_5               18                 45
  CLUS_6               26                 66
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) 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
D66V1, 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
D66V2, 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       22     38     21
  14Q LOSS WILD-TYPE    205     73    154
D66V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               22                205
  CLUS_2               38                 73
  CLUS_3               21                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       24     32     20      5
  14Q LOSS WILD-TYPE    185    102    137      8
D66V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               24                185
  CLUS_2               32                102
  CLUS_3               20                137
  CLUS_4                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       10     23     15     19
  14Q LOSS WILD-TYPE     81     72    110     96
D66V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               10                 81
  CLUS_2               23                 72
  CLUS_3               15                110
  CLUS_4               19                 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
  14Q LOSS MUTATED       10     22     35
  14Q LOSS WILD-TYPE     73    136    150
D66V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               10                 73
  CLUS_2               22                136
  CLUS_3               35                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q LOSS MUTATED       10     36     11     17      7
  14Q LOSS WILD-TYPE    120     79     94    116     23
D66V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               10                120
  CLUS_2               36                 79
  CLUS_3               11                 94
  CLUS_4               17                116
  CLUS_5                7                 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 CLUS_5 CLUS_6 CLUS_7
  14Q LOSS MUTATED       16     25      6      9      8     10      7
  14Q LOSS WILD-TYPE    119     46     30     59     82     31     65
D66V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               16                119
  CLUS_2               25                 46
  CLUS_3                6                 30
  CLUS_4                9                 59
  CLUS_5                8                 82
  CLUS_6               10                 31
  CLUS_7                7                 65
[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       34     13     11     22
  14Q LOSS WILD-TYPE    106     94     71    158
D66V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               34                106
  CLUS_2               13                 94
  CLUS_3               11                 71
  CLUS_4               22                158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       28     23     29
  14Q LOSS WILD-TYPE    194    161     74
D66V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               28                194
  CLUS_2               23                161
  CLUS_3               29                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       22     29     10     19
  14Q LOSS WILD-TYPE    105     90     95    135
D66V11, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               22                105
  CLUS_2               29                 90
  CLUS_3               10                 95
  CLUS_4               19                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 CLUS_5 CLUS_6
  14Q LOSS MUTATED       14     16     15      6     21      8
  14Q LOSS WILD-TYPE     85     61    103     50     42     84
D66V12, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               14                 85
  CLUS_2               16                 61
  CLUS_3               15                103
  CLUS_4                6                 50
  CLUS_5               21                 42
  CLUS_6                8                 84
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) 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
D67V1, 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
D67V2, 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       14     11     26
  15Q LOSS WILD-TYPE    213    100    149
D67V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               14                213
  CLUS_2               11                100
  CLUS_3               26                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED       13      5     28      5
  15Q LOSS WILD-TYPE    196    129    129      8
D67V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               13                196
  CLUS_2                5                129
  CLUS_3               28                129
  CLUS_4                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        6     16     14      5
  15Q LOSS WILD-TYPE     85     79    111    110
D67V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 85
  CLUS_2               16                 79
  CLUS_3               14                111
  CLUS_4                5                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9      9     23
  15Q LOSS WILD-TYPE     74    149    162
D67V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                9                 74
  CLUS_2                9                149
  CLUS_3               23                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q LOSS MUTATED        5     13     20     10      3
  15Q LOSS WILD-TYPE    125    102     85    123     27
D67V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                125
  CLUS_2               13                102
  CLUS_3               20                 85
  CLUS_4               10                123
  CLUS_5                3                 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 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED        7      2      6      2     18     10      6
  15Q LOSS WILD-TYPE    128     69     30     66     72     31     66
D67V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                128
  CLUS_2                2                 69
  CLUS_3                6                 30
  CLUS_4                2                 66
  CLUS_5               18                 72
  CLUS_6               10                 31
  CLUS_7                6                 66
[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       16     10     13     12
  15Q LOSS WILD-TYPE    124     97     69    168
D67V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               16                124
  CLUS_2               10                 97
  CLUS_3               13                 69
  CLUS_4               12                168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       25     19      7
  15Q LOSS WILD-TYPE    197    165     96
D67V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               25                197
  CLUS_2               19                165
  CLUS_3                7                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        8     16     15     12
  15Q LOSS WILD-TYPE    119    103     90    142
D67V11, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                119
  CLUS_2               16                103
  CLUS_3               15                 90
  CLUS_4               12                142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  15Q LOSS MUTATED        7     13      7     14      2      8
  15Q LOSS WILD-TYPE     92     64    111     42     61     84
D67V12, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                 92
  CLUS_2               13                 64
  CLUS_3                7                111
  CLUS_4               14                 42
  CLUS_5                2                 61
  CLUS_6                8                 84
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) 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
D68V1, 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
D68V2, 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        7      6      1
  16P LOSS WILD-TYPE    220    105    174
D68V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                7                220
  CLUS_2                6                105
  CLUS_3                1                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      6      2      0
  16P LOSS WILD-TYPE    203    128    155     13
D68V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                203
  CLUS_2                6                128
  CLUS_3                2                155
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      2
  16P LOSS WILD-TYPE     90     92    121    113
D68V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 90
  CLUS_2                3                 92
  CLUS_3                4                121
  CLUS_4                2                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
  16P LOSS MUTATED        0      2      8
  16P LOSS WILD-TYPE     83    156    177
D68V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                2                156
  CLUS_3                8                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    129    107    104    129     30
D68V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                129
  CLUS_2                8                107
  CLUS_3                1                104
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      0      5      2      2      0
  16P LOSS WILD-TYPE    134     67     36     63     88     39     72
D68V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                4                 67
  CLUS_3                0                 36
  CLUS_4                5                 63
  CLUS_5                2                 88
  CLUS_6                2                 39
  CLUS_7                0                 72
[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        3      2      3      6
  16P LOSS WILD-TYPE    137    105     79    174
D68V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                137
  CLUS_2                2                105
  CLUS_3                3                 79
  CLUS_4                6                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      4      5
  16P LOSS WILD-TYPE    217    180     98
D68V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                5                217
  CLUS_2                4                180
  CLUS_3                5                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      3      3
  16P LOSS WILD-TYPE    124    114    102    151
D68V11, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                124
  CLUS_2                5                114
  CLUS_3                3                102
  CLUS_4                3                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 CLUS_5 CLUS_6
  16P LOSS MUTATED        1      3      3      2      4      1
  16P LOSS WILD-TYPE     98     74    115     54     59     91
D68V12, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                3                 74
  CLUS_3                3                115
  CLUS_4                2                 54
  CLUS_5                4                 59
  CLUS_6                1                 91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) 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
D69V1, 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
D69V2, 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       10     10      2
  16Q LOSS WILD-TYPE    217    101    173
D69V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               10                217
  CLUS_2               10                101
  CLUS_3                2                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8     10      3      1
  16Q LOSS WILD-TYPE    201    124    154     12
D69V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                201
  CLUS_2               10                124
  CLUS_3                3                154
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        2      5      7      2
  16Q LOSS WILD-TYPE     89     90    118    113
D69V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                5                 90
  CLUS_3                7                118
  CLUS_4                2                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
  16Q LOSS MUTATED        0      3     13
  16Q LOSS WILD-TYPE     83    155    172
D69V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                3                155
  CLUS_3               13                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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    126    103    103    129     30
D69V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                126
  CLUS_2               12                103
  CLUS_3                2                103
  CLUS_4                4                129
  CLUS_5                0                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      8      1      5      2      2      0
  16Q LOSS WILD-TYPE    131     63     35     63     88     39     72
D69V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                131
  CLUS_2                8                 63
  CLUS_3                1                 35
  CLUS_4                5                 63
  CLUS_5                2                 88
  CLUS_6                2                 39
  CLUS_7                0                 72
[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        8      3      4      7
  16Q LOSS WILD-TYPE    132    104     78    173
D69V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                132
  CLUS_2                3                104
  CLUS_3                4                 78
  CLUS_4                7                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7      4     11
  16Q LOSS WILD-TYPE    215    180     92
D69V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                215
  CLUS_2                4                180
  CLUS_3               11                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        8      6      4      3
  16Q LOSS WILD-TYPE    119    113    101    151
D69V11, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                119
  CLUS_2                6                113
  CLUS_3                4                101
  CLUS_4                3                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 CLUS_5 CLUS_6
  16Q LOSS MUTATED        2      4      3      2      7      3
  16Q LOSS WILD-TYPE     97     73    115     54     56     89
D69V12, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                4                 73
  CLUS_3                3                115
  CLUS_4                2                 54
  CLUS_5                7                 56
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) 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
D70V1, 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
D70V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        4      9      1
  17P LOSS WILD-TYPE    223    102    174
D70V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                223
  CLUS_2                9                102
  CLUS_3                1                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2
  17P LOSS WILD-TYPE    206    127    155     11
D70V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                206
  CLUS_2                7                127
  CLUS_3                2                155
  CLUS_4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        2      3      4      2
  17P LOSS WILD-TYPE     89     92    121    113
D70V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 89
  CLUS_2                3                 92
  CLUS_3                4                121
  CLUS_4                2                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
  17P LOSS MUTATED        3      3      5
  17P LOSS WILD-TYPE     80    155    180
D70V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                3                155
  CLUS_3                5                180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        0      9      2      1      2
  17P LOSS WILD-TYPE    130    106    103    132     28
D70V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                130
  CLUS_2                9                106
  CLUS_3                2                103
  CLUS_4                1                132
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  17P LOSS MUTATED        3      5      1      1      1      3      0
  17P LOSS WILD-TYPE    132     66     35     67     89     38     72
D70V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                132
  CLUS_2                5                 66
  CLUS_3                1                 35
  CLUS_4                1                 67
  CLUS_5                1                 89
  CLUS_6                3                 38
  CLUS_7                0                 72
[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        8      2      2      2
  17P LOSS WILD-TYPE    132    105     80    178
D70V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                132
  CLUS_2                2                105
  CLUS_3                2                 80
  CLUS_4                2                178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      1      8
  17P LOSS WILD-TYPE    217    183     95
D70V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                217
  CLUS_2                1                183
  CLUS_3                8                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      1      3
  17P LOSS WILD-TYPE    123    114    104    151
D70V11, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                123
  CLUS_2                5                114
  CLUS_3                1                104
  CLUS_4                3                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 CLUS_5 CLUS_6
  17P LOSS MUTATED        3      2      0      1      5      2
  17P LOSS WILD-TYPE     96     75    118     55     58     90
D70V12, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 96
  CLUS_2                2                 75
  CLUS_3                0                118
  CLUS_4                1                 55
  CLUS_5                5                 58
  CLUS_6                2                 90
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) 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
D71V1, 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
D71V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        3      6      0
  17Q LOSS WILD-TYPE    224    105    175
D71V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                224
  CLUS_2                6                105
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      5      1      1
  17Q LOSS WILD-TYPE    207    129    156     12
D71V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                207
  CLUS_2                5                129
  CLUS_3                1                156
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        1      2      4      1
  17Q LOSS WILD-TYPE     90     93    121    114
D71V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 90
  CLUS_2                2                 93
  CLUS_3                4                121
  CLUS_4                1                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        3      1      4
  17Q LOSS WILD-TYPE     80    157    181
D71V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                1                157
  CLUS_3                4                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        0      5      1      1      2
  17Q LOSS WILD-TYPE    130    110    104    132     28
D71V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                130
  CLUS_2                5                110
  CLUS_3                1                104
  CLUS_4                1                132
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  17Q LOSS MUTATED        3      3      1      1      0      1      0
  17Q LOSS WILD-TYPE    132     68     35     67     90     40     72
D71V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                132
  CLUS_2                3                 68
  CLUS_3                1                 35
  CLUS_4                1                 67
  CLUS_5                0                 90
  CLUS_6                1                 40
  CLUS_7                0                 72
[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        6      1      1      1
  17Q LOSS WILD-TYPE    134    106     81    179
D71V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                134
  CLUS_2                1                106
  CLUS_3                1                 81
  CLUS_4                1                179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      1      4
  17Q LOSS WILD-TYPE    218    183     99
D71V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                218
  CLUS_2                1                183
  CLUS_3                4                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      2
  17Q LOSS WILD-TYPE    124    116    105    152
D71V11, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                124
  CLUS_2                3                116
  CLUS_3                0                105
  CLUS_4                2                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 CLUS_5 CLUS_6
  17Q LOSS MUTATED        2      2      0      0      3      1
  17Q LOSS WILD-TYPE     97     75    118     56     60     91
D71V12, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                2                 75
  CLUS_3                0                118
  CLUS_4                0                 56
  CLUS_5                3                 60
  CLUS_6                1                 91
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) 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
D72V1, 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
D72V2, 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       18     19     30
  18P LOSS WILD-TYPE    209     92    145
D72V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               18                209
  CLUS_2               19                 92
  CLUS_3               30                145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22     14     30      1
  18P LOSS WILD-TYPE    187    120    127     12
D72V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               22                187
  CLUS_2               14                120
  CLUS_3               30                127
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        8     14     18     15
  18P LOSS WILD-TYPE     83     81    107    100
D72V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                 83
  CLUS_2               14                 81
  CLUS_3               18                107
  CLUS_4               15                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
  18P LOSS MUTATED        7     17     31
  18P LOSS WILD-TYPE     76    141    154
D72V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 76
  CLUS_2               17                141
  CLUS_3               31                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     18     15      2
  18P LOSS WILD-TYPE    118     95     87    118     28
D72V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                118
  CLUS_2               20                 95
  CLUS_3               18                 87
  CLUS_4               15                118
  CLUS_5                2                 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 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED       12     12      7      6     18      6      6
  18P LOSS WILD-TYPE    123     59     29     62     72     35     66
D72V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                123
  CLUS_2               12                 59
  CLUS_3                7                 29
  CLUS_4                6                 62
  CLUS_5               18                 72
  CLUS_6                6                 35
  CLUS_7                6                 66
[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     12     16     20
  18P LOSS WILD-TYPE    121     95     66    160
D72V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               19                121
  CLUS_2               12                 95
  CLUS_3               16                 66
  CLUS_4               20                160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       29     23     15
  18P LOSS WILD-TYPE    193    161     88
D72V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               29                193
  CLUS_2               23                161
  CLUS_3               15                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       14     18     17     18
  18P LOSS WILD-TYPE    113    101     88    136
D72V11, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               14                113
  CLUS_2               18                101
  CLUS_3               17                 88
  CLUS_4               18                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 CLUS_5 CLUS_6
  18P LOSS MUTATED        9     10     15     11     10     12
  18P LOSS WILD-TYPE     90     67    103     45     53     80
D72V12, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                9                 90
  CLUS_2               10                 67
  CLUS_3               15                103
  CLUS_4               11                 45
  CLUS_5               10                 53
  CLUS_6               12                 80
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) 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
D73V1, 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
D73V2, 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     14     33
  18Q LOSS WILD-TYPE    212     97    142
D73V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               15                212
  CLUS_2               14                 97
  CLUS_3               33                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED       19     10     33      0
  18Q LOSS WILD-TYPE    190    124    124     13
D73V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               19                190
  CLUS_2               10                124
  CLUS_3               33                124
  CLUS_4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        6     13     16     15
  18Q LOSS WILD-TYPE     85     82    109    100
D73V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                6                 85
  CLUS_2               13                 82
  CLUS_3               16                109
  CLUS_4               15                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
  18Q LOSS MUTATED        5     17     28
  18Q LOSS WILD-TYPE     78    141    157
D73V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 78
  CLUS_2               17                141
  CLUS_3               28                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q LOSS MUTATED        9     14     21     15      3
  18Q LOSS WILD-TYPE    121    101     84    118     27
D73V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                121
  CLUS_2               14                101
  CLUS_3               21                 84
  CLUS_4               15                118
  CLUS_5                3                 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 CLUS_5 CLUS_6 CLUS_7
  18Q LOSS MUTATED        9      8      7      6     20      6      6
  18Q LOSS WILD-TYPE    126     63     29     62     70     35     66
D73V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                126
  CLUS_2                8                 63
  CLUS_3                7                 29
  CLUS_4                6                 62
  CLUS_5               20                 70
  CLUS_6                6                 35
  CLUS_7                6                 66
[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      7     18     20
  18Q LOSS WILD-TYPE    123    100     64    160
D73V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               17                123
  CLUS_2                7                100
  CLUS_3               18                 64
  CLUS_4               20                160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       29     23     10
  18Q LOSS WILD-TYPE    193    161     93
D73V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               29                193
  CLUS_2               23                161
  CLUS_3               10                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12     13     19     18
  18Q LOSS WILD-TYPE    115    106     86    136
D73V11, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                115
  CLUS_2               13                106
  CLUS_3               19                 86
  CLUS_4               18                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 CLUS_5 CLUS_6
  18Q LOSS MUTATED        8      9     13     12      7     13
  18Q LOSS WILD-TYPE     91     68    105     44     56     79
D73V12, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                8                 91
  CLUS_2                9                 68
  CLUS_3               13                105
  CLUS_4               12                 44
  CLUS_5                7                 56
  CLUS_6               13                 79
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) 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
D74V1, 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
D74V2, 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       12      6      8
  19P LOSS WILD-TYPE    215    105    167
D74V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               12                215
  CLUS_2                6                105
  CLUS_3                8                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED       11      6      8      1
  19P LOSS WILD-TYPE    198    128    149     12
D74V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               11                198
  CLUS_2                6                128
  CLUS_3                8                149
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        4      7      3      4
  19P LOSS WILD-TYPE     87     88    122    111
D74V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 87
  CLUS_2                7                 88
  CLUS_3                3                122
  CLUS_4                4                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
  19P LOSS MUTATED        2      5     11
  19P LOSS WILD-TYPE     81    153    174
D74V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                5                153
  CLUS_3               11                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED        5      8      7      5      1
  19P LOSS WILD-TYPE    125    107     98    128     29
D74V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                125
  CLUS_2                8                107
  CLUS_3                7                 98
  CLUS_4                5                128
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      2      3      2      4      6      3
  19P LOSS WILD-TYPE    129     69     33     66     86     35     69
D74V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                6                129
  CLUS_2                2                 69
  CLUS_3                3                 33
  CLUS_4                2                 66
  CLUS_5                4                 86
  CLUS_6                6                 35
  CLUS_7                3                 69
[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        8      6      7      5
  19P LOSS WILD-TYPE    132    101     75    175
D74V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                8                132
  CLUS_2                6                101
  CLUS_3                7                 75
  CLUS_4                5                175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       15      7      4
  19P LOSS WILD-TYPE    207    177     99
D74V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               15                207
  CLUS_2                7                177
  CLUS_3                4                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        3      9      9      4
  19P LOSS WILD-TYPE    124    110     96    150
D74V11, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                124
  CLUS_2                9                110
  CLUS_3                9                 96
  CLUS_4                4                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P LOSS MUTATED        4      9      3      4      2      3
  19P LOSS WILD-TYPE     95     68    115     52     61     89
D74V12, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 95
  CLUS_2                9                 68
  CLUS_3                3                115
  CLUS_4                4                 52
  CLUS_5                2                 61
  CLUS_6                3                 89
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) 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
D75V1, 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
D75V2, 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       22     22    165
  19Q LOSS WILD-TYPE    205     89     10
D75V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               22                205
  CLUS_2               22                 89
  CLUS_3              165                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       28     24    156      1
  19Q LOSS WILD-TYPE    181    110      1     12
D75V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               28                181
  CLUS_2               24                110
  CLUS_3              156                  1
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       30     42     50     59
  19Q LOSS WILD-TYPE     61     53     75     56
D75V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               30                 61
  CLUS_2               42                 53
  CLUS_3               50                 75
  CLUS_4               59                 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
  19Q LOSS MUTATED       28     82     71
  19Q LOSS WILD-TYPE     55     76    114
D75V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               28                 55
  CLUS_2               82                 76
  CLUS_3               71                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       16     16    103     63     11
  19Q LOSS WILD-TYPE    114     99      2     70     19
D75V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                114
  CLUS_2               16                 99
  CLUS_3              103                  2
  CLUS_4               63                 70
  CLUS_5               11                 19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      5     36      8     87      8     49
  19Q LOSS WILD-TYPE    119     66      0     60      3     33     23
D75V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                119
  CLUS_2                5                 66
  CLUS_3               36                  0
  CLUS_4                8                 60
  CLUS_5               87                  3
  CLUS_6                8                 33
  CLUS_7               49                 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
  19Q LOSS MUTATED       33     20     70     86
  19Q LOSS WILD-TYPE    107     87     12     94
D75V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               33                107
  CLUS_2               20                 87
  CLUS_3               70                 12
  CLUS_4               86                 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
  19Q LOSS MUTATED       97    103      9
  19Q LOSS WILD-TYPE    125     81     94
D75V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               97                125
  CLUS_2              103                 81
  CLUS_3                9                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22     26     87     73
  19Q LOSS WILD-TYPE    105     93     18     81
D75V11, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               22                105
  CLUS_2               26                 93
  CLUS_3               87                 18
  CLUS_4               73                 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 CLUS_5 CLUS_6
  19Q LOSS MUTATED       11     38     62     55      2     40
  19Q LOSS WILD-TYPE     88     39     56      1     61     52
D75V12, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               11                 88
  CLUS_2               38                 39
  CLUS_3               62                 56
  CLUS_4               55                  1
  CLUS_5                2                 61
  CLUS_6               40                 52
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) 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
D76V1, 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
D76V2, 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        7      0      0
  20P LOSS WILD-TYPE    220    111    175
D76V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                220
  CLUS_2                0                111
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      1
  20P LOSS WILD-TYPE    204    133    157     12
D76V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                204
  CLUS_2                1                133
  CLUS_3                0                157
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        0      2      1      2
  20P LOSS WILD-TYPE     91     93    124    113
D76V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 91
  CLUS_2                2                 93
  CLUS_3                1                124
  CLUS_4                2                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
  20P LOSS MUTATED        0      2      3
  20P LOSS WILD-TYPE     83    156    182
D76V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                2                156
  CLUS_3                3                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P LOSS MUTATED        2      3      0      1      1
  20P LOSS WILD-TYPE    128    112    105    132     29
D76V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                128
  CLUS_2                3                112
  CLUS_3                0                105
  CLUS_4                1                132
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      2      0      2      0
  20P LOSS WILD-TYPE    133     70     36     66     90     39     72
D76V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                133
  CLUS_2                1                 70
  CLUS_3                0                 36
  CLUS_4                2                 66
  CLUS_5                0                 90
  CLUS_6                2                 39
  CLUS_7                0                 72
[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        2      3      1      1
  20P LOSS WILD-TYPE    138    104     81    179
D76V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                138
  CLUS_2                3                104
  CLUS_3                1                 81
  CLUS_4                1                179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      1      2
  20P LOSS WILD-TYPE    218    183    101
D76V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                218
  CLUS_2                1                183
  CLUS_3                2                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      2      1
  20P LOSS WILD-TYPE    125    117    103    153
D76V11, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                125
  CLUS_2                2                117
  CLUS_3                2                103
  CLUS_4                1                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 CLUS_5 CLUS_6
  20P LOSS MUTATED        2      3      2      0      0      0
  20P LOSS WILD-TYPE     97     74    116     56     63     92
D76V12, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 97
  CLUS_2                3                 74
  CLUS_3                2                116
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                0                 92
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) 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
D77V1, 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
D77V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        3      0      0
  20Q LOSS WILD-TYPE    224    111    175
D77V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                224
  CLUS_2                0                111
  CLUS_3                0                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      1
  20Q LOSS WILD-TYPE    207    134    157     12
D77V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                207
  CLUS_2                0                134
  CLUS_3                0                157
  CLUS_4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        1      0      0      1
  20Q LOSS WILD-TYPE     90     95    125    114
D77V5, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                424 
        TCGA-CS-4938         TCGA-CS-4942         TCGA-CS-4943 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-4944         TCGA-CS-5390         TCGA-CS-5393 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5396         TCGA-CS-5397 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6186         TCGA-CS-6188         TCGA-CS-6665 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6666         TCGA-CS-6668         TCGA-CS-6669 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6670         TCGA-DB-5270         TCGA-DB-5273 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5279 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DB-A4X9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XA         TCGA-DB-A4XB         TCGA-DB-A4XC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XD         TCGA-DB-A4XE         TCGA-DB-A4XF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XG         TCGA-DB-A4XH         TCGA-DB-A64L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64O         TCGA-DB-A64P         TCGA-DB-A64Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64R         TCGA-DB-A64S         TCGA-DB-A64U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64V         TCGA-DB-A64W         TCGA-DB-A64X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A75K         TCGA-DB-A75L         TCGA-DB-A75M 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A75O         TCGA-DB-A75P         TCGA-DH-5140 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DH-A7US 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5847         TCGA-DU-5849         TCGA-DU-5851 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5872         TCGA-DU-5874         TCGA-DU-6392 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6393         TCGA-DU-6394         TCGA-DU-6395 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6397         TCGA-DU-6399 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6400         TCGA-DU-6401         TCGA-DU-6402 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6406         TCGA-DU-6407         TCGA-DU-6408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-6542         TCGA-DU-7006 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7007         TCGA-DU-7008         TCGA-DU-7009 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7010         TCGA-DU-7011         TCGA-DU-7012 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7019         TCGA-DU-7290 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7292         TCGA-DU-7294         TCGA-DU-7298 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7300         TCGA-DU-7301         TCGA-DU-7302 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8164         TCGA-DU-8165 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8166         TCGA-DU-8167         TCGA-DU-8168 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TP         TCGA-DU-A5TR         TCGA-DU-A5TS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TT         TCGA-DU-A5TU         TCGA-DU-A5TW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TY         TCGA-DU-A6S2         TCGA-DU-A6S3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A6S8         TCGA-DU-A76K         TCGA-DU-A76L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A76O         TCGA-DU-A76R         TCGA-DU-A7T6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A7TA         TCGA-DU-A7TB         TCGA-DU-A7TD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A7TG         TCGA-DU-A7TI         TCGA-DU-A7TJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YI         TCGA-E1-A7YJ         TCGA-E1-A7YL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YM         TCGA-E1-A7YN         TCGA-E1-A7YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YS         TCGA-E1-A7YV         TCGA-E1-A7YW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YY         TCGA-E1-A7Z2         TCGA-E1-A7Z3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7Z6         TCGA-EZ-7264         TCGA-F6-A8O3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F6-A8O4         TCGA-FG-5962         TCGA-FG-5963 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-5964         TCGA-FG-5965         TCGA-FG-6688 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-7634         TCGA-FG-7636         TCGA-FG-7638 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-7641         TCGA-FG-7643         TCGA-FG-8181 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8182         TCGA-FG-8185         TCGA-FG-8186 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8191         TCGA-FG-A4MT         TCGA-FG-A4MU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A4MY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A60J         TCGA-FG-A60L         TCGA-FG-A6IZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A6J3         TCGA-FG-A70Y         TCGA-FG-A70Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A710         TCGA-FG-A713         TCGA-FG-A87N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A87Q         TCGA-HT-7467         TCGA-HT-7468 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7469         TCGA-HT-7470         TCGA-HT-7471 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7472         TCGA-HT-7473         TCGA-HT-7474 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7476         TCGA-HT-7477 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7478         TCGA-HT-7479         TCGA-HT-7480 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7481         TCGA-HT-7482         TCGA-HT-7483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7601         TCGA-HT-7602 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7603         TCGA-HT-7604         TCGA-HT-7605 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7606         TCGA-HT-7607         TCGA-HT-7608 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7610         TCGA-HT-7611 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7616         TCGA-HT-7620         TCGA-HT-7676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7677         TCGA-HT-7680         TCGA-HT-7681 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7684         TCGA-HT-7686         TCGA-HT-7687 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7688         TCGA-HT-7689         TCGA-HT-7690 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7691         TCGA-HT-7692         TCGA-HT-7693 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7695         TCGA-HT-7854 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7855         TCGA-HT-7856         TCGA-HT-7857 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7858         TCGA-HT-7860         TCGA-HT-7873 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7874         TCGA-HT-7875         TCGA-HT-7877 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7879         TCGA-HT-7880         TCGA-HT-7881 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7882         TCGA-HT-7884         TCGA-HT-7902 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8010         TCGA-HT-8011         TCGA-HT-8012 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8013         TCGA-HT-8015         TCGA-HT-8018 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8019         TCGA-HT-8104         TCGA-HT-8105 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8106         TCGA-HT-8107         TCGA-HT-8109 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8110         TCGA-HT-8111         TCGA-HT-8113 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8114         TCGA-HT-8564         TCGA-HT-A4DV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A5R5         TCGA-HT-A5R7         TCGA-HT-A5R9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A5RB         TCGA-HT-A614         TCGA-HT-A615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A616         TCGA-HT-A617         TCGA-HT-A619 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A61B         TCGA-HT-A74H         TCGA-HT-A74J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A74L         TCGA-HT-A74O         TCGA-HW-7486 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-7487         TCGA-HW-7489         TCGA-HW-7490 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-7491         TCGA-HW-7493         TCGA-HW-7495 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-8319         TCGA-HW-8320         TCGA-HW-8321 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-8322         TCGA-HW-A5KJ         TCGA-HW-A5KK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-A5KM         TCGA-IK-7675         TCGA-IK-8125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KT-A74X         TCGA-P5-A5ET         TCGA-P5-A5EU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5EV         TCGA-P5-A5EW         TCGA-P5-A5EX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5EY         TCGA-P5-A5EZ         TCGA-P5-A5F0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5F1         TCGA-P5-A5F2         TCGA-P5-A5F4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5F6         TCGA-P5-A72U         TCGA-P5-A72W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A72X         TCGA-P5-A72Z         TCGA-P5-A730 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A731         TCGA-P5-A733         TCGA-P5-A735 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A736         TCGA-P5-A737         TCGA-P5-A77W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A77X         TCGA-P5-A780         TCGA-P5-A781 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A65S         TCGA-QH-A65V         TCGA-QH-A65X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A65Z         TCGA-QH-A6CS         TCGA-QH-A6CU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6CV         TCGA-QH-A6CW         TCGA-QH-A6CX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6CY         TCGA-QH-A6CZ         TCGA-QH-A6X4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6X5         TCGA-QH-A6X8         TCGA-QH-A6X9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6XA         TCGA-QH-A6XC         TCGA-QH-A86X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A870         TCGA-R8-A6MK         TCGA-R8-A6ML 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R8-A6MO         TCGA-R8-A6YH         TCGA-RY-A83X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RY-A83Y         TCGA-RY-A83Z         TCGA-RY-A843 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RY-A845         TCGA-S9-A6TS         TCGA-S9-A6TU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6TV         TCGA-S9-A6TX         TCGA-S9-A6TY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6U0         TCGA-S9-A6U1         TCGA-S9-A6U5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6U6         TCGA-S9-A6U9         TCGA-S9-A6WD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6WE         TCGA-S9-A6WG         TCGA-S9-A6WH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6WN         TCGA-S9-A6WP         TCGA-S9-A6WQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7IQ         TCGA-S9-A7IS         TCGA-S9-A7IY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7IZ         TCGA-S9-A7J0         TCGA-S9-A7J1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7J2         TCGA-S9-A7QX         TCGA-S9-A7QZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7R1         TCGA-S9-A7R4         TCGA-S9-A7R8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TM-A7C5         TCGA-TM-A84R         TCGA-TM-A84S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RF         TCGA-TQ-A7RG         TCGA-TQ-A7RH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RK         TCGA-TQ-A7RN         TCGA-TQ-A7RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RR         TCGA-TQ-A7RS         TCGA-TQ-A7RV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RW         TCGA-TQ-A8XE         TCGA-VM-A8C8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VM-A8C9         TCGA-VM-A8CA         TCGA-VM-A8CB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VM-A8CD         TCGA-VM-A8CE         TCGA-VM-A8CH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VV-A829         TCGA-VV-A86M         TCGA-VW-A7QS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-W9-A837         TCGA-WY-A85B         TCGA-WY-A85C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-WY-A85D 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        1      1      0
  20Q LOSS WILD-TYPE     82    157    185
D77V6, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                424 
        TCGA-CS-4938         TCGA-CS-4942         TCGA-CS-4943 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-4944         TCGA-CS-5390         TCGA-CS-5393 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5396         TCGA-CS-5397 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6186         TCGA-CS-6188         TCGA-CS-6665 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6666         TCGA-CS-6668         TCGA-CS-6669 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CS-6670         TCGA-DB-5270         TCGA-DB-5273 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5279 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DB-A4X9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XA         TCGA-DB-A4XB         TCGA-DB-A4XC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XD         TCGA-DB-A4XE         TCGA-DB-A4XF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A4XG         TCGA-DB-A4XH         TCGA-DB-A64L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64O         TCGA-DB-A64P         TCGA-DB-A64Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64R         TCGA-DB-A64S         TCGA-DB-A64U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A64V         TCGA-DB-A64W         TCGA-DB-A64X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A75K         TCGA-DB-A75L         TCGA-DB-A75M 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DB-A75O         TCGA-DB-A75P         TCGA-DH-5140 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DH-A7US 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5847         TCGA-DU-5849         TCGA-DU-5851 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-5872         TCGA-DU-5874         TCGA-DU-6392 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6393         TCGA-DU-6394         TCGA-DU-6395 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6397         TCGA-DU-6399 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6400         TCGA-DU-6401         TCGA-DU-6402 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6406         TCGA-DU-6407         TCGA-DU-6408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-6542         TCGA-DU-7006 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7007         TCGA-DU-7008         TCGA-DU-7009 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7010         TCGA-DU-7011         TCGA-DU-7012 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7019         TCGA-DU-7290 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7292         TCGA-DU-7294         TCGA-DU-7298 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7300         TCGA-DU-7301         TCGA-DU-7302 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8164         TCGA-DU-8165 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-8166         TCGA-DU-8167         TCGA-DU-8168 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TP         TCGA-DU-A5TR         TCGA-DU-A5TS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TT         TCGA-DU-A5TU         TCGA-DU-A5TW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A5TY         TCGA-DU-A6S2         TCGA-DU-A6S3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A6S8         TCGA-DU-A76K         TCGA-DU-A76L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A76O         TCGA-DU-A76R         TCGA-DU-A7T6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A7TA         TCGA-DU-A7TB         TCGA-DU-A7TD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DU-A7TG         TCGA-DU-A7TI         TCGA-DU-A7TJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YI         TCGA-E1-A7YJ         TCGA-E1-A7YL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YM         TCGA-E1-A7YN         TCGA-E1-A7YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YS         TCGA-E1-A7YV         TCGA-E1-A7YW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7YY         TCGA-E1-A7Z2         TCGA-E1-A7Z3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E1-A7Z6         TCGA-EZ-7264         TCGA-F6-A8O3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F6-A8O4         TCGA-FG-5962         TCGA-FG-5963 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-5964         TCGA-FG-5965         TCGA-FG-6688 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-7634         TCGA-FG-7636         TCGA-FG-7638 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-7641         TCGA-FG-7643         TCGA-FG-8181 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8182         TCGA-FG-8185         TCGA-FG-8186 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-8191         TCGA-FG-A4MT         TCGA-FG-A4MU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A4MY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A60J         TCGA-FG-A60L         TCGA-FG-A6IZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A6J3         TCGA-FG-A70Y         TCGA-FG-A70Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A710         TCGA-FG-A713         TCGA-FG-A87N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FG-A87Q         TCGA-HT-7467         TCGA-HT-7468 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7469         TCGA-HT-7470         TCGA-HT-7471 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7472         TCGA-HT-7473         TCGA-HT-7474 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7476         TCGA-HT-7477 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7478         TCGA-HT-7479         TCGA-HT-7480 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7481         TCGA-HT-7482         TCGA-HT-7483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7601         TCGA-HT-7602 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7603         TCGA-HT-7604         TCGA-HT-7605 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7606         TCGA-HT-7607         TCGA-HT-7608 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7610         TCGA-HT-7611 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7616         TCGA-HT-7620         TCGA-HT-7676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7677         TCGA-HT-7680         TCGA-HT-7681 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7684         TCGA-HT-7686         TCGA-HT-7687 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7688         TCGA-HT-7689         TCGA-HT-7690 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7691         TCGA-HT-7692         TCGA-HT-7693 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7695         TCGA-HT-7854 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7855         TCGA-HT-7856         TCGA-HT-7857 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7858         TCGA-HT-7860         TCGA-HT-7873 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7874         TCGA-HT-7875         TCGA-HT-7877 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7879         TCGA-HT-7880         TCGA-HT-7881 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-7882         TCGA-HT-7884         TCGA-HT-7902 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8010         TCGA-HT-8011         TCGA-HT-8012 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8013         TCGA-HT-8015         TCGA-HT-8018 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8019         TCGA-HT-8104         TCGA-HT-8105 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8106         TCGA-HT-8107         TCGA-HT-8109 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8110         TCGA-HT-8111         TCGA-HT-8113 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-8114         TCGA-HT-8564         TCGA-HT-A4DV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A5R5         TCGA-HT-A5R7         TCGA-HT-A5R9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A5RB         TCGA-HT-A614         TCGA-HT-A615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A616         TCGA-HT-A617         TCGA-HT-A619 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A61B         TCGA-HT-A74H         TCGA-HT-A74J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HT-A74L         TCGA-HT-A74O         TCGA-HW-7486 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-7487         TCGA-HW-7489         TCGA-HW-7490 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-7491         TCGA-HW-7493         TCGA-HW-7495 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-8319         TCGA-HW-8320         TCGA-HW-8321 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-8322         TCGA-HW-A5KJ         TCGA-HW-A5KK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HW-A5KM         TCGA-IK-7675         TCGA-IK-8125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KT-A74X         TCGA-P5-A5ET         TCGA-P5-A5EU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5EV         TCGA-P5-A5EW         TCGA-P5-A5EX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5EY         TCGA-P5-A5EZ         TCGA-P5-A5F0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5F1         TCGA-P5-A5F2         TCGA-P5-A5F4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A5F6         TCGA-P5-A72U         TCGA-P5-A72W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A72X         TCGA-P5-A72Z         TCGA-P5-A730 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A731         TCGA-P5-A733         TCGA-P5-A735 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A736         TCGA-P5-A737         TCGA-P5-A77W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P5-A77X         TCGA-P5-A780         TCGA-P5-A781 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A65S         TCGA-QH-A65V         TCGA-QH-A65X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A65Z         TCGA-QH-A6CS         TCGA-QH-A6CU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6CV         TCGA-QH-A6CW         TCGA-QH-A6CX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6CY         TCGA-QH-A6CZ         TCGA-QH-A6X4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6X5         TCGA-QH-A6X8         TCGA-QH-A6X9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A6XA         TCGA-QH-A6XC         TCGA-QH-A86X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QH-A870         TCGA-R8-A6MK         TCGA-R8-A6ML 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R8-A6MO         TCGA-R8-A6YH         TCGA-RY-A83X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RY-A83Y         TCGA-RY-A83Z         TCGA-RY-A843 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RY-A845         TCGA-S9-A6TS         TCGA-S9-A6TU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6TV         TCGA-S9-A6TX         TCGA-S9-A6TY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6U0         TCGA-S9-A6U1         TCGA-S9-A6U5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6U6         TCGA-S9-A6U9         TCGA-S9-A6WD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6WE         TCGA-S9-A6WG         TCGA-S9-A6WH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A6WN         TCGA-S9-A6WP         TCGA-S9-A6WQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7IQ         TCGA-S9-A7IS         TCGA-S9-A7IY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7IZ         TCGA-S9-A7J0         TCGA-S9-A7J1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7J2         TCGA-S9-A7QX         TCGA-S9-A7QZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-S9-A7R1         TCGA-S9-A7R4         TCGA-S9-A7R8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TM-A7C5         TCGA-TM-A84R         TCGA-TM-A84S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RF         TCGA-TQ-A7RG         TCGA-TQ-A7RH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RK         TCGA-TQ-A7RN         TCGA-TQ-A7RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RR         TCGA-TQ-A7RS         TCGA-TQ-A7RV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-TQ-A7RW         TCGA-TQ-A8XE         TCGA-VM-A8C8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VM-A8C9         TCGA-VM-A8CA         TCGA-VM-A8CB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VM-A8CD         TCGA-VM-A8CE         TCGA-VM-A8CH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VV-A829         TCGA-VV-A86M         TCGA-VW-A7QS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-W9-A837         TCGA-WY-A85B         TCGA-WY-A85C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-WY-A85D 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q LOSS MUTATED        0      2      0      0      1
  20Q LOSS WILD-TYPE    130    113    105    133     29
D77V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                130
  CLUS_2                2                113
  CLUS_3                0                105
  CLUS_4                0                133
  CLUS_5                1                 29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        1      0      0      0      0      2      0
  20Q LOSS WILD-TYPE    134     71     36     68     90     39     72
D77V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                134
  CLUS_2                0                 71
  CLUS_3                0                 36
  CLUS_4                0                 68
  CLUS_5                0                 90
  CLUS_6                2                 39
  CLUS_7                0                 72
[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    138    106     82    180
D77V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                138
  CLUS_2                1                106
  CLUS_3                0                 82
  CLUS_4                0                180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 LOSS MUTATED        2      1      0
  20Q LOSS WILD-TYPE    220    183    103
D77V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                220
  CLUS_2                1                183
  CLUS_3                0                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      2      1      0
  20Q LOSS WILD-TYPE    127    117    104    154
D77V11, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                127
  CLUS_2                2                117
  CLUS_3                1                104
  CLUS_4                0                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 CLUS_5 CLUS_6
  20Q LOSS MUTATED        1      2      0      0      0      0
  20Q LOSS WILD-TYPE     98     75    118     56     63     92
D77V12, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                 98
  CLUS_2                2                 75
  CLUS_3                0                118
  CLUS_4                0                 56
  CLUS_5                0                 63
  CLUS_6                0                 92
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        2      2      0
  21Q LOSS WILD-TYPE      7      8      8
D78V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  7
  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
  21Q LOSS MUTATED        0      4      0      0
  21Q LOSS WILD-TYPE      7      3      7      6
D78V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q 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
  21Q LOSS MUTATED       19     16      3
  21Q LOSS WILD-TYPE    208     95    172
D78V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               19                208
  CLUS_2               16                 95
  CLUS_3                3                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       23      9      2      4
  21Q LOSS WILD-TYPE    186    125    155      9
D78V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               23                186
  CLUS_2                9                125
  CLUS_3                2                155
  CLUS_4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        3     11     11      7
  21Q LOSS WILD-TYPE     88     84    114    108
D78V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 88
  CLUS_2               11                 84
  CLUS_3               11                114
  CLUS_4                7                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
  21Q LOSS MUTATED        4     11     17
  21Q LOSS WILD-TYPE     79    147    168
D78V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 79
  CLUS_2               11                147
  CLUS_3               17                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q LOSS MUTATED       13     13      1      6      5
  21Q LOSS WILD-TYPE    117    102    104    127     25
D78V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               13                117
  CLUS_2               13                102
  CLUS_3                1                104
  CLUS_4                6                127
  CLUS_5                5                 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 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED       16      3      2      4      0     11      2
  21Q LOSS WILD-TYPE    119     68     34     64     90     30     70
D78V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               16                119
  CLUS_2                3                 68
  CLUS_3                2                 34
  CLUS_4                4                 64
  CLUS_5                0                 90
  CLUS_6               11                 30
  CLUS_7                2                 70
[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       11     12      5     10
  21Q LOSS WILD-TYPE    129     95     77    170
D78V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                129
  CLUS_2               12                 95
  CLUS_3                5                 77
  CLUS_4               10                170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       21      7     10
  21Q LOSS WILD-TYPE    201    177     93
D78V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               21                201
  CLUS_2                7                177
  CLUS_3               10                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       10     14      4      9
  21Q LOSS WILD-TYPE    117    105    101    145
D78V11, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               10                117
  CLUS_2               14                105
  CLUS_3                4                101
  CLUS_4                9                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  21Q LOSS MUTATED       10     12      5      1      3      6
  21Q LOSS WILD-TYPE     89     65    113     55     60     86
D78V12, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               10                 89
  CLUS_2               12                 65
  CLUS_3                5                113
  CLUS_4                1                 55
  CLUS_5                3                 60
  CLUS_6                6                 86
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) 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
D79V1, 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
D79V2, 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       21     32      4
  22Q LOSS WILD-TYPE    206     79    171
D79V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               21                206
  CLUS_2               32                 79
  CLUS_3                4                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22     28      4      3
  22Q LOSS WILD-TYPE    187    106    153     10
D79V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               22                187
  CLUS_2               28                106
  CLUS_3                4                153
  CLUS_4                3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        5     23     10     10
  22Q LOSS WILD-TYPE     86     72    115    105
D79V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 86
  CLUS_2               23                 72
  CLUS_3               10                115
  CLUS_4               10                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
  22Q LOSS MUTATED        5     14     29
  22Q LOSS WILD-TYPE     78    144    156
D79V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 78
  CLUS_2               14                144
  CLUS_3               29                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q LOSS MUTATED        8     31      2     11      5
  22Q LOSS WILD-TYPE    122     84    103    122     25
D79V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                8                122
  CLUS_2               31                 84
  CLUS_3                2                103
  CLUS_4               11                122
  CLUS_5                5                 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 CLUS_5 CLUS_6 CLUS_7
  22Q LOSS MUTATED       11     21      2     11      2      9      1
  22Q LOSS WILD-TYPE    124     50     34     57     88     32     71
D79V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                124
  CLUS_2               21                 50
  CLUS_3                2                 34
  CLUS_4               11                 57
  CLUS_5                2                 88
  CLUS_6                9                 32
  CLUS_7                1                 71
[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       19     14      7     17
  22Q LOSS WILD-TYPE    121     93     75    163
D79V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               19                121
  CLUS_2               14                 93
  CLUS_3                7                 75
  CLUS_4               17                163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       18     15     24
  22Q LOSS WILD-TYPE    204    169     79
D79V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               18                204
  CLUS_2               15                169
  CLUS_3               24                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       17     23      5     11
  22Q LOSS WILD-TYPE    110     96    100    143
D79V11, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               17                110
  CLUS_2               23                 96
  CLUS_3                5                100
  CLUS_4               11                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  22Q LOSS MUTATED        3     15     10      3     17      8
  22Q LOSS WILD-TYPE     96     62    108     53     46     84
D79V12, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 96
  CLUS_2               15                 62
  CLUS_3               10                108
  CLUS_4                3                 53
  CLUS_5               17                 46
  CLUS_6                8                 84
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED        1      2      2
  XP LOSS WILD-TYPE      8      8      6
D80V1, multiclass
        clus
vv       XP LOSS MUTATED XP 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
  XP LOSS MUTATED        0      3      0      2
  XP LOSS WILD-TYPE      7      4      7      4
D80V2, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                 7
  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
  XP LOSS MUTATED       43     22     34
  XP LOSS WILD-TYPE    184     89    141
D80V3, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              43               184
  CLUS_2              22                89
  CLUS_3              34               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       44     16     32      7
  XP LOSS WILD-TYPE    165    118    125      6
D80V4, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              44               165
  CLUS_2              16               118
  CLUS_3              32               125
  CLUS_4               7                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       10     30     29     18
  XP LOSS WILD-TYPE     81     65     96     97
D80V5, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              10                81
  CLUS_2              30                65
  CLUS_3              29                96
  CLUS_4              18                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
  XP LOSS MUTATED       11     25     51
  XP LOSS WILD-TYPE     72    133    134
D80V6, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              11                72
  CLUS_2              25               133
  CLUS_3              51               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP LOSS MUTATED       24     29     24     17      5
  XP LOSS WILD-TYPE    106     86     81    116     25
D80V7, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              24               106
  CLUS_2              29                86
  CLUS_3              24                81
  CLUS_4              17               116
  CLUS_5               5                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 CLUS_5 CLUS_6 CLUS_7
  XP LOSS MUTATED       29     10     10      9     20     18      3
  XP LOSS WILD-TYPE    106     61     26     59     70     23     69
D80V8, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              29               106
  CLUS_2              10                61
  CLUS_3              10                26
  CLUS_4               9                59
  CLUS_5              20                70
  CLUS_6              18                23
  CLUS_7               3                69
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       22     24     25     28
  XP LOSS WILD-TYPE    118     83     57    152
D80V9, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              22               118
  CLUS_2              24                83
  CLUS_3              25                57
  CLUS_4              28               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
  XP LOSS MUTATED       48     29     22
  XP LOSS WILD-TYPE    174    155     81
D80V10, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              48               174
  CLUS_2              29               155
  CLUS_3              22                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       33     19     29     17
  XP LOSS WILD-TYPE     94    100     76    137
D80V11, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              33                94
  CLUS_2              19               100
  CLUS_3              29                76
  CLUS_4              17               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 CLUS_5 CLUS_6
  XP LOSS MUTATED       20     23      9     13      8     25
  XP LOSS WILD-TYPE     79     54    109     43     55     67
D80V12, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              20                79
  CLUS_2              23                54
  CLUS_3               9               109
  CLUS_4              13                43
  CLUS_5               8                55
  CLUS_6              25                67
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) 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
D81V1, 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
D81V2, 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       20     16     34
  XQ LOSS WILD-TYPE    207     95    141
D81V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              20               207
  CLUS_2              16                95
  CLUS_3              34               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       20     12     32      6
  XQ LOSS WILD-TYPE    189    122    125      7
D81V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              20               189
  CLUS_2              12               122
  CLUS_3              32               125
  CLUS_4               6                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4     27     15     15
  XQ LOSS WILD-TYPE     87     68    110    100
D81V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                87
  CLUS_2              27                68
  CLUS_3              15               110
  CLUS_4              15               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
  XQ LOSS MUTATED        5     21     35
  XQ LOSS WILD-TYPE     78    137    150
D81V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5                78
  CLUS_2              21               137
  CLUS_3              35               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED       10     23     24     13      0
  XQ LOSS WILD-TYPE    120     92     81    120     30
D81V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              10               120
  CLUS_2              23                92
  CLUS_3              24                81
  CLUS_4              13               120
  CLUS_5               0                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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        9      9     10      7     20     13      2
  XQ LOSS WILD-TYPE    126     62     26     61     70     28     70
D81V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               9               126
  CLUS_2               9                62
  CLUS_3              10                26
  CLUS_4               7                61
  CLUS_5              20                70
  CLUS_6              13                28
  CLUS_7               2                70
[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       11     16     26     17
  XQ LOSS WILD-TYPE    129     91     56    163
D81V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              11               129
  CLUS_2              16                91
  CLUS_3              26                56
  CLUS_4              17               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       30     21     19
  XQ LOSS WILD-TYPE    192    163     84
D81V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              30               192
  CLUS_2              21               163
  CLUS_3              19                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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     11     28     11
  XQ LOSS WILD-TYPE    108    108     77    143
D81V11, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              19               108
  CLUS_2              11               108
  CLUS_3              28                77
  CLUS_4              11               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  XQ LOSS MUTATED        9     17      6     13      7     17
  XQ LOSS WILD-TYPE     90     60    112     43     56     75
D81V12, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               9                90
  CLUS_2              17                60
  CLUS_3               6               112
  CLUS_4              13                43
  CLUS_5               7                56
  CLUS_6              17                75
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
