[1] "ofn"        "-oTUCEC-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/UCEC-TP/15120652/UCEC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/15106276/transformed.cor.cli.txt"

nPatients in clinical file=547, in cluster file=539, common to both=539
[1]  82 539
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               489 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               489 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              188               351 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              188               351 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               95               444 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               95               444 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               460 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               460 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               49               490 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               49               490 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               84               455 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               84               455 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               525 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               525 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               531 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               531 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               51               488 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               51               488 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               519 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               519 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               80               459 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               80               459 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               475 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               475 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               67               472 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               67               472 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               66               473 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               66               473 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               421 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               421 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              159               380 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              159               380 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               22               517 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               22               517 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               530 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               530 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               117                422 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               117                422 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               109                430 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               109                430 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                516 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                516 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                520 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                520 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                71                468 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                71                468 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                54                485 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                54                485 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                509 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                509 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                37                502 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                37                502 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                528 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                528 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                512 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                512 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                529 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                529 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                527 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                527 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                509 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                509 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                72                467 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                72                467 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                45                494 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                45                494 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                485 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                485 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                482 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                482 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               112                427 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               112                427 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                407 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                407 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                500 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                500 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                508 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                508 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               475 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               475 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               475 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               475 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               25               514 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               25               514 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               525 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               525 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               528 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               528 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               522 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               522 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               488 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               488 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               508 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               508 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105               434 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105               434 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              105               434 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              105               434 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               55               484 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               55               484 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               74               465 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               74               465 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               521 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               521 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               514 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               514 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               44               495 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               44               495 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               42               497 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               42               497 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               80               459 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               80               459 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               514 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               514 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              103               436 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              103               436 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              122               417 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              122               417 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                43                496 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                43                496 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                40                499 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                40                499 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                75                464 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                75                464 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                467 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                467 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                43                496 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                43                496 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                503 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                503 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                93                446 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                93                446 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                61                478 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                61                478 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               109                430 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               109                430 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                97                442 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                97                442 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               138                401 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               138                401 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               130                409 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               130                409 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                446 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                446 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                487 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                487 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                65                474 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                65                474 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                480 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                480 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                483 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                483 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                520 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                520 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                530 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                530 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                485 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                485 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               109                430 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               109                430 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               85               454 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               85               454 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               71               468 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               71               468 
[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 539 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 539 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=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        2      2      0      0
  1P GAIN WILD-TYPE     12     15     12     10
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                15
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  1P GAIN MUTATED        1      2      1      0      0
  1P GAIN WILD-TYPE     13      7      6      7     16
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 7
  CLUS_3               1                 6
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       38      6      2      0      4
  1P GAIN WILD-TYPE    131    299     17      9     33
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              38               131
  CLUS_2               6               299
  CLUS_3               2                17
  CLUS_4               0                 9
  CLUS_5               4                33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       30      5     10
  1P GAIN WILD-TYPE    135     84    161
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              30               135
  CLUS_2               5                84
  CLUS_3              10               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P GAIN MUTATED        2      6      0      1      1      2
  1P GAIN WILD-TYPE     39     31     39     11     40     22
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                39
  CLUS_2               6                31
  CLUS_3               0                39
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        6      2      2      2
  1P GAIN WILD-TYPE     61     65     41     15
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               6                61
  CLUS_2               2                65
  CLUS_3               2                41
  CLUS_4               2                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       39      6      5
  1P GAIN WILD-TYPE    195    147    145
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              39               195
  CLUS_2               6               147
  CLUS_3               5               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 CLUS_6 CLUS_7
  1P GAIN MUTATED       26      2      7      2      7      4      2
  1P GAIN WILD-TYPE     97     51     40     63    101     62     73
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              26                97
  CLUS_2               2                51
  CLUS_3               7                40
  CLUS_4               2                63
  CLUS_5               7               101
  CLUS_6               4                62
  CLUS_7               2                73
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       35     12      2
  1P GAIN WILD-TYPE    188    138    155
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              35               188
  CLUS_2              12               138
  CLUS_3               2               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
  1P GAIN MUTATED       21      1      4     23
  1P GAIN WILD-TYPE    198     57    133     93
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              21               198
  CLUS_2               1                57
  CLUS_3               4               133
  CLUS_4              23                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
  1P GAIN MUTATED       30      6      8
  1P GAIN WILD-TYPE    142     90    122
D1V11, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              30               142
  CLUS_2               6                90
  CLUS_3               8               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       26      6     12
  1P GAIN WILD-TYPE    118    109    127
D1V12, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              26               118
  CLUS_2               6               109
  CLUS_3              12               127
[1] 3 2
[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 CLUS_4
  1Q GAIN MUTATED        9      6      5      2
  1Q GAIN WILD-TYPE      5     11      7      8
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                 5
  CLUS_2               6                11
  CLUS_3               5                 7
  CLUS_4               2                 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 CLUS_5
  1Q GAIN MUTATED        6      2      6      5      3
  1Q GAIN WILD-TYPE      8      7      1      2     13
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               2                 7
  CLUS_3               6                 1
  CLUS_4               5                 2
  CLUS_5               3                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       57     90     12      8     21
  1Q GAIN WILD-TYPE    112    215      7      1     16
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              57               112
  CLUS_2              90               215
  CLUS_3              12                 7
  CLUS_4               8                 1
  CLUS_5              21                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       58     22     59
  1Q GAIN WILD-TYPE    107     67    112
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              58               107
  CLUS_2              22                67
  CLUS_3              59               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       10     10     16      8     17      8
  1Q GAIN WILD-TYPE     31     27     23      4     24     16
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              10                31
  CLUS_2              10                27
  CLUS_3              16                23
  CLUS_4               8                 4
  CLUS_5              17                24
  CLUS_6               8                16
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED       16     25     23      5
  1Q GAIN WILD-TYPE     51     42     20     12
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              16                51
  CLUS_2              25                42
  CLUS_3              23                20
  CLUS_4               5                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
  1Q GAIN MUTATED       76     75     37
  1Q GAIN WILD-TYPE    158     78    113
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              76               158
  CLUS_2              75                78
  CLUS_3              37               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       47     29     11     33     33     17     18
  1Q GAIN WILD-TYPE     76     24     36     32     75     49     57
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              47                76
  CLUS_2              29                24
  CLUS_3              11                36
  CLUS_4              33                32
  CLUS_5              33                75
  CLUS_6              17                49
  CLUS_7              18                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
  1Q GAIN MUTATED       69     79     39
  1Q GAIN WILD-TYPE    154     71    118
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              69               154
  CLUS_2              79                71
  CLUS_3              39               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       77     30     38     42
  1Q GAIN WILD-TYPE    142     28     99     74
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              77               142
  CLUS_2              30                28
  CLUS_3              38                99
  CLUS_4              42                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       61     32     43
  1Q GAIN WILD-TYPE    111     64     87
D2V11, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              61               111
  CLUS_2              32                64
  CLUS_3              43                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       59     32     45
  1Q GAIN WILD-TYPE     85     83     94
D2V12, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              59                85
  CLUS_2              32                83
  CLUS_3              45                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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED        1      3      2      1
  2P GAIN WILD-TYPE     13     14     10      9
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 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 CLUS_5
  2P GAIN MUTATED        1      3      1      0      2
  2P GAIN WILD-TYPE     13      6      6      7     14
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                 6
  CLUS_3               1                 6
  CLUS_4               0                 7
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       62      9     10      3     11
  2P GAIN WILD-TYPE    107    296      9      6     26
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              62               107
  CLUS_2               9               296
  CLUS_3              10                 9
  CLUS_4               3                 6
  CLUS_5              11                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
  2P GAIN MUTATED       53      9     11
  2P GAIN WILD-TYPE    112     80    160
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              53               112
  CLUS_2               9                80
  CLUS_3              11               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 CLUS_6
  2P GAIN MUTATED        5      7      1      1      6      7
  2P GAIN WILD-TYPE     36     30     38     11     35     17
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5                36
  CLUS_2               7                30
  CLUS_3               1                38
  CLUS_4               1                11
  CLUS_5               6                35
  CLUS_6               7                17
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED       10      8      4      5
  2P GAIN WILD-TYPE     57     59     39     12
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10                57
  CLUS_2               8                59
  CLUS_3               4                39
  CLUS_4               5                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
  2P GAIN MUTATED       70     15     10
  2P GAIN WILD-TYPE    164    138    140
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              70               164
  CLUS_2              15               138
  CLUS_3              10               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       49      7     11      4     14      6      4
  2P GAIN WILD-TYPE     74     46     36     61     94     60     71
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              49                74
  CLUS_2               7                46
  CLUS_3              11                36
  CLUS_4               4                61
  CLUS_5              14                94
  CLUS_6               6                60
  CLUS_7               4                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
  2P GAIN MUTATED       66     17     11
  2P GAIN WILD-TYPE    157    133    146
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              66               157
  CLUS_2              17               133
  CLUS_3              11               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       34      7     10     43
  2P GAIN WILD-TYPE    185     51    127     73
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              34               185
  CLUS_2               7                51
  CLUS_3              10               127
  CLUS_4              43                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       42     20      8
  2P GAIN WILD-TYPE    130     76    122
D3V11, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              42               130
  CLUS_2              20                76
  CLUS_3               8               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       35      7     28
  2P GAIN WILD-TYPE    109    108    111
D3V12, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              35               109
  CLUS_2               7               108
  CLUS_3              28               111
[1] 3 2
[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 CLUS_4
  2Q GAIN MUTATED        0      1      2      0
  2Q GAIN WILD-TYPE     14     16     10     10
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                16
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  2Q GAIN MUTATED        0      1      1      0      1
  2Q GAIN WILD-TYPE     14      8      6      7     15
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                 8
  CLUS_3               1                 6
  CLUS_4               0                 7
  CLUS_5               1                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       52      7      8      3      9
  2Q GAIN WILD-TYPE    117    298     11      6     28
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              52               117
  CLUS_2               7               298
  CLUS_3               8                11
  CLUS_4               3                 6
  CLUS_5               9                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
  2Q GAIN MUTATED       47      7     10
  2Q GAIN WILD-TYPE    118     82    161
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              47               118
  CLUS_2               7                82
  CLUS_3              10               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q GAIN MUTATED        4      5      1      1      4      7
  2Q GAIN WILD-TYPE     37     32     38     11     37     17
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                37
  CLUS_2               5                32
  CLUS_3               1                38
  CLUS_4               1                11
  CLUS_5               4                37
  CLUS_6               7                17
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED        7      7      3      5
  2Q GAIN WILD-TYPE     60     60     40     12
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               7                60
  CLUS_2               7                60
  CLUS_3               3                40
  CLUS_4               5                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
  2Q GAIN MUTATED       59     12      8
  2Q GAIN WILD-TYPE    175    141    142
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              59               175
  CLUS_2              12               141
  CLUS_3               8               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 CLUS_6 CLUS_7
  2Q GAIN MUTATED       41      5      9      3     12      5      4
  2Q GAIN WILD-TYPE     82     48     38     62     96     61     71
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              41                82
  CLUS_2               5                48
  CLUS_3               9                38
  CLUS_4               3                62
  CLUS_5              12                96
  CLUS_6               5                61
  CLUS_7               4                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
  2Q GAIN MUTATED       55     16      8
  2Q GAIN WILD-TYPE    168    134    149
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              55               168
  CLUS_2              16               134
  CLUS_3               8               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
  2Q GAIN MUTATED       30      5      8     36
  2Q GAIN WILD-TYPE    189     53    129     80
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              30               189
  CLUS_2               5                53
  CLUS_3               8               129
  CLUS_4              36                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       39     16      7
  2Q GAIN WILD-TYPE    133     80    123
D4V11, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              39               133
  CLUS_2              16                80
  CLUS_3               7               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       31      6     25
  2Q GAIN WILD-TYPE    113    109    114
D4V12, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              31               113
  CLUS_2               6               109
  CLUS_3              25               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"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        0      1      1      0
  3P GAIN WILD-TYPE     14     16     11     10
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-BG-A0LW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED        1      0      1      0      0
  3P GAIN WILD-TYPE     13      9      6      7     16
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-BG-A0LW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED       31      2      1      3     12
  3P GAIN WILD-TYPE    138    303     18      6     25
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              31               138
  CLUS_2               2               303
  CLUS_3               1                18
  CLUS_4               3                 6
  CLUS_5              12                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
  3P GAIN MUTATED       26      7     10
  3P GAIN WILD-TYPE    139     82    161
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              26               139
  CLUS_2               7                82
  CLUS_3              10               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P GAIN MUTATED        3      1      2      1      0      0
  3P GAIN WILD-TYPE     38     36     37     11     41     24
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               1                36
  CLUS_3               2                37
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        2      3      2      0
  3P GAIN WILD-TYPE     65     64     41     17
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               3                64
  CLUS_3               2                41
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       35      4     10
  3P GAIN WILD-TYPE    199    149    140
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              35               199
  CLUS_2               4               149
  CLUS_3              10               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       16      0      8      4     14      3      4
  3P GAIN WILD-TYPE    107     53     39     61     94     63     71
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              16               107
  CLUS_2               0                53
  CLUS_3               8                39
  CLUS_4               4                61
  CLUS_5              14                94
  CLUS_6               3                63
  CLUS_7               4                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
  3P GAIN MUTATED       33      8      8
  3P GAIN WILD-TYPE    190    142    149
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              33               190
  CLUS_2               8               142
  CLUS_3               8               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
  3P GAIN MUTATED       18      0     11     20
  3P GAIN WILD-TYPE    201     58    126     96
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              18               201
  CLUS_2               0                58
  CLUS_3              11               126
  CLUS_4              20                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
  3P GAIN MUTATED       25      9      6
  3P GAIN WILD-TYPE    147     87    124
D5V11, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              25               147
  CLUS_2               9                87
  CLUS_3               6               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
  3P GAIN MUTATED       22      7     11
  3P GAIN WILD-TYPE    122    108    128
D5V12, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              22               122
  CLUS_2               7               108
  CLUS_3              11               128
[1] 3 2
[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 CLUS_4
  3Q GAIN MUTATED        1      3      1      0
  3Q GAIN WILD-TYPE     13     14     11     10
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               1                11
  CLUS_4               0                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 CLUS_5
  3Q GAIN MUTATED        3      1      1      0      0
  3Q GAIN WILD-TYPE     11      8      6      7     16
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               1                 6
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       62      4      2      3     13
  3Q GAIN WILD-TYPE    107    301     17      6     24
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              62               107
  CLUS_2               4               301
  CLUS_3               2                17
  CLUS_4               3                 6
  CLUS_5              13                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
  3Q GAIN MUTATED       54      9     11
  3Q GAIN WILD-TYPE    111     80    160
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              54               111
  CLUS_2               9                80
  CLUS_3              11               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 CLUS_6
  3Q GAIN MUTATED        6      4      2      1      0      1
  3Q GAIN WILD-TYPE     35     33     37     11     41     23
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                35
  CLUS_2               4                33
  CLUS_3               2                37
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        9      3      2      0
  3Q GAIN WILD-TYPE     58     64     41     17
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9                58
  CLUS_2               3                64
  CLUS_3               2                41
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       68      5     11
  3Q GAIN WILD-TYPE    166    148    139
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              68               166
  CLUS_2               5               148
  CLUS_3              11               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       37      0     18      4     17      3      5
  3Q GAIN WILD-TYPE     86     53     29     61     91     63     70
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              37                86
  CLUS_2               0                53
  CLUS_3              18                29
  CLUS_4               4                61
  CLUS_5              17                91
  CLUS_6               3                63
  CLUS_7               5                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
  3Q GAIN MUTATED       63     12      9
  3Q GAIN WILD-TYPE    160    138    148
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              63               160
  CLUS_2              12               138
  CLUS_3               9               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
  3Q GAIN MUTATED       30      0     12     42
  3Q GAIN WILD-TYPE    189     58    125     74
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              30               189
  CLUS_2               0                58
  CLUS_3              12               125
  CLUS_4              42                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       43     17     10
  3Q GAIN WILD-TYPE    129     79    120
D6V11, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              43               129
  CLUS_2              17                79
  CLUS_3              10               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
  3Q GAIN MUTATED       41      8     21
  3Q GAIN WILD-TYPE    103    107    118
D6V12, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              41               103
  CLUS_2               8               107
  CLUS_3              21               118
[1] 3 2
[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 CLUS_4
  4P GAIN MUTATED        1      0      0      0
  4P GAIN WILD-TYPE     13     17     12     10
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED        1      0      0      0      0
  4P GAIN WILD-TYPE     13      9      7      7     16
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED       13      0      0      0      1
  4P GAIN WILD-TYPE    156    305     19      9     36
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              13               156
  CLUS_2               0               305
  CLUS_3               0                19
  CLUS_4               0                 9
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      3
  4P GAIN WILD-TYPE    160     87    168
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               160
  CLUS_2               2                87
  CLUS_3               3               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 CLUS_6
  4P GAIN MUTATED        2      2      0      0      0      1
  4P GAIN WILD-TYPE     39     35     39     12     41     23
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                39
  CLUS_2               2                35
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        5      0      0      0
  4P GAIN WILD-TYPE     62     67     43     17
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5                62
  CLUS_2               0                67
  CLUS_3               0                43
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       13      0      1
  4P GAIN WILD-TYPE    221    153    149
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              13               221
  CLUS_2               0               153
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  4P GAIN MUTATED        8      0      2      0      3      1      0
  4P GAIN WILD-TYPE    115     53     45     65    105     65     75
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8               115
  CLUS_2               0                53
  CLUS_3               2                45
  CLUS_4               0                65
  CLUS_5               3               105
  CLUS_6               1                65
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       12      1      1
  4P GAIN WILD-TYPE    211    149    156
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              12               211
  CLUS_2               1               149
  CLUS_3               1               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
  4P GAIN MUTATED        3      0      1     10
  4P GAIN WILD-TYPE    216     58    136    106
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               216
  CLUS_2               0                58
  CLUS_3               1               136
  CLUS_4              10               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
  4P GAIN MUTATED        7      1      2
  4P GAIN WILD-TYPE    165     95    128
D7V11, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7               165
  CLUS_2               1                95
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        5      1      4
  4P GAIN WILD-TYPE    139    114    135
D7V12, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               139
  CLUS_2               1               114
  CLUS_3               4               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"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        1      0      0      0
  4Q GAIN WILD-TYPE     13     17     12     10
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        1      0      0      0      0
  4Q GAIN WILD-TYPE     13      9      7      7     16
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        7      0      0      0      1
  4Q GAIN WILD-TYPE    162    305     19      9     36
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7               162
  CLUS_2               0               305
  CLUS_3               0                19
  CLUS_4               0                 9
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      1      2
  4Q GAIN WILD-TYPE    161     88    169
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               161
  CLUS_2               1                88
  CLUS_3               2               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 CLUS_6
  4Q GAIN MUTATED        1      1      0      0      0      0
  4Q GAIN WILD-TYPE     40     36     39     12     41     24
D8V5, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G9        TCGA-A5-A0GA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A13C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        2      0      0      0
  4Q GAIN WILD-TYPE     65     67     43     17
D8V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G9        TCGA-A5-A0GA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A13C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        7      0      1
  4Q GAIN WILD-TYPE    227    153    149
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7               227
  CLUS_2               0               153
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  4Q GAIN MUTATED        4      0      1      0      2      1      0
  4Q GAIN WILD-TYPE    119     53     46     65    106     65     75
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0                53
  CLUS_3               1                46
  CLUS_4               0                65
  CLUS_5               2               106
  CLUS_6               1                65
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        6      1      1
  4Q GAIN WILD-TYPE    217    149    156
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               6               217
  CLUS_2               1               149
  CLUS_3               1               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
  4Q GAIN MUTATED        2      0      1      5
  4Q GAIN WILD-TYPE    217     58    136    111
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               217
  CLUS_2               0                58
  CLUS_3               1               136
  CLUS_4               5               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
  4Q GAIN MUTATED        4      1      2
  4Q GAIN WILD-TYPE    168     95    128
D8V11, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               168
  CLUS_2               1                95
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      1      2
  4Q GAIN WILD-TYPE    140    114    137
D8V12, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               140
  CLUS_2               1               114
  CLUS_3               2               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"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        1      1      1      0
  5P GAIN WILD-TYPE     13     16     11     10
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                16
  CLUS_3               1                11
  CLUS_4               0                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 CLUS_5
  5P GAIN MUTATED        1      1      1      0      0
  5P GAIN WILD-TYPE     13      8      6      7     16
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 8
  CLUS_3               1                 6
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       43      3      4      1      0
  5P GAIN WILD-TYPE    126    302     15      8     37
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              43               126
  CLUS_2               3               302
  CLUS_3               4                15
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       34      5      5
  5P GAIN WILD-TYPE    131     84    166
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              34               131
  CLUS_2               5                84
  CLUS_3               5               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 CLUS_6
  5P GAIN MUTATED        1      3      0      0      4      3
  5P GAIN WILD-TYPE     40     34     39     12     37     21
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                40
  CLUS_2               3                34
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               4                37
  CLUS_6               3                21
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        3      3      4      1
  5P GAIN WILD-TYPE     64     64     39     16
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                64
  CLUS_2               3                64
  CLUS_3               4                39
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       45      5      1
  5P GAIN WILD-TYPE    189    148    149
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              45               189
  CLUS_2               5               148
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  5P GAIN MUTATED       28      3     12      1      5      2      0
  5P GAIN WILD-TYPE     95     50     35     64    103     64     75
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              28                95
  CLUS_2               3                50
  CLUS_3              12                35
  CLUS_4               1                64
  CLUS_5               5               103
  CLUS_6               2                64
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       40     10      1
  5P GAIN WILD-TYPE    183    140    156
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              40               183
  CLUS_2              10               140
  CLUS_3               1               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
  5P GAIN MUTATED       13      4      1     33
  5P GAIN WILD-TYPE    206     54    136     83
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               206
  CLUS_2               4                54
  CLUS_3               1               136
  CLUS_4              33                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       30      8      4
  5P GAIN WILD-TYPE    142     88    126
D9V11, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              30               142
  CLUS_2               8                88
  CLUS_3               4               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
  5P GAIN MUTATED       32      1      9
  5P GAIN WILD-TYPE    112    114    130
D9V12, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              32               112
  CLUS_2               1               114
  CLUS_3               9               130
[1] 3 2
[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 CLUS_4
  5Q GAIN MUTATED        0      0      0      0
  5Q GAIN WILD-TYPE     14     17     12     10
D10V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED        0      0      0      0      0
  5Q GAIN WILD-TYPE     14      9      7      7     16
D10V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED       15      1      3      1      0
  5Q GAIN WILD-TYPE    154    304     16      8     37
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              15               154
  CLUS_2               1               304
  CLUS_3               3                16
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       13      2      4
  5Q GAIN WILD-TYPE    152     87    167
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               152
  CLUS_2               2                87
  CLUS_3               4               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 CLUS_5 CLUS_6
  5Q GAIN MUTATED        0      2      0      0      2      0
  5Q GAIN WILD-TYPE     41     35     39     12     39     24
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                41
  CLUS_2               2                35
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               2                39
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED        0      2      2      0
  5Q GAIN WILD-TYPE     67     65     41     17
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2                65
  CLUS_3               2                41
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       17      3      0
  5Q GAIN WILD-TYPE    217    150    150
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              17               217
  CLUS_2               3               150
  CLUS_3               0               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 CLUS_6 CLUS_7
  5Q GAIN MUTATED        7      2      6      1      4      0      0
  5Q GAIN WILD-TYPE    116     51     41     64    104     66     75
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               7               116
  CLUS_2               2                51
  CLUS_3               6                41
  CLUS_4               1                64
  CLUS_5               4               104
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       13      7      0
  5Q GAIN WILD-TYPE    210    143    157
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               210
  CLUS_2               7               143
  CLUS_3               0               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
  5Q GAIN MUTATED        6      2      0     12
  5Q GAIN WILD-TYPE    213     56    137    104
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               6               213
  CLUS_2               2                56
  CLUS_3               0               137
  CLUS_4              12               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       11      3      3
  5Q GAIN WILD-TYPE    161     93    127
D10V11, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11               161
  CLUS_2               3                93
  CLUS_3               3               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       14      0      3
  5Q GAIN WILD-TYPE    130    115    136
D10V12, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              14               130
  CLUS_2               0               115
  CLUS_3               3               136
[1] 3 2
[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 CLUS_4
  6P GAIN MUTATED        0      3      2      0
  6P GAIN WILD-TYPE     14     14     10     10
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  6P GAIN MUTATED        1      2      0      0      2
  6P GAIN WILD-TYPE     13      7      7      7     14
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 7
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       61      5      1      1     12
  6P GAIN WILD-TYPE    108    300     18      8     25
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              61               108
  CLUS_2               5               300
  CLUS_3               1                18
  CLUS_4               1                 8
  CLUS_5              12                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
  6P GAIN MUTATED       49     12     11
  6P GAIN WILD-TYPE    116     77    160
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              49               116
  CLUS_2              12                77
  CLUS_3              11               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 CLUS_6
  6P GAIN MUTATED        4      6      2      1      0      2
  6P GAIN WILD-TYPE     37     31     37     11     41     22
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                37
  CLUS_2               6                31
  CLUS_3               2                37
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        7      5      2      1
  6P GAIN WILD-TYPE     60     62     41     16
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               7                60
  CLUS_2               5                62
  CLUS_3               2                41
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       61      5     14
  6P GAIN WILD-TYPE    173    148    136
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              61               173
  CLUS_2               5               148
  CLUS_3              14               136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       43      0      5      5     14      8      5
  6P GAIN WILD-TYPE     80     53     42     60     94     58     70
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              43                80
  CLUS_2               0                53
  CLUS_3               5                42
  CLUS_4               5                60
  CLUS_5              14                94
  CLUS_6               8                58
  CLUS_7               5                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
  6P GAIN MUTATED       55     14     11
  6P GAIN WILD-TYPE    168    136    146
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              55               168
  CLUS_2              14               136
  CLUS_3              11               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       34      0     11     35
  6P GAIN WILD-TYPE    185     58    126     81
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              34               185
  CLUS_2               0                58
  CLUS_3              11               126
  CLUS_4              35                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
  6P GAIN MUTATED       42     15     12
  6P GAIN WILD-TYPE    130     81    118
D11V11, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              42               130
  CLUS_2              15                81
  CLUS_3              12               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       34     12     23
  6P GAIN WILD-TYPE    110    103    116
D11V12, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              34               110
  CLUS_2              12               103
  CLUS_3              23               116
[1] 3 2
[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 = 6Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED        0      3      2      0
  6Q GAIN WILD-TYPE     14     14     10     10
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  6Q GAIN MUTATED        1      2      0      0      2
  6Q GAIN WILD-TYPE     13      7      7      7     14
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 7
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 GAIN MUTATED       46      5      1      1     11
  6Q GAIN WILD-TYPE    123    300     18      8     26
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              46               123
  CLUS_2               5               300
  CLUS_3               1                18
  CLUS_4               1                 8
  CLUS_5              11                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
  6Q GAIN MUTATED       35      9     12
  6Q GAIN WILD-TYPE    130     80    159
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              35               130
  CLUS_2               9                80
  CLUS_3              12               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 CLUS_6
  6Q GAIN MUTATED        4      6      1      1      0      2
  6Q GAIN WILD-TYPE     37     31     38     11     41     22
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               4                37
  CLUS_2               6                31
  CLUS_3               1                38
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED        7      4      2      1
  6Q GAIN WILD-TYPE     60     63     41     16
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               7                60
  CLUS_2               4                63
  CLUS_3               2                41
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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 GAIN MUTATED       45      5     14
  6Q GAIN WILD-TYPE    189    148    136
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              45               189
  CLUS_2               5               148
  CLUS_3              14               136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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 GAIN MUTATED       28      0      6      5     12      7      6
  6Q GAIN WILD-TYPE     95     53     41     60     96     59     69
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              28                95
  CLUS_2               0                53
  CLUS_3               6                41
  CLUS_4               5                60
  CLUS_5              12                96
  CLUS_6               7                59
  CLUS_7               6                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
  6Q GAIN MUTATED       41     12     11
  6Q GAIN WILD-TYPE    182    138    146
D12V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              41               182
  CLUS_2              12               138
  CLUS_3              11               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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 GAIN MUTATED       29      0     11     24
  6Q GAIN WILD-TYPE    190     58    126     92
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              29               190
  CLUS_2               0                58
  CLUS_3              11               126
  CLUS_4              24                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       31     13      9
  6Q GAIN WILD-TYPE    141     83    121
D12V11, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              31               141
  CLUS_2              13                83
  CLUS_3               9               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
  6Q GAIN MUTATED       23     11     19
  6Q GAIN WILD-TYPE    121    104    120
D12V12, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              23               121
  CLUS_2              11               104
  CLUS_3              19               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"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        1      3      2      1
  7P GAIN WILD-TYPE     13     14     10      9
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 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 CLUS_5
  7P GAIN MUTATED        1      2      1      1      2
  7P GAIN WILD-TYPE     13      7      6      6     14
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 7
  CLUS_3               1                 6
  CLUS_4               1                 6
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       33      9     12      2     11
  7P GAIN WILD-TYPE    136    296      7      7     26
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              33               136
  CLUS_2               9               296
  CLUS_3              12                 7
  CLUS_4               2                 7
  CLUS_5              11                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
  7P GAIN MUTATED       30      3     18
  7P GAIN WILD-TYPE    135     86    153
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              30               135
  CLUS_2               3                86
  CLUS_3              18               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 CLUS_5 CLUS_6
  7P GAIN MUTATED        3      5      3      1      5      1
  7P GAIN WILD-TYPE     38     32     36     11     36     23
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               5                32
  CLUS_3               3                36
  CLUS_4               1                11
  CLUS_5               5                36
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        5      7      5      1
  7P GAIN WILD-TYPE     62     60     38     16
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                62
  CLUS_2               7                60
  CLUS_3               5                38
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       39     15     13
  7P GAIN WILD-TYPE    195    138    137
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              39               195
  CLUS_2              15               138
  CLUS_3              13               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 CLUS_6 CLUS_7
  7P GAIN MUTATED       22      7      7      2     16      7      6
  7P GAIN WILD-TYPE    101     46     40     63     92     59     69
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22               101
  CLUS_2               7                46
  CLUS_3               7                40
  CLUS_4               2                63
  CLUS_5              16                92
  CLUS_6               7                59
  CLUS_7               6                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
  7P GAIN MUTATED       36     20     10
  7P GAIN WILD-TYPE    187    130    147
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              36               187
  CLUS_2              20               130
  CLUS_3              10               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       29      9     12     16
  7P GAIN WILD-TYPE    190     49    125    100
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              29               190
  CLUS_2               9                49
  CLUS_3              12               125
  CLUS_4              16               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
  7P GAIN MUTATED       26     14      8
  7P GAIN WILD-TYPE    146     82    122
D13V11, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              26               146
  CLUS_2              14                82
  CLUS_3               8               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       20      7     21
  7P GAIN WILD-TYPE    124    108    118
D13V12, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              20               124
  CLUS_2               7               108
  CLUS_3              21               118
[1] 3 2
[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 = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        1      3      2      1
  7Q GAIN WILD-TYPE     13     14     10      9
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 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 CLUS_5
  7Q GAIN MUTATED        1      2      1      1      2
  7Q GAIN WILD-TYPE     13      7      6      6     14
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                 7
  CLUS_3               1                 6
  CLUS_4               1                 6
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       30     12     12      2     10
  7Q GAIN WILD-TYPE    139    293      7      7     27
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              30               139
  CLUS_2              12               293
  CLUS_3              12                 7
  CLUS_4               2                 7
  CLUS_5              10                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
  7Q GAIN MUTATED       27      2     21
  7Q GAIN WILD-TYPE    138     87    150
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              27               138
  CLUS_2               2                87
  CLUS_3              21               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 CLUS_6
  7Q GAIN MUTATED        2      3      3      1      5      1
  7Q GAIN WILD-TYPE     39     34     36     11     36     23
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                39
  CLUS_2               3                34
  CLUS_3               3                36
  CLUS_4               1                11
  CLUS_5               5                36
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        3      6      5      1
  7Q GAIN WILD-TYPE     64     61     38     16
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                64
  CLUS_2               6                61
  CLUS_3               5                38
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       36     15     15
  7Q GAIN WILD-TYPE    198    138    135
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              36               198
  CLUS_2              15               138
  CLUS_3              15               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 CLUS_6 CLUS_7
  7Q GAIN MUTATED       20      8      8      1     15      8      6
  7Q GAIN WILD-TYPE    103     45     39     64     93     58     69
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              20               103
  CLUS_2               8                45
  CLUS_3               8                39
  CLUS_4               1                64
  CLUS_5              15                93
  CLUS_6               8                58
  CLUS_7               6                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
  7Q GAIN MUTATED       32     22     12
  7Q GAIN WILD-TYPE    191    128    145
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32               191
  CLUS_2              22               128
  CLUS_3              12               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
  7Q GAIN MUTATED       28     10     13     15
  7Q GAIN WILD-TYPE    191     48    124    101
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28               191
  CLUS_2              10                48
  CLUS_3              13               124
  CLUS_4              15               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       24     14      9
  7Q GAIN WILD-TYPE    148     82    121
D14V11, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              24               148
  CLUS_2              14                82
  CLUS_3               9               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
  7Q GAIN MUTATED       17      9     21
  7Q GAIN WILD-TYPE    127    106    118
D14V12, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              17               127
  CLUS_2               9               106
  CLUS_3              21               118
[1] 3 2
[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 = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        1      4      2      0
  8P GAIN WILD-TYPE     13     13     10     10
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                13
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  8P GAIN MUTATED        4      1      0      0      2
  8P GAIN WILD-TYPE     10      8      7      7     14
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                 8
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       43     29      8      2     36
  8P GAIN WILD-TYPE    126    276     11      7      1
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              43               126
  CLUS_2              29               276
  CLUS_3               8                11
  CLUS_4               2                 7
  CLUS_5              36                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       40     19     41
  8P GAIN WILD-TYPE    125     70    130
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              40               125
  CLUS_2              19                70
  CLUS_3              41               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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        7     10      4      2      2      8
  8P GAIN WILD-TYPE     34     27     35     10     39     16
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7                34
  CLUS_2              10                27
  CLUS_3               4                35
  CLUS_4               2                10
  CLUS_5               2                39
  CLUS_6               8                16
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        9     12      6      6
  8P GAIN WILD-TYPE     58     55     37     11
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               9                58
  CLUS_2              12                55
  CLUS_3               6                37
  CLUS_4               6                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
  8P GAIN MUTATED       61     28     29
  8P GAIN WILD-TYPE    173    125    121
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              61               173
  CLUS_2              28               125
  CLUS_3              29               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 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED       28     10     11      8     34     17     10
  8P GAIN WILD-TYPE     95     43     36     57     74     49     65
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              28                95
  CLUS_2              10                43
  CLUS_3              11                36
  CLUS_4               8                57
  CLUS_5              34                74
  CLUS_6              17                49
  CLUS_7              10                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
  8P GAIN MUTATED       54     35     28
  8P GAIN WILD-TYPE    169    115    129
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              54               169
  CLUS_2              35               115
  CLUS_3              28               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       60      6     27     24
  8P GAIN WILD-TYPE    159     52    110     92
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              60               159
  CLUS_2               6                52
  CLUS_3              27               110
  CLUS_4              24                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       48     23     23
  8P GAIN WILD-TYPE    124     73    107
D15V11, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              48               124
  CLUS_2              23                73
  CLUS_3              23               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       38     23     33
  8P GAIN WILD-TYPE    106     92    106
D15V12, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              38               106
  CLUS_2              23                92
  CLUS_3              33               106
[1] 3 2
[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 = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        1      8      2      0
  8Q GAIN WILD-TYPE     13      9     10     10
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               8                 9
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  8Q GAIN MUTATED        4      5      0      0      2
  8Q GAIN WILD-TYPE     10      4      7      7     14
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               5                 4
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               2                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       80     31      8      3     37
  8Q GAIN WILD-TYPE     89    274     11      6      0
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              80                89
  CLUS_2              31               274
  CLUS_3               8                11
  CLUS_4               3                 6
  CLUS_5              37                 0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       64     24     46
  8Q GAIN WILD-TYPE    101     65    125
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              64               101
  CLUS_2              24                65
  CLUS_3              46               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 CLUS_6
  8Q GAIN MUTATED        9     12      7      2      2     13
  8Q GAIN WILD-TYPE     32     25     32     10     39     11
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               9                32
  CLUS_2              12                25
  CLUS_3               7                32
  CLUS_4               2                10
  CLUS_5               2                39
  CLUS_6              13                11
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED       15     15      6      9
  8Q GAIN WILD-TYPE     52     52     37      8
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              15                52
  CLUS_2              15                52
  CLUS_3               6                37
  CLUS_4               9                 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
  8Q GAIN MUTATED       97     28     34
  8Q GAIN WILD-TYPE    137    125    116
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              97               137
  CLUS_2              28               125
  CLUS_3              34               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       53     10     18      8     37     23     10
  8Q GAIN WILD-TYPE     70     43     29     57     71     43     65
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              53                70
  CLUS_2              10                43
  CLUS_3              18                29
  CLUS_4               8                57
  CLUS_5              37                71
  CLUS_6              23                43
  CLUS_7              10                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
  8Q GAIN MUTATED       87     36     33
  8Q GAIN WILD-TYPE    136    114    124
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              87               136
  CLUS_2              36               114
  CLUS_3              33               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
  8Q GAIN MUTATED       68      6     31     51
  8Q GAIN WILD-TYPE    151     52    106     65
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              68               151
  CLUS_2               6                52
  CLUS_3              31               106
  CLUS_4              51                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       71     28     27
  8Q GAIN WILD-TYPE    101     68    103
D16V11, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              71               101
  CLUS_2              28                68
  CLUS_3              27               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
  8Q GAIN MUTATED       59     27     40
  8Q GAIN WILD-TYPE     85     88     99
D16V12, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              59                85
  CLUS_2              27                88
  CLUS_3              40                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"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        1      1      0      0
  9P GAIN WILD-TYPE     13     16     12     10
D17V1, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06F        TCGA-AX-A06J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED        1      0      1      0      0
  9P GAIN WILD-TYPE     13      9      6      7     16
D17V2, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06F        TCGA-AX-A06J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED       18      3      0      0      1
  9P GAIN WILD-TYPE    151    302     19      9     36
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              18               151
  CLUS_2               3               302
  CLUS_3               0                19
  CLUS_4               0                 9
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       15      2      3
  9P GAIN WILD-TYPE    150     87    168
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              15               150
  CLUS_2               2                87
  CLUS_3               3               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 CLUS_6
  9P GAIN MUTATED        3      3      0      0      0      0
  9P GAIN WILD-TYPE     38     34     39     12     41     24
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               3                34
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        4      2      0      0
  9P GAIN WILD-TYPE     63     65     43     17
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                63
  CLUS_2               2                65
  CLUS_3               0                43
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       17      2      3
  9P GAIN WILD-TYPE    217    151    147
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              17               217
  CLUS_2               2               151
  CLUS_3               3               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       11      0      1      1      7      2      0
  9P GAIN WILD-TYPE    112     53     46     64    101     64     75
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              11               112
  CLUS_2               0                53
  CLUS_3               1                46
  CLUS_4               1                64
  CLUS_5               7               101
  CLUS_6               2                64
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       16      4      2
  9P GAIN WILD-TYPE    207    146    155
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              16               207
  CLUS_2               4               146
  CLUS_3               2               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
  9P GAIN MUTATED       11      1      2      8
  9P GAIN WILD-TYPE    208     57    135    108
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              11               208
  CLUS_2               1                57
  CLUS_3               2               135
  CLUS_4               8               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
  9P GAIN MUTATED       10      6      2
  9P GAIN WILD-TYPE    162     90    128
D17V11, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              10               162
  CLUS_2               6                90
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        9      3      6
  9P GAIN WILD-TYPE    135    112    133
D17V12, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               9               135
  CLUS_2               3               112
  CLUS_3               6               133
[1] 3 2
[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 = 9Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        0      0      0      0
  9Q GAIN WILD-TYPE     14     17     12     10
D18V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        0      0      0      0      0
  9Q GAIN WILD-TYPE     14      9      7      7     16
D18V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        7      1      0      0      1
  9Q GAIN WILD-TYPE    162    304     19      9     36
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               162
  CLUS_2               1               304
  CLUS_3               0                19
  CLUS_4               0                 9
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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      0      3
  9Q GAIN WILD-TYPE    159     89    168
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6               159
  CLUS_2               0                89
  CLUS_3               3               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 CLUS_6
  9Q GAIN MUTATED        1      1      0      0      0      0
  9Q GAIN WILD-TYPE     40     36     39     12     41     24
D18V5, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        2      0      0      0
  9Q GAIN WILD-TYPE     65     67     43     17
D18V6, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        6      1      2
  9Q GAIN WILD-TYPE    228    152    148
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6               228
  CLUS_2               1               152
  CLUS_3               2               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 CLUS_5 CLUS_6 CLUS_7
  9Q GAIN MUTATED        4      0      0      0      4      1      0
  9Q GAIN WILD-TYPE    119     53     47     65    104     65     75
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               119
  CLUS_2               0                53
  CLUS_3               0                47
  CLUS_4               0                65
  CLUS_5               4               104
  CLUS_6               1                65
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        7      1      1
  9Q GAIN WILD-TYPE    216    149    156
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               216
  CLUS_2               1               149
  CLUS_3               1               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
  9Q GAIN MUTATED        5      0      1      3
  9Q GAIN WILD-TYPE    214     58    136    113
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               214
  CLUS_2               0                58
  CLUS_3               1               136
  CLUS_4               3               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        5      1      2
  9Q GAIN WILD-TYPE    167     95    128
D18V11, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               167
  CLUS_2               1                95
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      1
  9Q GAIN WILD-TYPE    139    113    138
D18V12, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               139
  CLUS_2               2               113
  CLUS_3               1               138
[1] 3 2
[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 = 10P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED        2      2      8      2
  10P GAIN WILD-TYPE     12     15      4      8
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 15
  CLUS_3                8                  4
  CLUS_4                2                  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 CLUS_5
  10P GAIN MUTATED        3      1      2      0      8
  10P GAIN WILD-TYPE     11      8      5      7      8
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                2                  5
  CLUS_4                0                  7
  CLUS_5                8                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       41     46      7      4     19
  10P GAIN WILD-TYPE    128    259     12      5     18
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               41                128
  CLUS_2               46                259
  CLUS_3                7                 12
  CLUS_4                4                  5
  CLUS_5               19                 18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       33     18     38
  10P GAIN WILD-TYPE    132     71    133
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               33                132
  CLUS_2               18                 71
  CLUS_3               38                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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        7      5      8      3     13      9
  10P GAIN WILD-TYPE     34     32     31      9     28     15
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                7                 34
  CLUS_2                5                 32
  CLUS_3                8                 31
  CLUS_4                3                  9
  CLUS_5               13                 28
  CLUS_6                9                 15
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       14     17      9      5
  10P GAIN WILD-TYPE     53     50     34     12
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               14                 53
  CLUS_2               17                 50
  CLUS_3                9                 34
  CLUS_4                5                 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
  10P GAIN MUTATED       51     25     40
  10P GAIN WILD-TYPE    183    128    110
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               51                183
  CLUS_2               25                128
  CLUS_3               40                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       30     14      7      8     21     20     16
  10P GAIN WILD-TYPE     93     39     40     57     87     46     59
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               30                 93
  CLUS_2               14                 39
  CLUS_3                7                 40
  CLUS_4                8                 57
  CLUS_5               21                 87
  CLUS_6               20                 46
  CLUS_7               16                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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     30     39
  10P GAIN WILD-TYPE    175    120    118
D19V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               48                175
  CLUS_2               30                120
  CLUS_3               39                118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       35     17     39     26
  10P GAIN WILD-TYPE    184     41     98     90
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               35                184
  CLUS_2               17                 41
  CLUS_3               39                 98
  CLUS_4               26                 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
  10P GAIN MUTATED       31     20     30
  10P GAIN WILD-TYPE    141     76    100
D19V11, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               31                141
  CLUS_2               20                 76
  CLUS_3               30                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
  10P GAIN MUTATED       24     33     24
  10P GAIN WILD-TYPE    120     82    115
D19V12, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               24                120
  CLUS_2               33                 82
  CLUS_3               24                115
[1] 3 2
[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 = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        1      3      8      2
  10Q GAIN WILD-TYPE     13     14      4      8
D20V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                 14
  CLUS_3                8                  4
  CLUS_4                2                  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 CLUS_5
  10Q GAIN MUTATED        3      1      2      0      8
  10Q GAIN WILD-TYPE     11      8      5      7      8
D20V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                2                  5
  CLUS_4                0                  7
  CLUS_5                8                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       36     45      8      4     16
  10Q GAIN WILD-TYPE    133    260     11      5     21
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               36                133
  CLUS_2               45                260
  CLUS_3                8                 11
  CLUS_4                4                  5
  CLUS_5               16                 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
  10Q GAIN MUTATED       29     17     36
  10Q GAIN WILD-TYPE    136     72    135
D20V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               29                136
  CLUS_2               17                 72
  CLUS_3               36                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 CLUS_6
  10Q GAIN MUTATED        7      4      8      2     14      8
  10Q GAIN WILD-TYPE     34     33     31     10     27     16
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                7                 34
  CLUS_2                4                 33
  CLUS_3                8                 31
  CLUS_4                2                 10
  CLUS_5               14                 27
  CLUS_6                8                 16
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED       13     17      8      5
  10Q GAIN WILD-TYPE     54     50     35     12
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               13                 54
  CLUS_2               17                 50
  CLUS_3                8                 35
  CLUS_4                5                 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
  10Q GAIN MUTATED       45     25     38
  10Q GAIN WILD-TYPE    189    128    112
D20V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               45                189
  CLUS_2               25                128
  CLUS_3               38                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       24     13      9      8     20     19     15
  10Q GAIN WILD-TYPE     99     40     38     57     88     47     60
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               24                 99
  CLUS_2               13                 40
  CLUS_3                9                 38
  CLUS_4                8                 57
  CLUS_5               20                 88
  CLUS_6               19                 47
  CLUS_7               15                 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
  10Q GAIN MUTATED       40     31     38
  10Q GAIN WILD-TYPE    183    119    119
D20V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               40                183
  CLUS_2               31                119
  CLUS_3               38                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       29     17     38     25
  10Q GAIN WILD-TYPE    190     41     99     91
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               29                190
  CLUS_2               17                 41
  CLUS_3               38                 99
  CLUS_4               25                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       28     19     27
  10Q GAIN WILD-TYPE    144     77    103
D20V11, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               28                144
  CLUS_2               19                 77
  CLUS_3               27                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
  10Q GAIN MUTATED       23     30     21
  10Q GAIN WILD-TYPE    121     85    118
D20V12, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               23                121
  CLUS_2               30                 85
  CLUS_3               21                118
[1] 3 2
[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 = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        0      4      0      0
  11P GAIN WILD-TYPE     14     13     12     10
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  11P GAIN MUTATED        2      2      0      0      0
  11P GAIN WILD-TYPE     12      7      7      7     16
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                  7
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       17      0      4      0      2
  11P GAIN WILD-TYPE    152    305     15      9     35
D21V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               17                152
  CLUS_2                0                305
  CLUS_3                4                 15
  CLUS_4                0                  9
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       12      4      3
  11P GAIN WILD-TYPE    153     85    168
D21V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               12                153
  CLUS_2                4                 85
  CLUS_3                3                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 CLUS_6
  11P GAIN MUTATED        3      1      0      0      1      4
  11P GAIN WILD-TYPE     38     36     39     12     40     20
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        2      3      1      3
  11P GAIN WILD-TYPE     65     64     42     14
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                3                 64
  CLUS_3                1                 42
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       18      2      3
  11P GAIN WILD-TYPE    216    151    147
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               18                216
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       14      1      1      0      5      2      0
  11P GAIN WILD-TYPE    109     52     46     65    103     64     75
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               14                109
  CLUS_2                1                 52
  CLUS_3                1                 46
  CLUS_4                0                 65
  CLUS_5                5                103
  CLUS_6                2                 64
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       18      2      3
  11P GAIN WILD-TYPE    205    148    154
D21V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               18                205
  CLUS_2                2                148
  CLUS_3                3                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
  11P GAIN MUTATED        8      1      2     12
  11P GAIN WILD-TYPE    211     57    135    104
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                211
  CLUS_2                1                 57
  CLUS_3                2                135
  CLUS_4               12                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       11      3      3
  11P GAIN WILD-TYPE    161     93    127
D21V11, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               11                161
  CLUS_2                3                 93
  CLUS_3                3                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        9      3      5
  11P GAIN WILD-TYPE    135    112    134
D21V12, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                9                135
  CLUS_2                3                112
  CLUS_3                5                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"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        0      2      0      0
  11Q GAIN WILD-TYPE     14     15     12     10
D22V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        1      1      0      0      0
  11Q GAIN WILD-TYPE     13      8      7      7     16
D22V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED       13      0      3      0      3
  11Q GAIN WILD-TYPE    156    305     16      9     34
D22V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               13                156
  CLUS_2                0                305
  CLUS_3                3                 16
  CLUS_4                0                  9
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       10      3      3
  11Q GAIN WILD-TYPE    155     86    168
D22V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               10                155
  CLUS_2                3                 86
  CLUS_3                3                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 CLUS_6
  11Q GAIN MUTATED        3      1      0      0      1      3
  11Q GAIN WILD-TYPE     38     36     39     12     40     21
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        1      4      0      3
  11Q GAIN WILD-TYPE     66     63     43     14
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                4                 63
  CLUS_3                0                 43
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       14      2      3
  11Q GAIN WILD-TYPE    220    151    147
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               14                220
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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        8      1      2      0      5      3      0
  11Q GAIN WILD-TYPE    115     52     45     65    103     63     75
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                115
  CLUS_2                1                 52
  CLUS_3                2                 45
  CLUS_4                0                 65
  CLUS_5                5                103
  CLUS_6                3                 63
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       12      3      4
  11Q GAIN WILD-TYPE    211    147    153
D22V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               12                211
  CLUS_2                3                147
  CLUS_3                4                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
  11Q GAIN MUTATED        6      1      3      9
  11Q GAIN WILD-TYPE    213     57    134    107
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                213
  CLUS_2                1                 57
  CLUS_3                3                134
  CLUS_4                9                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
  11Q GAIN MUTATED        6      4      4
  11Q GAIN WILD-TYPE    166     92    126
D22V11, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                166
  CLUS_2                4                 92
  CLUS_3                4                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
  11Q GAIN MUTATED        7      3      4
  11Q GAIN WILD-TYPE    137    112    135
D22V12, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                7                137
  CLUS_2                3                112
  CLUS_3                4                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"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED        1      2      3      0
  12P GAIN WILD-TYPE     13     15      9     10
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                3                  9
  CLUS_4                0                 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 CLUS_5
  12P GAIN MUTATED        3      1      1      0      1
  12P GAIN WILD-TYPE     11      8      6      7     15
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                1                  6
  CLUS_4                0                  7
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       42     14      7      3      5
  12P GAIN WILD-TYPE    127    291     12      6     32
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               42                127
  CLUS_2               14                291
  CLUS_3                7                 12
  CLUS_4                3                  6
  CLUS_5                5                 32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       35     14      8
  12P GAIN WILD-TYPE    130     75    163
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               35                130
  CLUS_2               14                 75
  CLUS_3                8                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 CLUS_6
  12P GAIN MUTATED        4      5      4      0      4      3
  12P GAIN WILD-TYPE     37     32     35     12     37     21
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                5                 32
  CLUS_3                4                 35
  CLUS_4                0                 12
  CLUS_5                4                 37
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED        7      8      4      1
  12P GAIN WILD-TYPE     60     59     39     16
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                8                 59
  CLUS_3                4                 39
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       51     10     10
  12P GAIN WILD-TYPE    183    143    140
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               51                183
  CLUS_2               10                143
  CLUS_3               10                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       31      1     10      6     13      3      7
  12P GAIN WILD-TYPE     92     52     37     59     95     63     68
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               31                 92
  CLUS_2                1                 52
  CLUS_3               10                 37
  CLUS_4                6                 59
  CLUS_5               13                 95
  CLUS_6                3                 63
  CLUS_7                7                 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
  12P GAIN MUTATED       44     17     10
  12P GAIN WILD-TYPE    179    133    147
D23V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               44                179
  CLUS_2               17                133
  CLUS_3               10                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       29      4     10     28
  12P GAIN WILD-TYPE    190     54    127     88
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               29                190
  CLUS_2                4                 54
  CLUS_3               10                127
  CLUS_4               28                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       34     11      9
  12P GAIN WILD-TYPE    138     85    121
D23V11, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               34                138
  CLUS_2               11                 85
  CLUS_3                9                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
  12P GAIN MUTATED       29      7     18
  12P GAIN WILD-TYPE    115    108    121
D23V12, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               29                115
  CLUS_2                7                108
  CLUS_3               18                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"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED        1      2      3      0
  12Q GAIN WILD-TYPE     13     15      9     10
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                3                  9
  CLUS_4                0                 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 CLUS_5
  12Q GAIN MUTATED        3      1      1      0      1
  12Q GAIN WILD-TYPE     11      8      6      7     15
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                1                  6
  CLUS_4                0                  7
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       26     14      6      3      5
  12Q GAIN WILD-TYPE    143    291     13      6     32
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               26                143
  CLUS_2               14                291
  CLUS_3                6                 13
  CLUS_4                3                  6
  CLUS_5                5                 32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       22     12      8
  12Q GAIN WILD-TYPE    143     77    163
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               22                143
  CLUS_2               12                 77
  CLUS_3                8                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 CLUS_6
  12Q GAIN MUTATED        4      4      4      0      3      2
  12Q GAIN WILD-TYPE     37     33     35     12     38     22
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                4                 33
  CLUS_3                4                 35
  CLUS_4                0                 12
  CLUS_5                3                 38
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED        6      7      3      1
  12Q GAIN WILD-TYPE     61     60     40     16
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                7                 60
  CLUS_3                3                 40
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       35      9     10
  12Q GAIN WILD-TYPE    199    144    140
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               35                199
  CLUS_2                9                144
  CLUS_3               10                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       19      1      8      6     10      3      7
  12Q GAIN WILD-TYPE    104     52     39     59     98     63     68
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               19                104
  CLUS_2                1                 52
  CLUS_3                8                 39
  CLUS_4                6                 59
  CLUS_5               10                 98
  CLUS_6                3                 63
  CLUS_7                7                 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
  12Q GAIN MUTATED       31     13     10
  12Q GAIN WILD-TYPE    192    137    147
D24V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               31                192
  CLUS_2               13                137
  CLUS_3               10                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       23      3     10     18
  12Q GAIN WILD-TYPE    196     55    127     98
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               23                196
  CLUS_2                3                 55
  CLUS_3               10                127
  CLUS_4               18                 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
  12Q GAIN MUTATED       21     10      8
  12Q GAIN WILD-TYPE    151     86    122
D24V11, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               21                151
  CLUS_2               10                 86
  CLUS_3                8                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       17      7     15
  12Q GAIN WILD-TYPE    127    108    124
D24V12, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               17                127
  CLUS_2                7                108
  CLUS_3               15                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"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        0      3      0      0
  13Q GAIN WILD-TYPE     14     14     12     10
D25V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  13Q GAIN MUTATED        0      3      0      0      0
  13Q GAIN WILD-TYPE     14      6      7      7     16
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       27      0      0      1      2
  13Q GAIN WILD-TYPE    142    305     19      8     35
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               27                142
  CLUS_2                0                305
  CLUS_3                0                 19
  CLUS_4                1                  8
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       18      7      1
  13Q GAIN WILD-TYPE    147     82    170
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               18                147
  CLUS_2                7                 82
  CLUS_3                1                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 CLUS_6
  13Q GAIN MUTATED        2      2      0      0      1      3
  13Q GAIN WILD-TYPE     39     35     39     12     40     21
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                2                 35
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        4      1      0      3
  13Q GAIN WILD-TYPE     63     66     43     14
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       27      1      2
  13Q GAIN WILD-TYPE    207    152    148
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               27                207
  CLUS_2                1                152
  CLUS_3                2                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 CLUS_5 CLUS_6 CLUS_7
  13Q GAIN MUTATED       26      0      1      0      1      1      1
  13Q GAIN WILD-TYPE     97     53     46     65    107     65     74
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               26                 97
  CLUS_2                0                 53
  CLUS_3                1                 46
  CLUS_4                0                 65
  CLUS_5                1                107
  CLUS_6                1                 65
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       27      1      2
  13Q GAIN WILD-TYPE    196    149    155
D25V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               27                196
  CLUS_2                1                149
  CLUS_3                2                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
  13Q GAIN MUTATED        5      0      2     23
  13Q GAIN WILD-TYPE    214     58    135     93
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                214
  CLUS_2                0                 58
  CLUS_3                2                135
  CLUS_4               23                 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
  13Q GAIN MUTATED       17      6      2
  13Q GAIN WILD-TYPE    155     90    128
D25V11, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               17                155
  CLUS_2                6                 90
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       14      2      9
  13Q GAIN WILD-TYPE    130    113    130
D25V12, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               14                130
  CLUS_2                2                113
  CLUS_3                9                130
[1] 3 2
[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 = 14Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        1      1      1      0
  14Q GAIN WILD-TYPE     13     16     11     10
D26V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 16
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  14Q GAIN MUTATED        1      0      0      1      1
  14Q GAIN WILD-TYPE     13      9      7      6     15
D26V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                0                  7
  CLUS_4                1                  6
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       26      4      1      0      6
  14Q GAIN WILD-TYPE    143    301     18      9     31
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               26                143
  CLUS_2                4                301
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                6                 31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       23      4      7
  14Q GAIN WILD-TYPE    142     85    164
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               23                142
  CLUS_2                4                 85
  CLUS_3                7                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 CLUS_5 CLUS_6
  14Q GAIN MUTATED        2      0      0      1      0      1
  14Q GAIN WILD-TYPE     39     37     39     11     41     23
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                0                 37
  CLUS_3                0                 39
  CLUS_4                1                 11
  CLUS_5                0                 41
  CLUS_6                1                 23
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        1      1      2      0
  14Q GAIN WILD-TYPE     66     66     41     17
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                1                 66
  CLUS_3                2                 41
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       28      3      6
  14Q GAIN WILD-TYPE    206    150    144
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               28                206
  CLUS_2                3                150
  CLUS_3                6                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       17      1      6      1      8      0      4
  14Q GAIN WILD-TYPE    106     52     41     64    100     66     71
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               17                106
  CLUS_2                1                 52
  CLUS_3                6                 41
  CLUS_4                1                 64
  CLUS_5                8                100
  CLUS_6                0                 66
  CLUS_7                4                 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
  14Q GAIN MUTATED       25      6      6
  14Q GAIN WILD-TYPE    198    144    151
D26V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               25                198
  CLUS_2                6                144
  CLUS_3                6                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
  14Q GAIN MUTATED       10      1      7     19
  14Q GAIN WILD-TYPE    209     57    130     97
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                209
  CLUS_2                1                 57
  CLUS_3                7                130
  CLUS_4               19                 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
  14Q GAIN MUTATED       20      8      6
  14Q GAIN WILD-TYPE    152     88    124
D26V11, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               20                152
  CLUS_2                8                 88
  CLUS_3                6                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
  14Q GAIN MUTATED       15      6     13
  14Q GAIN WILD-TYPE    129    109    126
D26V12, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               15                129
  CLUS_2                6                109
  CLUS_3               13                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"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        0      0      0      0
  15Q GAIN WILD-TYPE     14     17     12     10
D27V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q GAIN MUTATED        0      0      0      0      0
  15Q GAIN WILD-TYPE     14      9      7      7     16
D27V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q GAIN MUTATED        8      0      1      0      2
  15Q GAIN WILD-TYPE    161    305     18      9     35
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                161
  CLUS_2                0                305
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        3      2      5
  15Q GAIN WILD-TYPE    162     87    166
D27V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                162
  CLUS_2                2                 87
  CLUS_3                5                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 CLUS_6
  15Q GAIN MUTATED        1      0      0      0      0      1
  15Q GAIN WILD-TYPE     40     37     39     12     41     23
D27V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11N         TCGA-B5-A11Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        1      0      1      0
  15Q GAIN WILD-TYPE     66     67     42     17
D27V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11N         TCGA-B5-A11Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        6      2      3
  15Q GAIN WILD-TYPE    228    151    147
D27V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                228
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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      1      1      0      3      2      0
  15Q GAIN WILD-TYPE    119     52     46     65    105     64     75
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                119
  CLUS_2                1                 52
  CLUS_3                1                 46
  CLUS_4                0                 65
  CLUS_5                3                105
  CLUS_6                2                 64
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        6      3      2
  15Q GAIN WILD-TYPE    217    147    155
D27V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                217
  CLUS_2                3                147
  CLUS_3                2                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
  15Q GAIN MUTATED        6      1      2      2
  15Q GAIN WILD-TYPE    213     57    135    114
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                213
  CLUS_2                1                 57
  CLUS_3                2                135
  CLUS_4                2                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
  15Q GAIN MUTATED        4      2      3
  15Q GAIN WILD-TYPE    168     94    127
D27V11, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2                2                 94
  CLUS_3                3                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        1      4      4
  15Q GAIN WILD-TYPE    143    111    135
D27V12, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                143
  CLUS_2                4                111
  CLUS_3                4                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"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        0      1      0      0
  16P GAIN WILD-TYPE     14     16     12     10
D28V1, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED        0      1      0      0      0
  16P GAIN WILD-TYPE     14      8      7      7     16
D28V2, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED       22      1      1      0      3
  16P GAIN WILD-TYPE    147    304     18      9     34
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               22                147
  CLUS_2                1                304
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       16      0      9
  16P GAIN WILD-TYPE    149     89    162
D28V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               16                149
  CLUS_2                0                 89
  CLUS_3                9                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 CLUS_6
  16P GAIN MUTATED        1      1      0      0      3      3
  16P GAIN WILD-TYPE     40     36     39     12     38     21
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                3                 38
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        2      4      1      1
  16P GAIN WILD-TYPE     65     63     42     16
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                4                 63
  CLUS_3                1                 42
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       19      4      4
  16P GAIN WILD-TYPE    215    149    146
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               19                215
  CLUS_2                4                149
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       12      3      2      1      6      3      0
  16P GAIN WILD-TYPE    111     50     45     64    102     63     75
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               12                111
  CLUS_2                3                 50
  CLUS_3                2                 45
  CLUS_4                1                 64
  CLUS_5                6                102
  CLUS_6                3                 63
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       20      3      4
  16P GAIN WILD-TYPE    203    147    153
D28V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               20                203
  CLUS_2                3                147
  CLUS_3                4                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
  16P GAIN MUTATED       10      3      4     10
  16P GAIN WILD-TYPE    209     55    133    106
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               10                209
  CLUS_2                3                 55
  CLUS_3                4                133
  CLUS_4               10                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
  16P GAIN MUTATED       14      4      4
  16P GAIN WILD-TYPE    158     92    126
D28V11, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                158
  CLUS_2                4                 92
  CLUS_3                4                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
  16P GAIN MUTATED       11      4      7
  16P GAIN WILD-TYPE    133    111    132
D28V12, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               11                133
  CLUS_2                4                111
  CLUS_3                7                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"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        0      0      0      0
  16Q GAIN WILD-TYPE     14     17     12     10
D29V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        0      0      0      0      0
  16Q GAIN WILD-TYPE     14      9      7      7     16
D29V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        8      1      0      0      1
  16Q GAIN WILD-TYPE    161    304     19      9     36
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                161
  CLUS_2                1                304
  CLUS_3                0                 19
  CLUS_4                0                  9
  CLUS_5                1                 36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        7      0      2
  16Q GAIN WILD-TYPE    158     89    169
D29V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                7                158
  CLUS_2                0                 89
  CLUS_3                2                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 CLUS_6
  16Q GAIN MUTATED        1      1      0      0      1      0
  16Q GAIN WILD-TYPE     40     36     39     12     40     24
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        2      1      0      0
  16Q GAIN WILD-TYPE     65     66     43     17
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8      1      1
  16Q GAIN WILD-TYPE    226    152    149
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                226
  CLUS_2                1                152
  CLUS_3                1                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 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        5      1      1      0      3      0      0
  16Q GAIN WILD-TYPE    118     52     46     65    105     66     75
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                118
  CLUS_2                1                 52
  CLUS_3                1                 46
  CLUS_4                0                 65
  CLUS_5                3                105
  CLUS_6                0                 66
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        8      1      1
  16Q GAIN WILD-TYPE    215    149    156
D29V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                215
  CLUS_2                1                149
  CLUS_3                1                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
  16Q GAIN MUTATED        3      1      1      5
  16Q GAIN WILD-TYPE    216     57    136    111
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                216
  CLUS_2                1                 57
  CLUS_3                1                136
  CLUS_4                5                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
  16Q GAIN MUTATED        4      2      1
  16Q GAIN WILD-TYPE    168     94    129
D29V11, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2                2                 94
  CLUS_3                1                129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      1      3
  16Q GAIN WILD-TYPE    141    114    136
D29V12, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                141
  CLUS_2                1                114
  CLUS_3                3                136
[1] 3 2
[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 = 17P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        0      1      0      0
  17P GAIN WILD-TYPE     14     16     12     10
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P GAIN MUTATED        1      0      0      0      0
  17P GAIN WILD-TYPE     13      9      7      7     16
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P GAIN MUTATED        8      1      0      1      2
  17P GAIN WILD-TYPE    161    304     19      8     35
D30V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                161
  CLUS_2                1                304
  CLUS_3                0                 19
  CLUS_4                1                  8
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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      1      2
  17P GAIN WILD-TYPE    158     88    169
D30V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                158
  CLUS_2                1                 88
  CLUS_3                2                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 CLUS_6
  17P GAIN MUTATED        1      1      0      1      0      0
  17P GAIN WILD-TYPE     40     36     39     11     41     24
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                1                 11
  CLUS_5                0                 41
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        1      1      1      0
  17P GAIN WILD-TYPE     66     66     42     17
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                1                 66
  CLUS_3                1                 42
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        9      2      1
  17P GAIN WILD-TYPE    225    151    149
D30V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                9                225
  CLUS_2                2                151
  CLUS_3                1                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 CLUS_5 CLUS_6 CLUS_7
  17P GAIN MUTATED        8      0      1      1      2      0      0
  17P GAIN WILD-TYPE    115     53     46     64    106     66     75
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                115
  CLUS_2                0                 53
  CLUS_3                1                 46
  CLUS_4                1                 64
  CLUS_5                2                106
  CLUS_6                0                 66
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        9      2      1
  17P GAIN WILD-TYPE    214    148    156
D30V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                9                214
  CLUS_2                2                148
  CLUS_3                1                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
  17P GAIN MUTATED        4      1      1      6
  17P GAIN WILD-TYPE    215     57    136    110
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                215
  CLUS_2                1                 57
  CLUS_3                1                136
  CLUS_4                6                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
  17P GAIN MUTATED        7      1      2
  17P GAIN WILD-TYPE    165     95    128
D30V11, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                165
  CLUS_2                1                 95
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        3      2      5
  17P GAIN WILD-TYPE    141    113    134
D30V12, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                141
  CLUS_2                2                113
  CLUS_3                5                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"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        0      1      0      0
  17Q GAIN WILD-TYPE     14     16     12     10
D31V1, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED        1      0      0      0      0
  17Q GAIN WILD-TYPE     13      9      7      7     16
D31V2, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED       25      1      0      1      3
  17Q GAIN WILD-TYPE    144    304     19      8     34
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               25                144
  CLUS_2                1                304
  CLUS_3                0                 19
  CLUS_4                1                  8
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       23      2      2
  17Q GAIN WILD-TYPE    142     87    169
D31V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               23                142
  CLUS_2                2                 87
  CLUS_3                2                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 CLUS_6
  17Q GAIN MUTATED        4      1      0      1      0      0
  17Q GAIN WILD-TYPE     37     36     39     11     41     24
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                1                 36
  CLUS_3                0                 39
  CLUS_4                1                 11
  CLUS_5                0                 41
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        2      3      1      0
  17Q GAIN WILD-TYPE     65     64     42     17
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                3                 64
  CLUS_3                1                 42
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       25      2      3
  17Q GAIN WILD-TYPE    209    151    147
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               25                209
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       19      0      5      1      3      2      0
  17Q GAIN WILD-TYPE    104     53     42     64    105     64     75
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               19                104
  CLUS_2                0                 53
  CLUS_3                5                 42
  CLUS_4                1                 64
  CLUS_5                3                105
  CLUS_6                2                 64
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       24      3      3
  17Q GAIN WILD-TYPE    199    147    154
D31V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               24                199
  CLUS_2                3                147
  CLUS_3                3                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
  17Q GAIN MUTATED       11      1      3     15
  17Q GAIN WILD-TYPE    208     57    134    101
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               11                208
  CLUS_2                1                 57
  CLUS_3                3                134
  CLUS_4               15                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       17      5      4
  17Q GAIN WILD-TYPE    155     91    126
D31V11, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               17                155
  CLUS_2                5                 91
  CLUS_3                4                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
  17Q GAIN MUTATED       13      3     10
  17Q GAIN WILD-TYPE    131    112    129
D31V12, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               13                131
  CLUS_2                3                112
  CLUS_3               10                129
[1] 3 2
[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 = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        1      4      1      0
  18P GAIN WILD-TYPE     13     13     11     10
D32V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                 13
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  18P GAIN MUTATED        2      3      0      0      1
  18P GAIN WILD-TYPE     12      6      7      7     15
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       65      3      3      0      1
  18P GAIN WILD-TYPE    104    302     16      9     36
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               65                104
  CLUS_2                3                302
  CLUS_3                3                 16
  CLUS_4                0                  9
  CLUS_5                1                 36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       45     13      4
  18P GAIN WILD-TYPE    120     76    167
D32V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               45                120
  CLUS_2               13                 76
  CLUS_3                4                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 CLUS_5 CLUS_6
  18P GAIN MUTATED        7      3      0      0      1      4
  18P GAIN WILD-TYPE     34     34     39     12     40     20
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 34
  CLUS_2                3                 34
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        9      4      1      1
  18P GAIN WILD-TYPE     58     63     42     16
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                 58
  CLUS_2                4                 63
  CLUS_3                1                 42
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       65      3      4
  18P GAIN WILD-TYPE    169    150    146
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               65                169
  CLUS_2                3                150
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       47      1     13      1      7      2      1
  18P GAIN WILD-TYPE     76     52     34     64    101     64     74
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               47                 76
  CLUS_2                1                 52
  CLUS_3               13                 34
  CLUS_4                1                 64
  CLUS_5                7                101
  CLUS_6                2                 64
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       60      9      3
  18P GAIN WILD-TYPE    163    141    154
D32V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               60                163
  CLUS_2                9                141
  CLUS_3                3                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
  18P GAIN MUTATED       24      1      2     45
  18P GAIN WILD-TYPE    195     57    135     71
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               24                195
  CLUS_2                1                 57
  CLUS_3                2                135
  CLUS_4               45                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       40     16      3
  18P GAIN WILD-TYPE    132     80    127
D32V11, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               40                132
  CLUS_2               16                 80
  CLUS_3                3                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       33      2     24
  18P GAIN WILD-TYPE    111    113    115
D32V12, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               33                111
  CLUS_2                2                113
  CLUS_3               24                115
[1] 3 2
[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 = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        0      3      1      0
  18Q GAIN WILD-TYPE     14     14     11     10
D33V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  18Q GAIN MUTATED        0      3      0      0      1
  18Q GAIN WILD-TYPE     14      6      7      7     15
D33V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       39      3      2      0      1
  18Q GAIN WILD-TYPE    130    302     17      9     36
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               39                130
  CLUS_2                3                302
  CLUS_3                2                 17
  CLUS_4                0                  9
  CLUS_5                1                 36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       29      7      3
  18Q GAIN WILD-TYPE    136     82    168
D33V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               29                136
  CLUS_2                7                 82
  CLUS_3                3                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 CLUS_6
  18Q GAIN MUTATED        4      2      0      0      1      2
  18Q GAIN WILD-TYPE     37     35     39     12     40     22
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                2                 35
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        5      2      0      2
  18Q GAIN WILD-TYPE     62     65     43     15
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                 62
  CLUS_2                2                 65
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       40      2      3
  18Q GAIN WILD-TYPE    194    151    147
D33V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               40                194
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       30      1      5      0      6      2      1
  18Q GAIN WILD-TYPE     93     52     42     65    102     64     74
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               30                 93
  CLUS_2                1                 52
  CLUS_3                5                 42
  CLUS_4                0                 65
  CLUS_5                6                102
  CLUS_6                2                 64
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       35      9      1
  18Q GAIN WILD-TYPE    188    141    156
D33V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               35                188
  CLUS_2                9                141
  CLUS_3                1                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
  18Q GAIN MUTATED       19      1      1     24
  18Q GAIN WILD-TYPE    200     57    136     92
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               19                200
  CLUS_2                1                 57
  CLUS_3                1                136
  CLUS_4               24                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       27      8      1
  18Q GAIN WILD-TYPE    145     88    129
D33V11, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               27                145
  CLUS_2                8                 88
  CLUS_3                1                129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       22      1     13
  18Q GAIN WILD-TYPE    122    114    126
D33V12, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               22                122
  CLUS_2                1                114
  CLUS_3               13                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"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      4      0      0
  19P GAIN WILD-TYPE     14     13     12     10
D34V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  19P GAIN MUTATED        1      3      0      0      0
  19P GAIN WILD-TYPE     13      6      7      7     16
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       49      0      1      0      4
  19P GAIN WILD-TYPE    120    305     18      9     33
D34V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               49                120
  CLUS_2                0                305
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                4                 33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       30     11      8
  19P GAIN WILD-TYPE    135     78    163
D34V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               30                135
  CLUS_2               11                 78
  CLUS_3                8                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 CLUS_6
  19P GAIN MUTATED        3      2      1      0      1      1
  19P GAIN WILD-TYPE     38     35     38     12     40     23
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                2                 35
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                1                 23
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        6      1      0      1
  19P GAIN WILD-TYPE     61     66     43     16
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       47      2      4
  19P GAIN WILD-TYPE    187    151    146
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               47                187
  CLUS_2                2                151
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       36      1      3      2      8      2      1
  19P GAIN WILD-TYPE     87     52     44     63    100     64     74
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               36                 87
  CLUS_2                1                 52
  CLUS_3                3                 44
  CLUS_4                2                 63
  CLUS_5                8                100
  CLUS_6                2                 64
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       45      4      5
  19P GAIN WILD-TYPE    178    146    152
D34V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               45                178
  CLUS_2                4                146
  CLUS_3                5                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
  19P GAIN MUTATED       17      1      6     30
  19P GAIN WILD-TYPE    202     57    131     86
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               17                202
  CLUS_2                1                 57
  CLUS_3                6                131
  CLUS_4               30                 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
  19P GAIN MUTATED       28     14      4
  19P GAIN WILD-TYPE    144     82    126
D34V11, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               28                144
  CLUS_2               14                 82
  CLUS_3                4                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
  19P GAIN MUTATED       20      7     19
  19P GAIN WILD-TYPE    124    108    120
D34V12, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               20                124
  CLUS_2                7                108
  CLUS_3               19                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"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        0      2      0      0
  19Q GAIN WILD-TYPE     14     15     12     10
D35V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED        0      2      0      0      0
  19Q GAIN WILD-TYPE     14      7      7      7     16
D35V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED       51      0      2      0      4
  19Q GAIN WILD-TYPE    118    305     17      9     33
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               51                118
  CLUS_2                0                305
  CLUS_3                2                 17
  CLUS_4                0                  9
  CLUS_5                4                 33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       33     11      7
  19Q GAIN WILD-TYPE    132     78    164
D35V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               33                132
  CLUS_2               11                 78
  CLUS_3                7                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 CLUS_5 CLUS_6
  19Q GAIN MUTATED        1      2      1      0      1      3
  19Q GAIN WILD-TYPE     40     35     38     12     40     21
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                2                 35
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        5      1      0      2
  19Q GAIN WILD-TYPE     62     66     43     15
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                5                 62
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       52      2      3
  19Q GAIN WILD-TYPE    182    151    147
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               52                182
  CLUS_2                2                151
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       39      1      6      1      8      1      1
  19Q GAIN WILD-TYPE     84     52     41     64    100     65     74
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               39                 84
  CLUS_2                1                 52
  CLUS_3                6                 41
  CLUS_4                1                 64
  CLUS_5                8                100
  CLUS_6                1                 65
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       48      5      4
  19Q GAIN WILD-TYPE    175    145    153
D35V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               48                175
  CLUS_2                5                145
  CLUS_3                4                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
  19Q GAIN MUTATED       14      1      5     37
  19Q GAIN WILD-TYPE    205     57    132     79
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               14                205
  CLUS_2                1                 57
  CLUS_3                5                132
  CLUS_4               37                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       29     15      4
  19Q GAIN WILD-TYPE    143     81    126
D35V11, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               29                143
  CLUS_2               15                 81
  CLUS_3                4                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
  19Q GAIN MUTATED       24      6     18
  19Q GAIN WILD-TYPE    120    109    121
D35V12, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               24                120
  CLUS_2                6                109
  CLUS_3               18                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"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        0      5      0      0
  20P GAIN WILD-TYPE     14     12     12     10
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                5                 12
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  20P GAIN MUTATED        2      3      0      0      0
  20P GAIN WILD-TYPE     12      6      7      7     16
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       85      7     12      2      6
  20P GAIN WILD-TYPE     84    298      7      7     31
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               85                 84
  CLUS_2                7                298
  CLUS_3               12                  7
  CLUS_4                2                  7
  CLUS_5                6                 31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       73     13     17
  20P GAIN WILD-TYPE     92     76    154
D36V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               73                 92
  CLUS_2               13                 76
  CLUS_3               17                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 CLUS_6
  20P GAIN MUTATED        5      6      2      0      2      5
  20P GAIN WILD-TYPE     36     31     37     12     39     19
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                 36
  CLUS_2                6                 31
  CLUS_3                2                 37
  CLUS_4                0                 12
  CLUS_5                2                 39
  CLUS_6                5                 19
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        7      6      4      3
  20P GAIN WILD-TYPE     60     61     39     14
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                6                 61
  CLUS_3                4                 39
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       89      9     14
  20P GAIN WILD-TYPE    145    144    136
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               89                145
  CLUS_2                9                144
  CLUS_3               14                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       62      4     15      2     15     12      2
  20P GAIN WILD-TYPE     61     49     32     63     93     54     73
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               62                 61
  CLUS_2                4                 49
  CLUS_3               15                 32
  CLUS_4                2                 63
  CLUS_5               15                 93
  CLUS_6               12                 54
  CLUS_7                2                 73
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       81     16     14
  20P GAIN WILD-TYPE    142    134    143
D36V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               81                142
  CLUS_2               16                134
  CLUS_3               14                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       36      5     13     57
  20P GAIN WILD-TYPE    183     53    124     59
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               36                183
  CLUS_2                5                 53
  CLUS_3               13                124
  CLUS_4               57                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       58     20     18
  20P GAIN WILD-TYPE    114     76    112
D36V11, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               58                114
  CLUS_2               20                 76
  CLUS_3               18                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       56     15     25
  20P GAIN WILD-TYPE     88    100    114
D36V12, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               56                 88
  CLUS_2               15                100
  CLUS_3               25                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"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        0      6      0      0
  20Q GAIN WILD-TYPE     14     11     12     10
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  20Q GAIN MUTATED        2      4      0      0      0
  20Q GAIN WILD-TYPE     12      5      7      7     16
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                  5
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      103      8     12      2      7
  20Q GAIN WILD-TYPE     66    297      7      7     30
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              103                 66
  CLUS_2                8                297
  CLUS_3               12                  7
  CLUS_4                2                  7
  CLUS_5                7                 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
  20Q GAIN MUTATED       83     16     21
  20Q GAIN WILD-TYPE     82     73    150
D37V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               83                 82
  CLUS_2               16                 73
  CLUS_3               21                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 CLUS_6
  20Q GAIN MUTATED        6      8      2      0      2      6
  20Q GAIN WILD-TYPE     35     29     37     12     39     18
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                 35
  CLUS_2                8                 29
  CLUS_3                2                 37
  CLUS_4                0                 12
  CLUS_5                2                 39
  CLUS_6                6                 18
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       10      7      4      3
  20Q GAIN WILD-TYPE     57     60     39     14
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                 57
  CLUS_2                7                 60
  CLUS_3                4                 39
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      104     10     18
  20Q GAIN WILD-TYPE    130    143    132
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              104                130
  CLUS_2               10                143
  CLUS_3               18                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 CLUS_6 CLUS_7
  20Q GAIN MUTATED       71      4     19      3     18     14      3
  20Q GAIN WILD-TYPE     52     49     28     62     90     52     72
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               71                 52
  CLUS_2                4                 49
  CLUS_3               19                 28
  CLUS_4                3                 62
  CLUS_5               18                 90
  CLUS_6               14                 52
  CLUS_7                3                 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
  20Q GAIN MUTATED       95     17     18
  20Q GAIN WILD-TYPE    128    133    139
D37V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               95                128
  CLUS_2               17                133
  CLUS_3               18                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       43      5     17     65
  20Q GAIN WILD-TYPE    176     53    120     51
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               43                176
  CLUS_2                5                 53
  CLUS_3               17                120
  CLUS_4               65                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       70     23     19
  20Q GAIN WILD-TYPE    102     73    111
D37V11, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               70                102
  CLUS_2               23                 73
  CLUS_3               19                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       64     18     30
  20Q GAIN WILD-TYPE     80     97    109
D37V12, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               64                 80
  CLUS_2               18                 97
  CLUS_3               30                109
[1] 3 2
[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 = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        1      1      0      0
  21Q GAIN WILD-TYPE     13     16     12     10
D38V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        1      1      0      0      0
  21Q GAIN WILD-TYPE     13      8      7      7     16
D38V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED       35      1      0      0      3
  21Q GAIN WILD-TYPE    134    304     19      9     34
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               35                134
  CLUS_2                1                304
  CLUS_3                0                 19
  CLUS_4                0                  9
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       24      7      5
  21Q GAIN WILD-TYPE    141     82    166
D38V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               24                141
  CLUS_2                7                 82
  CLUS_3                5                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 CLUS_6
  21Q GAIN MUTATED        1      2      0      0      0      1
  21Q GAIN WILD-TYPE     40     35     39     12     41     23
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                2                 35
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                1                 23
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        2      1      0      1
  21Q GAIN WILD-TYPE     65     66     43     16
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       33      2      4
  21Q GAIN WILD-TYPE    201    151    146
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               33                201
  CLUS_2                2                151
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       24      0      7      1      3      1      3
  21Q GAIN WILD-TYPE     99     53     40     64    105     65     72
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               24                 99
  CLUS_2                0                 53
  CLUS_3                7                 40
  CLUS_4                1                 64
  CLUS_5                3                105
  CLUS_6                1                 65
  CLUS_7                3                 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
  21Q GAIN MUTATED       34      2      3
  21Q GAIN WILD-TYPE    189    148    154
D38V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               34                189
  CLUS_2                2                148
  CLUS_3                3                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
  21Q GAIN MUTATED        9      1      4     25
  21Q GAIN WILD-TYPE    210     57    133     91
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                9                210
  CLUS_2                1                 57
  CLUS_3                4                133
  CLUS_4               25                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       23     10      2
  21Q GAIN WILD-TYPE    149     86    128
D38V11, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               23                149
  CLUS_2               10                 86
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       16      6     13
  21Q GAIN WILD-TYPE    128    109    126
D38V12, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               16                128
  CLUS_2                6                109
  CLUS_3               13                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"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        1      1      0      0
  22Q GAIN WILD-TYPE     13     16     12     10
D39V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05D         TCGA-AP-A05H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q GAIN MUTATED        1      1      0      0      0
  22Q GAIN WILD-TYPE     13      8      7      7     16
D39V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05D         TCGA-AP-A05H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q GAIN MUTATED       27      3      0      1      0
  22Q GAIN WILD-TYPE    142    302     19      8     37
D39V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               27                142
  CLUS_2                3                302
  CLUS_3                0                 19
  CLUS_4                1                  8
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       26      1      1
  22Q GAIN WILD-TYPE    139     88    170
D39V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               26                139
  CLUS_2                1                 88
  CLUS_3                1                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 CLUS_6
  22Q GAIN MUTATED        1      2      0      0      0      0
  22Q GAIN WILD-TYPE     40     35     39     12     41     24
D39V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                2                 35
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        3      0      0      0
  22Q GAIN WILD-TYPE     64     67     43     17
D39V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                0                 67
  CLUS_3                0                 43
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       31      0      0
  22Q GAIN WILD-TYPE    203    153    150
D39V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               31                203
  CLUS_2                0                153
  CLUS_3                0                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 CLUS_6 CLUS_7
  22Q GAIN MUTATED       16      0     12      0      3      0      0
  22Q GAIN WILD-TYPE    107     53     35     65    105     66     75
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               16                107
  CLUS_2                0                 53
  CLUS_3               12                 35
  CLUS_4                0                 65
  CLUS_5                3                105
  CLUS_6                0                 66
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       28      1      1
  22Q GAIN WILD-TYPE    195    149    156
D39V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               28                195
  CLUS_2                1                149
  CLUS_3                1                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
  22Q GAIN MUTATED        9      0      1     20
  22Q GAIN WILD-TYPE    210     58    136     96
D39V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                9                210
  CLUS_2                0                 58
  CLUS_3                1                136
  CLUS_4               20                 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
  22Q GAIN MUTATED       24      2      2
  22Q GAIN WILD-TYPE    148     94    128
D39V11, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               24                148
  CLUS_2                2                 94
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       22      1      5
  22Q GAIN WILD-TYPE    122    114    134
D39V12, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               22                122
  CLUS_2                1                114
  CLUS_3                5                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"

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        1      3      2      0
  XP GAIN WILD-TYPE     13     14     10     10
D40V1, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  XP GAIN MUTATED        2      1      1      1      1
  XP GAIN WILD-TYPE     12      8      6      6     15
D40V2, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                 8
  CLUS_3               1                 6
  CLUS_4               1                 6
  CLUS_5               1                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       23      7      8      3     23
  XP GAIN WILD-TYPE    146    298     11      6     14
D40V3, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              23               146
  CLUS_2               7               298
  CLUS_3               8                11
  CLUS_4               3                 6
  CLUS_5              23                14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       25      6     17
  XP GAIN WILD-TYPE    140     83    154
D40V4, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              25               140
  CLUS_2               6                83
  CLUS_3              17               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 CLUS_6
  XP GAIN MUTATED        6      4      4      2      3      3
  XP GAIN WILD-TYPE     35     33     35     10     38     21
D40V5, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               6                35
  CLUS_2               4                33
  CLUS_3               4                35
  CLUS_4               2                10
  CLUS_5               3                38
  CLUS_6               3                21
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        5      8      7      2
  XP GAIN WILD-TYPE     62     59     36     15
D40V6, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               5                62
  CLUS_2               8                59
  CLUS_3               7                36
  CLUS_4               2                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       32     15     17
  XP GAIN WILD-TYPE    202    138    133
D40V7, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              32               202
  CLUS_2              15               138
  CLUS_3              17               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       16      5      9      6     12      8      8
  XP GAIN WILD-TYPE    107     48     38     59     96     58     67
D40V8, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              16               107
  CLUS_2               5                48
  CLUS_3               9                38
  CLUS_4               6                59
  CLUS_5              12                96
  CLUS_6               8                58
  CLUS_7               8                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
  XP GAIN MUTATED       33     16     15
  XP GAIN WILD-TYPE    190    134    142
D40V9, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              33               190
  CLUS_2              16               134
  CLUS_3              15               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
  XP GAIN MUTATED       25      6     16     17
  XP GAIN WILD-TYPE    194     52    121     99
D40V10, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              25               194
  CLUS_2               6                52
  CLUS_3              16               121
  CLUS_4              17                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
  XP GAIN MUTATED       26      9     12
  XP GAIN WILD-TYPE    146     87    118
D40V11, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              26               146
  CLUS_2               9                87
  CLUS_3              12               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       20     10     17
  XP GAIN WILD-TYPE    124    105    122
D40V12, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              20               124
  CLUS_2              10               105
  CLUS_3              17               122
[1] 3 2
[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 = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        1      2      2      0
  XQ GAIN WILD-TYPE     13     15     10     10
D41V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                15
  CLUS_3               2                10
  CLUS_4               0                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 CLUS_5
  XQ GAIN MUTATED        1      1      1      1      1
  XQ GAIN WILD-TYPE     13      8      6      6     15
D41V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 8
  CLUS_3               1                 6
  CLUS_4               1                 6
  CLUS_5               1                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       24      7      8      3     22
  XQ GAIN WILD-TYPE    145    298     11      6     15
D41V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              24               145
  CLUS_2               7               298
  CLUS_3               8                11
  CLUS_4               3                 6
  CLUS_5              22                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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      8     18
  XQ GAIN WILD-TYPE    143     81    153
D41V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              22               143
  CLUS_2               8                81
  CLUS_3              18               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 CLUS_5 CLUS_6
  XQ GAIN MUTATED        3      4      4      2      3      3
  XQ GAIN WILD-TYPE     38     33     35     10     38     21
D41V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               4                33
  CLUS_3               4                35
  CLUS_4               2                10
  CLUS_5               3                38
  CLUS_6               3                21
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        4      7      7      1
  XQ GAIN WILD-TYPE     63     60     36     16
D41V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4                63
  CLUS_2               7                60
  CLUS_3               7                36
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       30     15     19
  XQ GAIN WILD-TYPE    204    138    131
D41V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              30               204
  CLUS_2              15               138
  CLUS_3              19               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 CLUS_5 CLUS_6 CLUS_7
  XQ GAIN MUTATED       19      5      5      6     12      9      8
  XQ GAIN WILD-TYPE    104     48     42     59     96     57     67
D41V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              19               104
  CLUS_2               5                48
  CLUS_3               5                42
  CLUS_4               6                59
  CLUS_5              12                96
  CLUS_6               9                57
  CLUS_7               8                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
  XQ GAIN MUTATED       31     17     16
  XQ GAIN WILD-TYPE    192    133    141
D41V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              31               192
  CLUS_2              17               133
  CLUS_3              16               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 GAIN MUTATED       27      6     16     15
  XQ GAIN WILD-TYPE    192     52    121    101
D41V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              27               192
  CLUS_2               6                52
  CLUS_3              16               121
  CLUS_4              15               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       26      9     12
  XQ GAIN WILD-TYPE    146     87    118
D41V11, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              26               146
  CLUS_2               9                87
  CLUS_3              12               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       18     12     17
  XQ GAIN WILD-TYPE    126    103    122
D41V12, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              18               126
  CLUS_2              12               103
  CLUS_3              17               122
[1] 3 2
[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 = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        1      1      0      0
  1P LOSS WILD-TYPE     13     16     12     10
D42V1, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED        1      1      0      0      0
  1P LOSS WILD-TYPE     13      8      7      7     16
D42V2, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED       18      0      3      4      0
  1P LOSS WILD-TYPE    151    305     16      5     37
D42V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              18               151
  CLUS_2               0               305
  CLUS_3               3                16
  CLUS_4               4                 5
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       20      1      0
  1P LOSS WILD-TYPE    145     88    171
D42V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              20               145
  CLUS_2               1                88
  CLUS_3               0               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 CLUS_6
  1P LOSS MUTATED        2      1      0      0      1      0
  1P LOSS WILD-TYPE     39     36     39     12     40     24
D42V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                39
  CLUS_2               1                36
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               1                40
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        3      0      1      0
  1P LOSS WILD-TYPE     64     67     42     17
D42V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                64
  CLUS_2               0                67
  CLUS_3               1                42
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      1      1
  1P LOSS WILD-TYPE    211    152    149
D42V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              23               211
  CLUS_2               1               152
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  1P LOSS MUTATED       13      1      7      0      4      0      0
  1P LOSS WILD-TYPE    110     52     40     65    104     66     75
D42V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              13               110
  CLUS_2               1                52
  CLUS_3               7                40
  CLUS_4               0                65
  CLUS_5               4               104
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       21      3      1
  1P LOSS WILD-TYPE    202    147    156
D42V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              21               202
  CLUS_2               3               147
  CLUS_3               1               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
  1P LOSS MUTATED        6      0      0     19
  1P LOSS WILD-TYPE    213     58    137     97
D42V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6               213
  CLUS_2               0                58
  CLUS_3               0               137
  CLUS_4              19                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
  1P LOSS MUTATED       11      7      4
  1P LOSS WILD-TYPE    161     89    126
D42V11, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              11               161
  CLUS_2               7                89
  CLUS_3               4               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
  1P LOSS MUTATED       14      0      8
  1P LOSS WILD-TYPE    130    115    131
D42V12, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              14               130
  CLUS_2               0               115
  CLUS_3               8               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"

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        1      1      0      0
  1Q LOSS WILD-TYPE     13     16     12     10
D43V1, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q LOSS MUTATED        1      1      0      0      0
  1Q LOSS WILD-TYPE     13      8      7      7     16
D43V2, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q LOSS MUTATED       12      0      1      1      0
  1Q LOSS WILD-TYPE    157    305     18      8     37
D43V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              12               157
  CLUS_2               0               305
  CLUS_3               1                18
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       12      0      0
  1Q LOSS WILD-TYPE    153     89    171
D43V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              12               153
  CLUS_2               0                89
  CLUS_3               0               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 CLUS_6
  1Q LOSS MUTATED        1      1      0      0      0      0
  1Q LOSS WILD-TYPE     40     36     39     12     41     24
D43V5, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G5        TCGA-A5-A0G9        TCGA-A5-A0GA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM        TCGA-AP-A0LN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D        TCGA-AX-A06F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS        TCGA-AX-A0IW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1        TCGA-B5-A0JN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        2      0      0      0
  1Q LOSS WILD-TYPE     65     67     43     17
D43V6, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G5        TCGA-A5-A0G9        TCGA-A5-A0GA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM        TCGA-AP-A0LN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D        TCGA-AX-A06F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS        TCGA-AX-A0IW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1        TCGA-B5-A0JN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED       14      0      0
  1Q LOSS WILD-TYPE    220    153    150
D43V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              14               220
  CLUS_2               0               153
  CLUS_3               0               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 CLUS_6 CLUS_7
  1Q LOSS MUTATED        7      0      5      0      2      0      0
  1Q LOSS WILD-TYPE    116     53     42     65    106     66     75
D43V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               116
  CLUS_2               0                53
  CLUS_3               5                42
  CLUS_4               0                65
  CLUS_5               2               106
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       13      1      0
  1Q LOSS WILD-TYPE    210    149    157
D43V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              13               210
  CLUS_2               1               149
  CLUS_3               0               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
  1Q LOSS MUTATED        2      0      0     12
  1Q LOSS WILD-TYPE    217     58    137    104
D43V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               217
  CLUS_2               0                58
  CLUS_3               0               137
  CLUS_4              12               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        7      3      2
  1Q LOSS WILD-TYPE    165     93    128
D43V11, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               165
  CLUS_2               3                93
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        9      0      3
  1Q LOSS WILD-TYPE    135    115    136
D43V12, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               9               135
  CLUS_2               0               115
  CLUS_3               3               136
[1] 3 2
[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 = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        0      0      0      0
  2P LOSS WILD-TYPE     14     17     12     10
D44V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P LOSS MUTATED        0      0      0      0      0
  2P LOSS WILD-TYPE     14      9      7      7     16
D44V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P LOSS MUTATED       10      0      1      0      0
  2P LOSS WILD-TYPE    159    305     18      9     37
D44V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               159
  CLUS_2               0               305
  CLUS_3               1                18
  CLUS_4               0                 9
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        6      3      2
  2P LOSS WILD-TYPE    159     86    169
D44V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               159
  CLUS_2               3                86
  CLUS_3               2               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 CLUS_6
  2P LOSS MUTATED        1      1      0      0      0      0
  2P LOSS WILD-TYPE     40     36     39     12     41     24
D44V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        1      1      0      0
  2P LOSS WILD-TYPE     66     66     43     17
D44V6, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       10      0      1
  2P LOSS WILD-TYPE    224    153    149
D44V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               224
  CLUS_2               0               153
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  2P LOSS MUTATED        6      0      1      0      4      0      0
  2P LOSS WILD-TYPE    117     53     46     65    104     66     75
D44V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               117
  CLUS_2               0                53
  CLUS_3               1                46
  CLUS_4               0                65
  CLUS_5               4               104
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        7      2      2
  2P LOSS WILD-TYPE    216    148    155
D44V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               7               216
  CLUS_2               2               148
  CLUS_3               2               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
  2P LOSS MUTATED        3      0      2      6
  2P LOSS WILD-TYPE    216     58    135    110
D44V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               216
  CLUS_2               0                58
  CLUS_3               2               135
  CLUS_4               6               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
  2P LOSS MUTATED        6      1      3
  2P LOSS WILD-TYPE    166     95    127
D44V11, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               6               166
  CLUS_2               1                95
  CLUS_3               3               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        5      2      3
  2P LOSS WILD-TYPE    139    113    136
D44V12, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5               139
  CLUS_2               2               113
  CLUS_3               3               136
[1] 3 2
[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 = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        0      1      0      0
  2Q LOSS WILD-TYPE     14     16     12     10
D45V1, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q LOSS MUTATED        0      1      0      0      0
  2Q LOSS WILD-TYPE     14      8      7      7     16
D45V2, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q LOSS MUTATED       16      0      1      0      0
  2Q LOSS WILD-TYPE    153    305     18      9     37
D45V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              16               153
  CLUS_2               0               305
  CLUS_3               1                18
  CLUS_4               0                 9
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      3      3
  2Q LOSS WILD-TYPE    155     86    168
D45V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10               155
  CLUS_2               3                86
  CLUS_3               3               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 CLUS_6
  2Q LOSS MUTATED        1      1      0      0      0      0
  2Q LOSS WILD-TYPE     40     36     39     12     41     24
D45V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        1      1      0      0
  2Q LOSS WILD-TYPE     66     66     43     17
D45V6, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       15      0      2
  2Q LOSS WILD-TYPE    219    153    148
D45V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              15               219
  CLUS_2               0               153
  CLUS_3               2               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 CLUS_5 CLUS_6 CLUS_7
  2Q LOSS MUTATED        9      0      1      0      6      1      0
  2Q LOSS WILD-TYPE    114     53     46     65    102     65     75
D45V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9               114
  CLUS_2               0                53
  CLUS_3               1                46
  CLUS_4               0                65
  CLUS_5               6               102
  CLUS_6               1                65
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       13      2      2
  2Q LOSS WILD-TYPE    210    148    155
D45V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              13               210
  CLUS_2               2               148
  CLUS_3               2               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
  2Q LOSS MUTATED        5      0      3      9
  2Q LOSS WILD-TYPE    214     58    134    107
D45V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               214
  CLUS_2               0                58
  CLUS_3               3               134
  CLUS_4               9               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
  2Q LOSS MUTATED        9      3      3
  2Q LOSS WILD-TYPE    163     93    127
D45V11, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9               163
  CLUS_2               3                93
  CLUS_3               3               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        6      3      6
  2Q LOSS WILD-TYPE    138    112    133
D45V12, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               6               138
  CLUS_2               3               112
  CLUS_3               6               133
[1] 3 2
[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 = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      4      0      0
  3P LOSS WILD-TYPE     14     13     12     10
D46V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  3P LOSS MUTATED        0      4      0      0      0
  3P LOSS WILD-TYPE     14      5      7      7     16
D46V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                 5
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       45      0      3      2      1
  3P LOSS WILD-TYPE    124    305     16      7     36
D46V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              45               124
  CLUS_2               0               305
  CLUS_3               3                16
  CLUS_4               2                 7
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       33      6      3
  3P LOSS WILD-TYPE    132     83    168
D46V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              33               132
  CLUS_2               6                83
  CLUS_3               3               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 CLUS_6
  3P LOSS MUTATED        2      8      1      0      1      2
  3P LOSS WILD-TYPE     39     29     38     12     40     22
D46V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                39
  CLUS_2               8                29
  CLUS_3               1                38
  CLUS_4               0                12
  CLUS_5               1                40
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        9      2      2      1
  3P LOSS WILD-TYPE     58     65     41     16
D46V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9                58
  CLUS_2               2                65
  CLUS_3               2                41
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       47      1      2
  3P LOSS WILD-TYPE    187    152    148
D46V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              47               187
  CLUS_2               1               152
  CLUS_3               2               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 CLUS_5 CLUS_6 CLUS_7
  3P LOSS MUTATED       36      0      6      0      6      2      0
  3P LOSS WILD-TYPE     87     53     41     65    102     64     75
D46V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              36                87
  CLUS_2               0                53
  CLUS_3               6                41
  CLUS_4               0                65
  CLUS_5               6               102
  CLUS_6               2                64
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       38      8      3
  3P LOSS WILD-TYPE    185    142    154
D46V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              38               185
  CLUS_2               8               142
  CLUS_3               3               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
  3P LOSS MUTATED       19      1      2     27
  3P LOSS WILD-TYPE    200     57    135     89
D46V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              19               200
  CLUS_2               1                57
  CLUS_3               2               135
  CLUS_4              27                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       25      9      6
  3P LOSS WILD-TYPE    147     87    124
D46V11, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              25               147
  CLUS_2               9                87
  CLUS_3               6               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
  3P LOSS MUTATED       26      3     11
  3P LOSS WILD-TYPE    118    112    128
D46V12, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              26               118
  CLUS_2               3               112
  CLUS_3              11               128
[1] 3 2
[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 = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        0      4      0      0
  3Q LOSS WILD-TYPE     14     13     12     10
D47V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  3Q LOSS MUTATED        0      4      0      0      0
  3Q LOSS WILD-TYPE     14      5      7      7     16
D47V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                 5
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       27      0      1      2      1
  3Q LOSS WILD-TYPE    142    305     18      7     36
D47V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              27               142
  CLUS_2               0               305
  CLUS_3               1                18
  CLUS_4               2                 7
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       20      3      2
  3Q LOSS WILD-TYPE    145     86    169
D47V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              20               145
  CLUS_2               3                86
  CLUS_3               2               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 CLUS_6
  3Q LOSS MUTATED        1      4      0      0      0      1
  3Q LOSS WILD-TYPE     40     33     39     12     41     23
D47V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                40
  CLUS_2               4                33
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        4      1      0      1
  3Q LOSS WILD-TYPE     63     66     43     16
D47V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4                63
  CLUS_2               1                66
  CLUS_3               0                43
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       28      0      2
  3Q LOSS WILD-TYPE    206    153    148
D47V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              28               206
  CLUS_2               0               153
  CLUS_3               2               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 CLUS_5 CLUS_6 CLUS_7
  3Q LOSS MUTATED       21      0      4      0      3      2      0
  3Q LOSS WILD-TYPE    102     53     43     65    105     64     75
D47V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              21               102
  CLUS_2               0                53
  CLUS_3               4                43
  CLUS_4               0                65
  CLUS_5               3               105
  CLUS_6               2                64
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       25      1      3
  3Q LOSS WILD-TYPE    198    149    154
D47V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              25               198
  CLUS_2               1               149
  CLUS_3               3               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
  3Q LOSS MUTATED       12      0      2     15
  3Q LOSS WILD-TYPE    207     58    135    101
D47V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              12               207
  CLUS_2               0                58
  CLUS_3               2               135
  CLUS_4              15               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      2
  3Q LOSS WILD-TYPE    156     89    128
D47V11, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              16               156
  CLUS_2               7                89
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       13      3      9
  3Q LOSS WILD-TYPE    131    112    130
D47V12, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              13               131
  CLUS_2               3               112
  CLUS_3               9               130
[1] 3 2
[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 = 4P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        1      7      0      0
  4P LOSS WILD-TYPE     13     10     12     10
D48V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               7                10
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  4P LOSS MUTATED        3      5      0      0      0
  4P LOSS WILD-TYPE     11      4      7      7     16
D48V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               5                 4
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       91      4      4      4      2
  4P LOSS WILD-TYPE     78    301     15      5     35
D48V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              91                78
  CLUS_2               4               301
  CLUS_3               4                15
  CLUS_4               4                 5
  CLUS_5               2                35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       72     16      6
  4P LOSS WILD-TYPE     93     73    165
D48V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              72                93
  CLUS_2              16                73
  CLUS_3               6               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 CLUS_6
  4P LOSS MUTATED        5      8      0      1      1      6
  4P LOSS WILD-TYPE     36     29     39     11     40     18
D48V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               8                29
  CLUS_3               0                39
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               6                18
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        9      5      3      4
  4P LOSS WILD-TYPE     58     62     40     13
D48V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                58
  CLUS_2               5                62
  CLUS_3               3                40
  CLUS_4               4                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
  4P LOSS MUTATED       91      6      8
  4P LOSS WILD-TYPE    143    147    142
D48V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              91               143
  CLUS_2               6               147
  CLUS_3               8               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 CLUS_6 CLUS_7
  4P LOSS MUTATED       62      2     15      2     18      5      1
  4P LOSS WILD-TYPE     61     51     32     63     90     61     74
D48V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              62                61
  CLUS_2               2                51
  CLUS_3              15                32
  CLUS_4               2                63
  CLUS_5              18                90
  CLUS_6               5                61
  CLUS_7               1                74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       81     14      8
  4P LOSS WILD-TYPE    142    136    149
D48V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              81               142
  CLUS_2              14               136
  CLUS_3               8               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
  4P LOSS MUTATED       38      1      5     59
  4P LOSS WILD-TYPE    181     57    132     57
D48V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              38               181
  CLUS_2               1                57
  CLUS_3               5               132
  CLUS_4              59                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
  4P LOSS MUTATED       55     26     12
  4P LOSS WILD-TYPE    117     70    118
D48V11, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              55               117
  CLUS_2              26                70
  CLUS_3              12               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       52      9     32
  4P LOSS WILD-TYPE     92    106    107
D48V12, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              52                92
  CLUS_2               9               106
  CLUS_3              32               107
[1] 3 2
[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 = 4Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        1      4      0      0
  4Q LOSS WILD-TYPE     13     13     12     10
D49V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  4Q LOSS MUTATED        1      4      0      0      0
  4Q LOSS WILD-TYPE     13      5      7      7     16
D49V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                 5
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       92      3      4      4      2
  4Q LOSS WILD-TYPE     77    302     15      5     35
D49V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              92                77
  CLUS_2               3               302
  CLUS_3               4                15
  CLUS_4               4                 5
  CLUS_5               2                35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       73     15      5
  4Q LOSS WILD-TYPE     92     74    166
D49V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              73                92
  CLUS_2              15                74
  CLUS_3               5               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 CLUS_6
  4Q LOSS MUTATED        5      7      1      1      1      6
  4Q LOSS WILD-TYPE     36     30     38     11     40     18
D49V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               7                30
  CLUS_3               1                38
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               6                18
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        9      5      3      4
  4Q LOSS WILD-TYPE     58     62     40     13
D49V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                58
  CLUS_2               5                62
  CLUS_3               3                40
  CLUS_4               4                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
  4Q LOSS MUTATED       91      6      8
  4Q LOSS WILD-TYPE    143    147    142
D49V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              91               143
  CLUS_2               6               147
  CLUS_3               8               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 CLUS_6 CLUS_7
  4Q LOSS MUTATED       65      2     13      2     17      6      0
  4Q LOSS WILD-TYPE     58     51     34     63     91     60     75
D49V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              65                58
  CLUS_2               2                51
  CLUS_3              13                34
  CLUS_4               2                63
  CLUS_5              17                91
  CLUS_6               6                60
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       82     13      8
  4Q LOSS WILD-TYPE    141    137    149
D49V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              82               141
  CLUS_2              13               137
  CLUS_3               8               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
  4Q LOSS MUTATED       39      1      4     59
  4Q LOSS WILD-TYPE    180     57    133     57
D49V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              39               180
  CLUS_2               1                57
  CLUS_3               4               133
  CLUS_4              59                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
  4Q LOSS MUTATED       53     28     11
  4Q LOSS WILD-TYPE    119     68    119
D49V11, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              53               119
  CLUS_2              28                68
  CLUS_3              11               119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       49      8     35
  4Q LOSS WILD-TYPE     95    107    104
D49V12, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              49                95
  CLUS_2               8               107
  CLUS_3              35               104
[1] 3 2
[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 = 5P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED        1      5      0      0
  5P LOSS WILD-TYPE     13     12     12     10
D50V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               5                12
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  5P LOSS MUTATED        3      3      0      0      0
  5P LOSS WILD-TYPE     11      6      7      7     16
D50V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               3                 6
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       46      0      3      2      4
  5P LOSS WILD-TYPE    123    305     16      7     33
D50V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              46               123
  CLUS_2               0               305
  CLUS_3               3                16
  CLUS_4               2                 7
  CLUS_5               4                33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       38      5      2
  5P LOSS WILD-TYPE    127     84    169
D50V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              38               127
  CLUS_2               5                84
  CLUS_3               2               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 CLUS_6
  5P LOSS MUTATED        5      6      0      1      0      4
  5P LOSS WILD-TYPE     36     31     39     11     41     20
D50V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               6                31
  CLUS_3               0                39
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               4                20
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED        8      4      1      3
  5P LOSS WILD-TYPE     59     63     42     14
D50V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               8                59
  CLUS_2               4                63
  CLUS_3               1                42
  CLUS_4               3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       47      4      4
  5P LOSS WILD-TYPE    187    149    146
D50V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              47               187
  CLUS_2               4               149
  CLUS_3               4               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       33      0      8      1      9      4      0
  5P LOSS WILD-TYPE     90     53     39     64     99     62     75
D50V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              33                90
  CLUS_2               0                53
  CLUS_3               8                39
  CLUS_4               1                64
  CLUS_5               9                99
  CLUS_6               4                62
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       43      6      5
  5P LOSS WILD-TYPE    180    144    152
D50V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              43               180
  CLUS_2               6               144
  CLUS_3               5               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
  5P LOSS MUTATED       20      0      2     32
  5P LOSS WILD-TYPE    199     58    135     84
D50V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              20               199
  CLUS_2               0                58
  CLUS_3               2               135
  CLUS_4              32                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       30     10      3
  5P LOSS WILD-TYPE    142     86    127
D50V11, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              30               142
  CLUS_2              10                86
  CLUS_3               3               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       22      3     18
  5P LOSS WILD-TYPE    122    112    121
D50V12, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              22               122
  CLUS_2               3               112
  CLUS_3              18               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"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        1      6      0      0
  5Q LOSS WILD-TYPE     13     11     12     10
D51V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               6                11
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  5Q LOSS MUTATED        3      4      0      0      0
  5Q LOSS WILD-TYPE     11      5      7      7     16
D51V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               4                 5
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       66      0      2      2      4
  5Q LOSS WILD-TYPE    103    305     17      7     33
D51V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              66               103
  CLUS_2               0               305
  CLUS_3               2                17
  CLUS_4               2                 7
  CLUS_5               4                33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       54      6      2
  5Q LOSS WILD-TYPE    111     83    169
D51V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              54               111
  CLUS_2               6                83
  CLUS_3               2               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 CLUS_6
  5Q LOSS MUTATED        5      7      1      0      0      6
  5Q LOSS WILD-TYPE     36     30     38     12     41     18
D51V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               7                30
  CLUS_3               1                38
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               6                18
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED       11      4      0      4
  5Q LOSS WILD-TYPE     56     63     43     13
D51V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              11                56
  CLUS_2               4                63
  CLUS_3               0                43
  CLUS_4               4                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
  5Q LOSS MUTATED       65      4      5
  5Q LOSS WILD-TYPE    169    149    145
D51V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              65               169
  CLUS_2               4               149
  CLUS_3               5               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 CLUS_6 CLUS_7
  5Q LOSS MUTATED       50      0      7      1     11      5      0
  5Q LOSS WILD-TYPE     73     53     40     64     97     61     75
D51V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              50                73
  CLUS_2               0                53
  CLUS_3               7                40
  CLUS_4               1                64
  CLUS_5              11                97
  CLUS_6               5                61
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       61      7      5
  5Q LOSS WILD-TYPE    162    143    152
D51V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              61               162
  CLUS_2               7               143
  CLUS_3               5               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
  5Q LOSS MUTATED       29      0      3     41
  5Q LOSS WILD-TYPE    190     58    134     75
D51V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              29               190
  CLUS_2               0                58
  CLUS_3               3               134
  CLUS_4              41                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       38     14      7
  5Q LOSS WILD-TYPE    134     82    123
D51V11, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              38               134
  CLUS_2              14                82
  CLUS_3               7               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       31      4     24
  5Q LOSS WILD-TYPE    113    111    115
D51V12, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              31               113
  CLUS_2               4               111
  CLUS_3              24               115
[1] 3 2
[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 = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        1      3      0      0
  6P LOSS WILD-TYPE     13     14     12     10
D52V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  6P LOSS MUTATED        1      3      0      0      0
  6P LOSS WILD-TYPE     13      6      7      7     16
D52V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                 6
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       15      0      2      1      0
  6P LOSS WILD-TYPE    154    305     17      8     37
D52V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              15               154
  CLUS_2               0               305
  CLUS_3               2                17
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       10      2      0
  6P LOSS WILD-TYPE    155     87    171
D52V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              10               155
  CLUS_2               2                87
  CLUS_3               0               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 CLUS_6
  6P LOSS MUTATED        1      3      0      0      1      0
  6P LOSS WILD-TYPE     40     34     39     12     40     24
D52V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                40
  CLUS_2               3                34
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               1                40
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        2      2      1      0
  6P LOSS WILD-TYPE     65     65     42     17
D52V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                65
  CLUS_2               2                65
  CLUS_3               1                42
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       16      1      1
  6P LOSS WILD-TYPE    218    152    149
D52V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              16               218
  CLUS_2               1               152
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  6P LOSS MUTATED       13      1      2      0      2      0      0
  6P LOSS WILD-TYPE    110     52     45     65    106     66     75
D52V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              13               110
  CLUS_2               1                52
  CLUS_3               2                45
  CLUS_4               0                65
  CLUS_5               2               106
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       13      2      1
  6P LOSS WILD-TYPE    210    148    156
D52V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              13               210
  CLUS_2               2               148
  CLUS_3               1               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
  6P LOSS MUTATED        8      0      0      8
  6P LOSS WILD-TYPE    211     58    137    108
D52V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8               211
  CLUS_2               0                58
  CLUS_3               0               137
  CLUS_4               8               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        9      2      1
  6P LOSS WILD-TYPE    163     94    129
D52V11, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               9               163
  CLUS_2               2                94
  CLUS_3               1               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        8      0      4
  6P LOSS WILD-TYPE    136    115    135
D52V12, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8               136
  CLUS_2               0               115
  CLUS_3               4               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"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        1      3      0      0
  6Q LOSS WILD-TYPE     13     14     12     10
D53V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  6Q LOSS MUTATED        1      3      0      0      0
  6Q LOSS WILD-TYPE     13      6      7      7     16
D53V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                 6
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       22      0      2      1      0
  6Q LOSS WILD-TYPE    147    305     17      8     37
D53V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              22               147
  CLUS_2               0               305
  CLUS_3               2                17
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       15      4      0
  6Q LOSS WILD-TYPE    150     85    171
D53V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              15               150
  CLUS_2               4                85
  CLUS_3               0               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 CLUS_6
  6Q LOSS MUTATED        1      3      0      0      1      1
  6Q LOSS WILD-TYPE     40     34     39     12     40     23
D53V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                40
  CLUS_2               3                34
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               1                40
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        2      2      1      1
  6Q LOSS WILD-TYPE     65     65     42     16
D53V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                65
  CLUS_2               2                65
  CLUS_3               1                42
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       23      1      1
  6Q LOSS WILD-TYPE    211    152    149
D53V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              23               211
  CLUS_2               1               152
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED       20      1      2      0      2      0      0
  6Q LOSS WILD-TYPE    103     52     45     65    106     66     75
D53V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              20               103
  CLUS_2               1                52
  CLUS_3               2                45
  CLUS_4               0                65
  CLUS_5               2               106
  CLUS_6               0                66
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       19      3      1
  6Q LOSS WILD-TYPE    204    147    156
D53V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              19               204
  CLUS_2               3               147
  CLUS_3               1               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
  6Q LOSS MUTATED       10      0      0     13
  6Q LOSS WILD-TYPE    209     58    137    103
D53V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              10               209
  CLUS_2               0                58
  CLUS_3               0               137
  CLUS_4              13               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       13      5      1
  6Q LOSS WILD-TYPE    159     91    129
D53V11, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              13               159
  CLUS_2               5                91
  CLUS_3               1               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       11      0      8
  6Q LOSS WILD-TYPE    133    115    131
D53V12, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              11               133
  CLUS_2               0               115
  CLUS_3               8               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"

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        0      4      0      0
  7P LOSS WILD-TYPE     14     13     12     10
D54V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  7P LOSS MUTATED        3      1      0      0      0
  7P LOSS WILD-TYPE     11      8      7      7     16
D54V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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 LOSS MUTATED       39      3      1      1      0
  7P LOSS WILD-TYPE    130    302     18      8     37
D54V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              39               130
  CLUS_2               3               302
  CLUS_3               1                18
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       24     10      5
  7P LOSS WILD-TYPE    141     79    166
D54V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              24               141
  CLUS_2              10                79
  CLUS_3               5               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 CLUS_6
  7P LOSS MUTATED        3      4      0      1      0      0
  7P LOSS WILD-TYPE     38     33     39     11     41     24
D54V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3                38
  CLUS_2               4                33
  CLUS_3               0                39
  CLUS_4               1                11
  CLUS_5               0                41
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        5      2      1      0
  7P LOSS WILD-TYPE     62     65     42     17
D54V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               5                62
  CLUS_2               2                65
  CLUS_3               1                42
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       39      1      4
  7P LOSS WILD-TYPE    195    152    146
D54V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              39               195
  CLUS_2               1               152
  CLUS_3               4               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       30      0      2      0      8      4      0
  7P LOSS WILD-TYPE     93     53     45     65    100     62     75
D54V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              30                93
  CLUS_2               0                53
  CLUS_3               2                45
  CLUS_4               0                65
  CLUS_5               8               100
  CLUS_6               4                62
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       35      3      6
  7P LOSS WILD-TYPE    188    147    151
D54V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              35               188
  CLUS_2               3               147
  CLUS_3               6               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
  7P LOSS MUTATED       14      0      3     27
  7P LOSS WILD-TYPE    205     58    134     89
D54V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              14               205
  CLUS_2               0                58
  CLUS_3               3               134
  CLUS_4              27                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       21     10      6
  7P LOSS WILD-TYPE    151     86    124
D54V11, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              21               151
  CLUS_2              10                86
  CLUS_3               6               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
  7P LOSS MUTATED       18      5     14
  7P LOSS WILD-TYPE    126    110    125
D54V12, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              18               126
  CLUS_2               5               110
  CLUS_3              14               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"

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        0      1      0      0
  7Q LOSS WILD-TYPE     14     16     12     10
D55V1, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED        1      0      0      0      0
  7Q LOSS WILD-TYPE     13      9      7      7     16
D55V2, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED       41      0      0      1      0
  7Q LOSS WILD-TYPE    128    305     19      8     37
D55V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              41               128
  CLUS_2               0               305
  CLUS_3               0                19
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       29      9      1
  7Q LOSS WILD-TYPE    136     80    170
D55V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              29               136
  CLUS_2               9                80
  CLUS_3               1               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 CLUS_6
  7Q LOSS MUTATED        4      4      0      0      0      2
  7Q LOSS WILD-TYPE     37     33     39     12     41     22
D55V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4                37
  CLUS_2               4                33
  CLUS_3               0                39
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        8      1      0      1
  7Q LOSS WILD-TYPE     59     66     43     16
D55V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               8                59
  CLUS_2               1                66
  CLUS_3               0                43
  CLUS_4               1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       41      0      1
  7Q LOSS WILD-TYPE    193    153    149
D55V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              41               193
  CLUS_2               0               153
  CLUS_3               1               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 CLUS_5 CLUS_6 CLUS_7
  7Q LOSS MUTATED       32      0      4      0      4      2      0
  7Q LOSS WILD-TYPE     91     53     43     65    104     64     75
D55V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              32                91
  CLUS_2               0                53
  CLUS_3               4                43
  CLUS_4               0                65
  CLUS_5               4               104
  CLUS_6               2                64
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       38      2      2
  7Q LOSS WILD-TYPE    185    148    155
D55V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              38               185
  CLUS_2               2               148
  CLUS_3               2               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 LOSS MUTATED       10      0      1     31
  7Q LOSS WILD-TYPE    209     58    136     85
D55V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              10               209
  CLUS_2               0                58
  CLUS_3               1               136
  CLUS_4              31                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       25      8      4
  7Q LOSS WILD-TYPE    147     88    126
D55V11, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              25               147
  CLUS_2               8                88
  CLUS_3               4               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
  7Q LOSS MUTATED       22      2     13
  7Q LOSS WILD-TYPE    122    113    126
D55V12, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              22               122
  CLUS_2               2               113
  CLUS_3              13               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"

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        0      5      0      0
  8P LOSS WILD-TYPE     14     12     12     10
D56V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               5                12
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  8P LOSS MUTATED        0      5      0      0      0
  8P LOSS WILD-TYPE     14      4      7      7     16
D56V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               5                 4
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       75      3      1      1      0
  8P LOSS WILD-TYPE     94    302     18      8     37
D56V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              75                94
  CLUS_2               3               302
  CLUS_3               1                18
  CLUS_4               1                 8
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       58     11      2
  8P LOSS WILD-TYPE    107     78    169
D56V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              58               107
  CLUS_2              11                78
  CLUS_3               2               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 CLUS_6
  8P LOSS MUTATED        5      2      3      0      0      5
  8P LOSS WILD-TYPE     36     35     36     12     41     19
D56V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               2                35
  CLUS_3               3                36
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               5                19
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        8      4      0      3
  8P LOSS WILD-TYPE     59     63     43     14
D56V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                59
  CLUS_2               4                63
  CLUS_3               0                43
  CLUS_4               3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       73      3      3
  8P LOSS WILD-TYPE    161    150    147
D56V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              73               161
  CLUS_2               3               150
  CLUS_3               3               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       57      0     11      1      6      3      1
  8P LOSS WILD-TYPE     66     53     36     64    102     63     74
D56V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              57                66
  CLUS_2               0                53
  CLUS_3              11                36
  CLUS_4               1                64
  CLUS_5               6               102
  CLUS_6               3                63
  CLUS_7               1                74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       68      5      4
  8P LOSS WILD-TYPE    155    145    153
D56V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              68               155
  CLUS_2               5               145
  CLUS_3               4               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
  8P LOSS MUTATED       19      0      4     54
  8P LOSS WILD-TYPE    200     58    133     62
D56V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              19               200
  CLUS_2               0                58
  CLUS_3               4               133
  CLUS_4              54                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       45     15      6
  8P LOSS WILD-TYPE    127     81    124
D56V11, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              45               127
  CLUS_2              15                81
  CLUS_3               6               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
  8P LOSS MUTATED       41      3     22
  8P LOSS WILD-TYPE    103    112    117
D56V12, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              41               103
  CLUS_2               3               112
  CLUS_3              22               117
[1] 3 2
[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 = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        0      1      0      0
  8Q LOSS WILD-TYPE     14     16     12     10
D57V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED        0      1      0      0      0
  8Q LOSS WILD-TYPE     14      8      7      7     16
D57V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED       23      1      1      0      0
  8Q LOSS WILD-TYPE    146    304     18      9     37
D57V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              23               146
  CLUS_2               1               304
  CLUS_3               1                18
  CLUS_4               0                 9
  CLUS_5               0                37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       20      3      0
  8Q LOSS WILD-TYPE    145     86    171
D57V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              20               145
  CLUS_2               3                86
  CLUS_3               0               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 CLUS_6
  8Q LOSS MUTATED        0      2      1      0      0      0
  8Q LOSS WILD-TYPE     41     35     38     12     41     24
D57V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                41
  CLUS_2               2                35
  CLUS_3               1                38
  CLUS_4               0                12
  CLUS_5               0                41
  CLUS_6               0                24
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        1      2      0      0
  8Q LOSS WILD-TYPE     66     65     43     17
D57V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                66
  CLUS_2               2                65
  CLUS_3               0                43
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       23      0      2
  8Q LOSS WILD-TYPE    211    153    148
D57V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              23               211
  CLUS_2               0               153
  CLUS_3               2               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 CLUS_5 CLUS_6 CLUS_7
  8Q LOSS MUTATED       19      0      3      0      1      1      1
  8Q LOSS WILD-TYPE    104     53     44     65    107     65     74
D57V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              19               104
  CLUS_2               0                53
  CLUS_3               3                44
  CLUS_4               0                65
  CLUS_5               1               107
  CLUS_6               1                65
  CLUS_7               1                74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       21      1      2
  8Q LOSS WILD-TYPE    202    149    155
D57V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              21               202
  CLUS_2               1               149
  CLUS_3               2               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
  8Q LOSS MUTATED        6      0      2     16
  8Q LOSS WILD-TYPE    213     58    135    100
D57V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6               213
  CLUS_2               0                58
  CLUS_3               2               135
  CLUS_4              16               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
  8Q LOSS MUTATED       17      3      1
  8Q LOSS WILD-TYPE    155     93    129
D57V11, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              17               155
  CLUS_2               3                93
  CLUS_3               1               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       13      1      7
  8Q LOSS WILD-TYPE    131    114    132
D57V12, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              13               131
  CLUS_2               1               114
  CLUS_3               7               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"

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED        1      8      0      0
  9P LOSS WILD-TYPE     13      9     12     10
D58V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               8                 9
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  9P LOSS MUTATED        2      7      0      0      0
  9P LOSS WILD-TYPE     12      2      7      7     16
D58V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               7                 2
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       90      2      6      1      4
  9P LOSS WILD-TYPE     79    303     13      8     33
D58V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              90                79
  CLUS_2               2               303
  CLUS_3               6                13
  CLUS_4               1                 8
  CLUS_5               4                33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       59     20      9
  9P LOSS WILD-TYPE    106     69    162
D58V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              59               106
  CLUS_2              20                69
  CLUS_3               9               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 CLUS_6
  9P LOSS MUTATED        5      9      1      1      1      6
  9P LOSS WILD-TYPE     36     28     38     11     40     18
D58V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               9                28
  CLUS_3               1                38
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               6                18
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       10      6      4      3
  9P LOSS WILD-TYPE     57     61     39     14
D58V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              10                57
  CLUS_2               6                61
  CLUS_3               4                39
  CLUS_4               3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       84      6     13
  9P LOSS WILD-TYPE    150    147    137
D58V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              84               150
  CLUS_2               6               147
  CLUS_3              13               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 CLUS_6 CLUS_7
  9P LOSS MUTATED       58      0     18      2     13     11      1
  9P LOSS WILD-TYPE     65     53     29     63     95     55     74
D58V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              58                65
  CLUS_2               0                53
  CLUS_3              18                29
  CLUS_4               2                63
  CLUS_5              13                95
  CLUS_6              11                55
  CLUS_7               1                74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       74     12     14
  9P LOSS WILD-TYPE    149    138    143
D58V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              74               149
  CLUS_2              12               138
  CLUS_3              14               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       30      1     11     58
  9P LOSS WILD-TYPE    189     57    126     58
D58V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              30               189
  CLUS_2               1                57
  CLUS_3              11               126
  CLUS_4              58                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       47     22     17
  9P LOSS WILD-TYPE    125     74    113
D58V11, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              47               125
  CLUS_2              22                74
  CLUS_3              17               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     13     29
  9P LOSS WILD-TYPE    100    102    110
D58V12, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              44               100
  CLUS_2              13               102
  CLUS_3              29               110
[1] 3 2
[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 = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED        0      9      0      0
  9Q LOSS WILD-TYPE     14      8     12     10
D59V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               9                 8
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  9Q LOSS MUTATED        2      7      0      0      0
  9Q LOSS WILD-TYPE     12      2      7      7     16
D59V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               7                 2
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      105      3      7      2      5
  9Q LOSS WILD-TYPE     64    302     12      7     32
D59V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1             105                64
  CLUS_2               3               302
  CLUS_3               7                12
  CLUS_4               2                 7
  CLUS_5               5                32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       71     22     13
  9Q LOSS WILD-TYPE     94     67    158
D59V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              71                94
  CLUS_2              22                67
  CLUS_3              13               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 CLUS_6
  9Q LOSS MUTATED        6     12      1      2      1      6
  9Q LOSS WILD-TYPE     35     25     38     10     40     18
D59V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               6                35
  CLUS_2              12                25
  CLUS_3               1                38
  CLUS_4               2                10
  CLUS_5               1                40
  CLUS_6               6                18
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       12      8      5      3
  9Q LOSS WILD-TYPE     55     59     38     14
D59V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              12                55
  CLUS_2               8                59
  CLUS_3               5                38
  CLUS_4               3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       99      8     15
  9Q LOSS WILD-TYPE    135    145    135
D59V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              99               135
  CLUS_2               8               145
  CLUS_3              15               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 CLUS_6 CLUS_7
  9Q LOSS MUTATED       70      0     18      3     17     13      1
  9Q LOSS WILD-TYPE     53     53     29     62     91     53     74
D59V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              70                53
  CLUS_2               0                53
  CLUS_3              18                29
  CLUS_4               3                62
  CLUS_5              17                91
  CLUS_6              13                53
  CLUS_7               1                74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       86     17     16
  9Q LOSS WILD-TYPE    137    133    141
D59V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              86               137
  CLUS_2              17               133
  CLUS_3              16               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
  9Q LOSS MUTATED       43      1     12     63
  9Q LOSS WILD-TYPE    176     57    125     53
D59V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              43               176
  CLUS_2               1                57
  CLUS_3              12               125
  CLUS_4              63                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       56     28     19
  9Q LOSS WILD-TYPE    116     68    111
D59V11, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              56               116
  CLUS_2              28                68
  CLUS_3              19               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       55     15     33
  9Q LOSS WILD-TYPE     89    100    106
D59V12, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              55                89
  CLUS_2              15               100
  CLUS_3              33               106
[1] 3 2
[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 = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        0      4      0      0
  10P LOSS WILD-TYPE     14     13     12     10
D60V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  10P LOSS MUTATED        1      3      0      0      0
  10P LOSS WILD-TYPE     13      6      7      7     16
D60V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       42      0      1      0      0
  10P LOSS WILD-TYPE    127    305     18      9     37
D60V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               42                127
  CLUS_2                0                305
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       31      5      1
  10P LOSS WILD-TYPE    134     84    170
D60V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               31                134
  CLUS_2                5                 84
  CLUS_3                1                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 CLUS_6
  10P LOSS MUTATED        2      3      0      0      0      3
  10P LOSS WILD-TYPE     39     34     39     12     41     21
D60V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                3                 34
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        3      3      0      2
  10P LOSS WILD-TYPE     64     64     43     15
D60V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                3                 64
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       39      1      3
  10P LOSS WILD-TYPE    195    152    147
D60V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               39                195
  CLUS_2                1                152
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       28      0      7      1      4      3      0
  10P LOSS WILD-TYPE     95     53     40     64    104     63     75
D60V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               28                 95
  CLUS_2                0                 53
  CLUS_3                7                 40
  CLUS_4                1                 64
  CLUS_5                4                104
  CLUS_6                3                 63
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       35      4      2
  10P LOSS WILD-TYPE    188    146    155
D60V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               35                188
  CLUS_2                4                146
  CLUS_3                2                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
  10P LOSS MUTATED       12      0      2     27
  10P LOSS WILD-TYPE    207     58    135     89
D60V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                207
  CLUS_2                0                 58
  CLUS_3                2                135
  CLUS_4               27                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       21     10      5
  10P LOSS WILD-TYPE    151     86    125
D60V11, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               21                151
  CLUS_2               10                 86
  CLUS_3                5                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
  10P LOSS MUTATED       20      3     13
  10P LOSS WILD-TYPE    124    112    126
D60V12, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               20                124
  CLUS_2                3                112
  CLUS_3               13                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"

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        0      3      0      0
  10Q LOSS WILD-TYPE     14     14     12     10
D61V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  10Q LOSS MUTATED        1      2      0      0      0
  10Q LOSS WILD-TYPE     13      7      7      7     16
D61V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       38      1      1      0      0
  10Q LOSS WILD-TYPE    131    304     18      9     37
D61V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               38                131
  CLUS_2                1                304
  CLUS_3                1                 18
  CLUS_4                0                  9
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       28      6      1
  10Q LOSS WILD-TYPE    137     83    170
D61V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               28                137
  CLUS_2                6                 83
  CLUS_3                1                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 CLUS_6
  10Q LOSS MUTATED        3      3      0      0      0      3
  10Q LOSS WILD-TYPE     38     34     39     12     41     21
D61V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                3                 34
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        3      4      0      2
  10Q LOSS WILD-TYPE     64     63     43     15
D61V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                4                 63
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       35      1      4
  10Q LOSS WILD-TYPE    199    152    146
D61V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               35                199
  CLUS_2                1                152
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       25      0      5      1      5      4      0
  10Q LOSS WILD-TYPE     98     53     42     64    103     62     75
D61V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               25                 98
  CLUS_2                0                 53
  CLUS_3                5                 42
  CLUS_4                1                 64
  CLUS_5                5                103
  CLUS_6                4                 62
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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      4      3
  10Q LOSS WILD-TYPE    191    146    154
D61V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               32                191
  CLUS_2                4                146
  CLUS_3                3                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
  10Q LOSS MUTATED       14      0      3     22
  10Q LOSS WILD-TYPE    205     58    134     94
D61V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                205
  CLUS_2                0                 58
  CLUS_3                3                134
  CLUS_4               22                 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
  10Q LOSS MUTATED       22      6      6
  10Q LOSS WILD-TYPE    150     90    124
D61V11, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               22                150
  CLUS_2                6                 90
  CLUS_3                6                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
  10Q LOSS MUTATED       21      4      9
  10Q LOSS WILD-TYPE    123    111    130
D61V12, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               21                123
  CLUS_2                4                111
  CLUS_3                9                130
[1] 3 2
[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 = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        0      2      0      0
  11P LOSS WILD-TYPE     14     15     12     10
D62V1, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P LOSS MUTATED        1      1      0      0      0
  11P LOSS WILD-TYPE     13      8      7      7     16
D62V2, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P LOSS MUTATED       66      0      3      4      2
  11P LOSS WILD-TYPE    103    305     16      5     35
D62V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               66                103
  CLUS_2                0                305
  CLUS_3                3                 16
  CLUS_4                4                  5
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       53     12      5
  11P LOSS WILD-TYPE    112     77    166
D62V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               53                112
  CLUS_2               12                 77
  CLUS_3                5                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 CLUS_6
  11P LOSS MUTATED        3      5      3      0      1      0
  11P LOSS WILD-TYPE     38     32     36     12     40     24
D62V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                5                 32
  CLUS_3                3                 36
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        7      4      1      0
  11P LOSS WILD-TYPE     60     63     42     17
D62V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                4                 63
  CLUS_3                1                 42
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       65      3      7
  11P LOSS WILD-TYPE    169    150    143
D62V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               65                169
  CLUS_2                3                150
  CLUS_3                7                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED       44      1     11      1     11      7      0
  11P LOSS WILD-TYPE     79     52     36     64     97     59     75
D62V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               44                 79
  CLUS_2                1                 52
  CLUS_3               11                 36
  CLUS_4                1                 64
  CLUS_5               11                 97
  CLUS_6                7                 59
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       57      9      8
  11P LOSS WILD-TYPE    166    141    149
D62V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               57                166
  CLUS_2                9                141
  CLUS_3                8                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
  11P LOSS MUTATED       28      0      6     40
  11P LOSS WILD-TYPE    191     58    131     76
D62V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               28                191
  CLUS_2                0                 58
  CLUS_3                6                131
  CLUS_4               40                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       44     15     11
  11P LOSS WILD-TYPE    128     81    119
D62V11, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               44                128
  CLUS_2               15                 81
  CLUS_3               11                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       44      8     18
  11P LOSS WILD-TYPE    100    107    121
D62V12, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               44                100
  CLUS_2                8                107
  CLUS_3               18                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"

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        0      0      0      0
  11Q LOSS WILD-TYPE     14     17     12     10
D63V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q LOSS MUTATED        0      0      0      0      0
  11Q LOSS WILD-TYPE     14      9      7      7     16
D63V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q LOSS MUTATED       62      0      4      4      2
  11Q LOSS WILD-TYPE    107    305     15      5     35
D63V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               62                107
  CLUS_2                0                305
  CLUS_3                4                 15
  CLUS_4                4                  5
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       52     11      6
  11Q LOSS WILD-TYPE    113     78    165
D63V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               52                113
  CLUS_2               11                 78
  CLUS_3                6                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 CLUS_6
  11Q LOSS MUTATED        2      3      3      0      1      1
  11Q LOSS WILD-TYPE     39     34     36     12     40     23
D63V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                3                 34
  CLUS_3                3                 36
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                1                 23
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        5      3      2      0
  11Q LOSS WILD-TYPE     62     64     41     17
D63V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 62
  CLUS_2                3                 64
  CLUS_3                2                 41
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       60      3      9
  11Q LOSS WILD-TYPE    174    150    141
D63V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               60                174
  CLUS_2                3                150
  CLUS_3                9                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 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED       44      1     10      1     10      6      0
  11Q LOSS WILD-TYPE     79     52     37     64     98     60     75
D63V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               44                 79
  CLUS_2                1                 52
  CLUS_3               10                 37
  CLUS_4                1                 64
  CLUS_5               10                 98
  CLUS_6                6                 60
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       55      8      9
  11Q LOSS WILD-TYPE    168    142    148
D63V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               55                168
  CLUS_2                8                142
  CLUS_3                9                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
  11Q LOSS MUTATED       26      0      7     39
  11Q LOSS WILD-TYPE    193     58    130     77
D63V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               26                193
  CLUS_2                0                 58
  CLUS_3                7                130
  CLUS_4               39                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       49     10     10
  11Q LOSS WILD-TYPE    123     86    120
D63V11, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               49                123
  CLUS_2               10                 86
  CLUS_3               10                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
  11Q LOSS MUTATED       46      8     15
  11Q LOSS WILD-TYPE     98    107    124
D63V12, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               46                 98
  CLUS_2                8                107
  CLUS_3               15                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"

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        0      3      0      0
  12P LOSS WILD-TYPE     14     14     12     10
D64V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  12P LOSS MUTATED        1      2      0      0      0
  12P LOSS WILD-TYPE     13      7      7      7     16
D64V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       41      0      0      0      2
  12P LOSS WILD-TYPE    128    305     19      9     35
D64V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               41                128
  CLUS_2                0                305
  CLUS_3                0                 19
  CLUS_4                0                  9
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       29      3      4
  12P LOSS WILD-TYPE    136     86    167
D64V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               29                136
  CLUS_2                3                 86
  CLUS_3                4                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 CLUS_5 CLUS_6
  12P LOSS MUTATED        2      6      1      0      0      2
  12P LOSS WILD-TYPE     39     31     38     12     41     22
D64V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                6                 31
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        7      2      0      2
  12P LOSS WILD-TYPE     60     65     43     15
D64V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                2                 65
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       38      0      5
  12P LOSS WILD-TYPE    196    153    145
D64V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               38                196
  CLUS_2                0                153
  CLUS_3                5                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 CLUS_6 CLUS_7
  12P LOSS MUTATED       27      0      7      1      3      5      0
  12P LOSS WILD-TYPE     96     53     40     64    105     61     75
D64V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               27                 96
  CLUS_2                0                 53
  CLUS_3                7                 40
  CLUS_4                1                 64
  CLUS_5                3                105
  CLUS_6                5                 61
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       35      2      4
  12P LOSS WILD-TYPE    188    148    153
D64V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               35                188
  CLUS_2                2                148
  CLUS_3                4                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
  12P LOSS MUTATED        9      0      3     29
  12P LOSS WILD-TYPE    210     58    134     87
D64V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                9                210
  CLUS_2                0                 58
  CLUS_3                3                134
  CLUS_4               29                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       26      5      4
  12P LOSS WILD-TYPE    146     91    126
D64V11, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               26                146
  CLUS_2                5                 91
  CLUS_3                4                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
  12P LOSS MUTATED       22      4      9
  12P LOSS WILD-TYPE    122    111    130
D64V12, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               22                122
  CLUS_2                4                111
  CLUS_3                9                130
[1] 3 2
[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 = 12Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        0      2      0      0
  12Q LOSS WILD-TYPE     14     15     12     10
D65V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A053         TCGA-AP-A054 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q LOSS MUTATED        0      2      0      0      0
  12Q LOSS WILD-TYPE     14      7      7      7     16
D65V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A053         TCGA-AP-A054 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q LOSS MUTATED       34      0      0      0      2
  12Q LOSS WILD-TYPE    135    305     19      9     35
D65V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               34                135
  CLUS_2                0                305
  CLUS_3                0                 19
  CLUS_4                0                  9
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       27      1      2
  12Q LOSS WILD-TYPE    138     88    169
D65V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               27                138
  CLUS_2                1                 88
  CLUS_3                2                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 CLUS_6
  12Q LOSS MUTATED        2      5      1      0      0      2
  12Q LOSS WILD-TYPE     39     32     38     12     41     22
D65V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                5                 32
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                0                 41
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        7      1      0      2
  12Q LOSS WILD-TYPE     60     66     43     15
D65V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                1                 66
  CLUS_3                0                 43
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       33      0      3
  12Q LOSS WILD-TYPE    201    153    147
D65V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               33                201
  CLUS_2                0                153
  CLUS_3                3                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       25      0      6      0      2      3      0
  12Q LOSS WILD-TYPE     98     53     41     65    106     63     75
D65V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               25                 98
  CLUS_2                0                 53
  CLUS_3                6                 41
  CLUS_4                0                 65
  CLUS_5                2                106
  CLUS_6                3                 63
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       29      3      2
  12Q LOSS WILD-TYPE    194    147    155
D65V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               29                194
  CLUS_2                3                147
  CLUS_3                2                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
  12Q LOSS MUTATED        9      0      1     24
  12Q LOSS WILD-TYPE    210     58    136     92
D65V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                9                210
  CLUS_2                0                 58
  CLUS_3                1                136
  CLUS_4               24                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       24      3      2
  12Q LOSS WILD-TYPE    148     93    128
D65V11, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               24                148
  CLUS_2                3                 93
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       20      2      7
  12Q LOSS WILD-TYPE    124    113    132
D65V12, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               20                124
  CLUS_2                2                113
  CLUS_3                7                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"

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        1      2      1      0
  13Q LOSS WILD-TYPE     13     15     11     10
D66V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  13Q LOSS MUTATED        3      1      0      0      0
  13Q LOSS WILD-TYPE     11      8      7      7     16
D66V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       71      6      8      3      5
  13Q LOSS WILD-TYPE     98    299     11      6     32
D66V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               71                 98
  CLUS_2                6                299
  CLUS_3                8                 11
  CLUS_4                3                  6
  CLUS_5                5                 32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       51     17     13
  13Q LOSS WILD-TYPE    114     72    158
D66V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               51                114
  CLUS_2               17                 72
  CLUS_3               13                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 CLUS_6
  13Q LOSS MUTATED        4      8      0      1      3      4
  13Q LOSS WILD-TYPE     37     29     39     11     38     20
D66V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                8                 29
  CLUS_3                0                 39
  CLUS_4                1                 11
  CLUS_5                3                 38
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        9      4      5      2
  13Q LOSS WILD-TYPE     58     63     38     15
D66V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                 58
  CLUS_2                4                 63
  CLUS_3                5                 38
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       68      9     16
  13Q LOSS WILD-TYPE    166    144    134
D66V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               68                166
  CLUS_2                9                144
  CLUS_3               16                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 CLUS_6 CLUS_7
  13Q LOSS MUTATED       38      4     14      0     24     12      1
  13Q LOSS WILD-TYPE     85     49     33     65     84     54     74
D66V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               38                 85
  CLUS_2                4                 49
  CLUS_3               14                 33
  CLUS_4                0                 65
  CLUS_5               24                 84
  CLUS_6               12                 54
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       60     18     14
  13Q LOSS WILD-TYPE    163    132    143
D66V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               60                163
  CLUS_2               18                132
  CLUS_3               14                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       44      3     11     34
  13Q LOSS WILD-TYPE    175     55    126     82
D66V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               44                175
  CLUS_2                3                 55
  CLUS_3               11                126
  CLUS_4               34                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       42     19     20
  13Q LOSS WILD-TYPE    130     77    110
D66V11, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               42                130
  CLUS_2               19                 77
  CLUS_3               20                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       43     16     22
  13Q LOSS WILD-TYPE    101     99    117
D66V12, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               43                101
  CLUS_2               16                 99
  CLUS_3               22                117
[1] 3 2
[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 = 14Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED        0      6      0      0
  14Q LOSS WILD-TYPE     14     11     12     10
D67V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  14Q LOSS MUTATED        1      5      0      0      0
  14Q LOSS WILD-TYPE     13      4      7      7     16
D67V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                5                  4
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       54      0      2      3      2
  14Q LOSS WILD-TYPE    115    305     17      6     35
D67V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               54                115
  CLUS_2                0                305
  CLUS_3                2                 17
  CLUS_4                3                  6
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       40      7      1
  14Q LOSS WILD-TYPE    125     82    170
D67V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               40                125
  CLUS_2                7                 82
  CLUS_3                1                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 CLUS_6
  14Q LOSS MUTATED        5      6      0      0      1      4
  14Q LOSS WILD-TYPE     36     31     39     12     40     20
D67V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 36
  CLUS_2                6                 31
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED        9      3      1      3
  14Q LOSS WILD-TYPE     58     64     42     14
D67V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                9                 58
  CLUS_2                3                 64
  CLUS_3                1                 42
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       54      3      4
  14Q LOSS WILD-TYPE    180    150    146
D67V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               54                180
  CLUS_2                3                150
  CLUS_3                4                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       45      1      4      0      7      4      0
  14Q LOSS WILD-TYPE     78     52     43     65    101     62     75
D67V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               45                 78
  CLUS_2                1                 52
  CLUS_3                4                 43
  CLUS_4                0                 65
  CLUS_5                7                101
  CLUS_6                4                 62
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       49      8      2
  14Q LOSS WILD-TYPE    174    142    155
D67V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               49                174
  CLUS_2                8                142
  CLUS_3                2                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
  14Q LOSS MUTATED       20      0      2     37
  14Q LOSS WILD-TYPE    199     58    135     79
D67V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               20                199
  CLUS_2                0                 58
  CLUS_3                2                135
  CLUS_4               37                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       30     10      7
  14Q LOSS WILD-TYPE    142     86    123
D67V11, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               30                142
  CLUS_2               10                 86
  CLUS_3                7                123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       31      3     13
  14Q LOSS WILD-TYPE    113    112    126
D67V12, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               31                113
  CLUS_2                3                112
  CLUS_3               13                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"

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      7      0      0
  15Q LOSS WILD-TYPE     14     10     12     10
D68V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                7                 10
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  15Q LOSS MUTATED        1      6      0      0      0
  15Q LOSS WILD-TYPE     13      3      7      7     16
D68V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                6                  3
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       91      4      6      5      3
  15Q LOSS WILD-TYPE     78    301     13      4     34
D68V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               91                 78
  CLUS_2                4                301
  CLUS_3                6                 13
  CLUS_4                5                  4
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       70     18      8
  15Q LOSS WILD-TYPE     95     71    163
D68V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               70                 95
  CLUS_2               18                 71
  CLUS_3                8                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 CLUS_6
  15Q LOSS MUTATED        1     11      2      1      1      3
  15Q LOSS WILD-TYPE     40     26     37     11     40     21
D68V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 40
  CLUS_2               11                 26
  CLUS_3                2                 37
  CLUS_4                1                 11
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        8      5      3      3
  15Q LOSS WILD-TYPE     59     62     40     14
D68V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                5                 62
  CLUS_3                3                 40
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       94      6      9
  15Q LOSS WILD-TYPE    140    147    141
D68V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               94                140
  CLUS_2                6                147
  CLUS_3                9                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 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED       71      1      9      2     18      7      1
  15Q LOSS WILD-TYPE     52     52     38     63     90     59     74
D68V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               71                 52
  CLUS_2                1                 52
  CLUS_3                9                 38
  CLUS_4                2                 63
  CLUS_5               18                 90
  CLUS_6                7                 59
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       86     13      8
  15Q LOSS WILD-TYPE    137    137    149
D68V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               86                137
  CLUS_2               13                137
  CLUS_3                8                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       41      0      5     61
  15Q LOSS WILD-TYPE    178     58    132     55
D68V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               41                178
  CLUS_2                0                 58
  CLUS_3                5                132
  CLUS_4               61                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       58     23     13
  15Q LOSS WILD-TYPE    114     73    117
D68V11, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               58                114
  CLUS_2               23                 73
  CLUS_3               13                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       55      8     31
  15Q LOSS WILD-TYPE     89    107    108
D68V12, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               55                 89
  CLUS_2                8                107
  CLUS_3               31                108
[1] 3 2
[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 = 16P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED        0      6      0      0
  16P LOSS WILD-TYPE     14     11     12     10
D69V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  16P LOSS MUTATED        2      4      0      0      0
  16P LOSS WILD-TYPE     12      5      7      7     16
D69V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                  5
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       85      4      4      1      3
  16P LOSS WILD-TYPE     84    301     15      8     34
D69V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               85                 84
  CLUS_2                4                301
  CLUS_3                4                 15
  CLUS_4                1                  8
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       61     20      6
  16P LOSS WILD-TYPE    104     69    165
D69V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               61                104
  CLUS_2               20                 69
  CLUS_3                6                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 CLUS_6
  16P LOSS MUTATED        8      7      2      0      2      2
  16P LOSS WILD-TYPE     33     30     37     12     39     22
D69V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                8                 33
  CLUS_2                7                 30
  CLUS_3                2                 37
  CLUS_4                0                 12
  CLUS_5                2                 39
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED       11      5      3      2
  16P LOSS WILD-TYPE     56     62     40     15
D69V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               11                 56
  CLUS_2                5                 62
  CLUS_3                3                 40
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       85      4      8
  16P LOSS WILD-TYPE    149    149    142
D69V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               85                149
  CLUS_2                4                149
  CLUS_3                8                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 CLUS_6 CLUS_7
  16P LOSS MUTATED       60      3     11      1     14      7      1
  16P LOSS WILD-TYPE     63     50     36     64     94     59     74
D69V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               60                 63
  CLUS_2                3                 50
  CLUS_3               11                 36
  CLUS_4                1                 64
  CLUS_5               14                 94
  CLUS_6                7                 59
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       74     11      9
  16P LOSS WILD-TYPE    149    139    148
D69V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               74                149
  CLUS_2               11                139
  CLUS_3                9                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
  16P LOSS MUTATED       34      1      6     53
  16P LOSS WILD-TYPE    185     57    131     63
D69V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               34                185
  CLUS_2                1                 57
  CLUS_3                6                131
  CLUS_4               53                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       47     23     16
  16P LOSS WILD-TYPE    125     73    114
D69V11, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               47                125
  CLUS_2               23                 73
  CLUS_3               16                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
  16P LOSS MUTATED       46      7     33
  16P LOSS WILD-TYPE     98    108    106
D69V12, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               46                 98
  CLUS_2                7                108
  CLUS_3               33                106
[1] 3 2
[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 = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      8      1      0
  16Q LOSS WILD-TYPE     14      9     11     10
D70V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                8                  9
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  16Q LOSS MUTATED        2      6      0      0      1
  16Q LOSS WILD-TYPE     12      3      7      7     15
D70V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                6                  3
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                1                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      112     14      7      1      4
  16Q LOSS WILD-TYPE     57    291     12      8     33
D70V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              112                 57
  CLUS_2               14                291
  CLUS_3                7                 12
  CLUS_4                1                  8
  CLUS_5                4                 33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       80     26     15
  16Q LOSS WILD-TYPE     85     63    156
D70V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               80                 85
  CLUS_2               26                 63
  CLUS_3               15                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 CLUS_6
  16Q LOSS MUTATED        7     10      3      1      6      4
  16Q LOSS WILD-TYPE     34     27     36     11     35     20
D70V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 34
  CLUS_2               10                 27
  CLUS_3                3                 36
  CLUS_4                1                 11
  CLUS_5                6                 35
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED       11     11      6      3
  16Q LOSS WILD-TYPE     56     56     37     14
D70V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               11                 56
  CLUS_2               11                 56
  CLUS_3                6                 37
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      110     14     14
  16Q LOSS WILD-TYPE    124    139    136
D70V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              110                124
  CLUS_2               14                139
  CLUS_3               14                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       78      7     16      3     21      9      4
  16Q LOSS WILD-TYPE     45     46     31     62     87     57     71
D70V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               78                 45
  CLUS_2                7                 46
  CLUS_3               16                 31
  CLUS_4                3                 62
  CLUS_5               21                 87
  CLUS_6                9                 57
  CLUS_7                4                 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
  16Q LOSS MUTATED       96     23     15
  16Q LOSS WILD-TYPE    127    127    142
D70V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               96                127
  CLUS_2               23                127
  CLUS_3               15                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
  16Q LOSS MUTATED       49      6     12     67
  16Q LOSS WILD-TYPE    170     52    125     49
D70V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               49                170
  CLUS_2                6                 52
  CLUS_3               12                125
  CLUS_4               67                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED       66     30     22
  16Q LOSS WILD-TYPE    106     66    108
D70V11, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               66                106
  CLUS_2               30                 66
  CLUS_3               22                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       61     13     44
  16Q LOSS WILD-TYPE     83    102     95
D70V12, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               61                 83
  CLUS_2               13                102
  CLUS_3               44                 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"

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        0      7      1      0
  17P LOSS WILD-TYPE     14     10     11     10
D71V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                7                 10
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  17P LOSS MUTATED        1      6      1      0      0
  17P LOSS WILD-TYPE     13      3      6      7     16
D71V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                6                  3
  CLUS_3                1                  6
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      120      3      4      1      2
  17P LOSS WILD-TYPE     49    302     15      8     35
D71V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              120                 49
  CLUS_2                3                302
  CLUS_3                4                 15
  CLUS_4                1                  8
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       83     21     11
  17P LOSS WILD-TYPE     82     68    160
D71V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               83                 82
  CLUS_2               21                 68
  CLUS_3               11                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 CLUS_6
  17P LOSS MUTATED        5      8      3      0      1      8
  17P LOSS WILD-TYPE     36     29     36     12     40     16
D71V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                 36
  CLUS_2                8                 29
  CLUS_3                3                 36
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                8                 16
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        9      9      3      4
  17P LOSS WILD-TYPE     58     58     40     13
D71V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                9                 58
  CLUS_2                9                 58
  CLUS_3                3                 40
  CLUS_4                4                 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
  17P LOSS MUTATED      110      4     15
  17P LOSS WILD-TYPE    124    149    135
D71V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              110                124
  CLUS_2                4                149
  CLUS_3               15                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 CLUS_6 CLUS_7
  17P LOSS MUTATED       84      1     10      3     17     13      1
  17P LOSS WILD-TYPE     39     52     37     62     91     53     74
D71V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               84                 39
  CLUS_2                1                 52
  CLUS_3               10                 37
  CLUS_4                3                 62
  CLUS_5               17                 91
  CLUS_6               13                 53
  CLUS_7                1                 74
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       99     12     16
  17P LOSS WILD-TYPE    124    138    141
D71V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               99                124
  CLUS_2               12                138
  CLUS_3               16                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
  17P LOSS MUTATED       45      0     13     69
  17P LOSS WILD-TYPE    174     58    124     47
D71V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               45                174
  CLUS_2                0                 58
  CLUS_3               13                124
  CLUS_4               69                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED       66     28     16
  17P LOSS WILD-TYPE    106     68    114
D71V11, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               66                106
  CLUS_2               28                 68
  CLUS_3               16                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
  17P LOSS MUTATED       59     16     35
  17P LOSS WILD-TYPE     85     99    104
D71V12, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               59                 85
  CLUS_2               16                 99
  CLUS_3               35                104
[1] 3 2
[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 = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      6      0      0
  17Q LOSS WILD-TYPE     14     11     12     10
D72V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  17Q LOSS MUTATED        0      6      0      0      0
  17Q LOSS WILD-TYPE     14      3      7      7     16
D72V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                  3
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       84      2      4      1      2
  17Q LOSS WILD-TYPE     85    303     15      8     35
D72V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               84                 85
  CLUS_2                2                303
  CLUS_3                4                 15
  CLUS_4                1                  8
  CLUS_5                2                 35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       54     18     10
  17Q LOSS WILD-TYPE    111     71    161
D72V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               54                111
  CLUS_2               18                 71
  CLUS_3               10                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q LOSS MUTATED        3      7      3      0      1      4
  17Q LOSS WILD-TYPE     38     30     36     12     40     20
D72V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                7                 30
  CLUS_3                3                 36
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        7      6      3      2
  17Q LOSS WILD-TYPE     60     61     40     15
D72V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                6                 61
  CLUS_3                3                 40
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       75      4     13
  17Q LOSS WILD-TYPE    159    149    137
D72V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               75                159
  CLUS_2                4                149
  CLUS_3               13                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 CLUS_6 CLUS_7
  17Q LOSS MUTATED       55      1      6      3     15     12      0
  17Q LOSS WILD-TYPE     68     52     41     62     93     54     75
D72V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               55                 68
  CLUS_2                1                 52
  CLUS_3                6                 41
  CLUS_4                3                 62
  CLUS_5               15                 93
  CLUS_6               12                 54
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       66     10     14
  17Q LOSS WILD-TYPE    157    140    143
D72V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               66                157
  CLUS_2               10                140
  CLUS_3               14                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED       34      0     11     45
  17Q LOSS WILD-TYPE    185     58    126     71
D72V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               34                185
  CLUS_2                0                 58
  CLUS_3               11                126
  CLUS_4               45                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       46     19     15
  17Q LOSS WILD-TYPE    126     77    115
D72V11, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               46                126
  CLUS_2               19                 77
  CLUS_3               15                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       44     14     22
  17Q LOSS WILD-TYPE    100    101    117
D72V12, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               44                100
  CLUS_2               14                101
  CLUS_3               22                117
[1] 3 2
[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 = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      1      1      0
  18P LOSS WILD-TYPE     14     16     11     10
D73V1, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED        0      1      1      0      0
  18P LOSS WILD-TYPE     14      8      6      7     16
D73V2, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED       38      1      6      4      3
  18P LOSS WILD-TYPE    131    304     13      5     34
D73V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               38                131
  CLUS_2                1                304
  CLUS_3                6                 13
  CLUS_4                4                  5
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       34      8      4
  18P LOSS WILD-TYPE    131     81    167
D73V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               34                131
  CLUS_2                8                 81
  CLUS_3                4                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 CLUS_5 CLUS_6
  18P LOSS MUTATED        1      4      2      0      2      3
  18P LOSS WILD-TYPE     40     33     37     12     39     21
D73V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                4                 33
  CLUS_3                2                 37
  CLUS_4                0                 12
  CLUS_5                2                 39
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        3      5      2      2
  18P LOSS WILD-TYPE     64     62     41     15
D73V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                5                 62
  CLUS_3                2                 41
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       40      5      7
  18P LOSS WILD-TYPE    194    148    143
D73V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               40                194
  CLUS_2                5                148
  CLUS_3                7                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED       21      1      6      1     17      6      0
  18P LOSS WILD-TYPE    102     52     41     64     91     60     75
D73V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               21                102
  CLUS_2                1                 52
  CLUS_3                6                 41
  CLUS_4                1                 64
  CLUS_5               17                 91
  CLUS_6                6                 60
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       36      8      7
  18P LOSS WILD-TYPE    187    142    150
D73V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               36                187
  CLUS_2                8                142
  CLUS_3                7                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
  18P LOSS MUTATED       24      1      5     21
  18P LOSS WILD-TYPE    195     57    132     95
D73V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               24                195
  CLUS_2                1                 57
  CLUS_3                5                132
  CLUS_4               21                 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
  18P LOSS MUTATED       29      8      9
  18P LOSS WILD-TYPE    143     88    121
D73V11, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               29                143
  CLUS_2                8                 88
  CLUS_3                9                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
  18P LOSS MUTATED       27      7     12
  18P LOSS WILD-TYPE    117    108    127
D73V12, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               27                117
  CLUS_2                7                108
  CLUS_3               12                127
[1] 3 2
[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 = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      2      1      0
  18Q LOSS WILD-TYPE     14     15     11     10
D74V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 15
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  18Q LOSS MUTATED        1      1      1      0      0
  18Q LOSS WILD-TYPE     13      8      6      7     16
D74V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  8
  CLUS_3                1                  6
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       50      1      7      4      3
  18Q LOSS WILD-TYPE    119    304     12      5     34
D74V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               50                119
  CLUS_2                1                304
  CLUS_3                7                 12
  CLUS_4                4                  5
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       42     11      6
  18Q LOSS WILD-TYPE    123     78    165
D74V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               42                123
  CLUS_2               11                 78
  CLUS_3                6                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 CLUS_6
  18Q LOSS MUTATED        4      4      2      1      1      3
  18Q LOSS WILD-TYPE     37     33     37     11     40     21
D74V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                4                 33
  CLUS_3                2                 37
  CLUS_4                1                 11
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        5      6      3      1
  18Q LOSS WILD-TYPE     62     61     40     16
D74V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 62
  CLUS_2                6                 61
  CLUS_3                3                 40
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       52      5      8
  18Q LOSS WILD-TYPE    182    148    142
D74V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               52                182
  CLUS_2                5                148
  CLUS_3                8                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 CLUS_6 CLUS_7
  18Q LOSS MUTATED       27      1     11      1     19      6      0
  18Q LOSS WILD-TYPE     96     52     36     64     89     60     75
D74V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               27                 96
  CLUS_2                1                 52
  CLUS_3               11                 36
  CLUS_4                1                 64
  CLUS_5               19                 89
  CLUS_6                6                 60
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       48      7      9
  18Q LOSS WILD-TYPE    175    143    148
D74V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               48                175
  CLUS_2                7                143
  CLUS_3                9                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
  18Q LOSS MUTATED       25      0      6     33
  18Q LOSS WILD-TYPE    194     58    131     83
D74V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               25                194
  CLUS_2                0                 58
  CLUS_3                6                131
  CLUS_4               33                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       36     11     12
  18Q LOSS WILD-TYPE    136     85    118
D74V11, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               36                136
  CLUS_2               11                 85
  CLUS_3               12                118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       34      8     17
  18Q LOSS WILD-TYPE    110    107    122
D74V12, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               34                110
  CLUS_2                8                107
  CLUS_3               17                122
[1] 3 2
[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 = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        0      2      0      0
  19P LOSS WILD-TYPE     14     15     12     10
D75V1, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED        0      2      0      0      0
  19P LOSS WILD-TYPE     14      7      7      7     16
D75V2, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED       51      0      5      2      1
  19P LOSS WILD-TYPE    118    305     14      7     36
D75V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               51                118
  CLUS_2                0                305
  CLUS_3                5                 14
  CLUS_4                2                  7
  CLUS_5                1                 36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       45      6      2
  19P LOSS WILD-TYPE    120     83    169
D75V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               45                120
  CLUS_2                6                 83
  CLUS_3                2                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 CLUS_6
  19P LOSS MUTATED        3      3      1      0      1      5
  19P LOSS WILD-TYPE     38     34     38     12     40     19
D75V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                3                 34
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                5                 19
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        5      3      2      3
  19P LOSS WILD-TYPE     62     64     41     14
D75V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                 62
  CLUS_2                3                 64
  CLUS_3                2                 41
  CLUS_4                3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       50      4      5
  19P LOSS WILD-TYPE    184    149    145
D75V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               50                184
  CLUS_2                4                149
  CLUS_3                5                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 CLUS_6 CLUS_7
  19P LOSS MUTATED       34      1      9      1     11      3      0
  19P LOSS WILD-TYPE     89     52     38     64     97     63     75
D75V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               34                 89
  CLUS_2                1                 52
  CLUS_3                9                 38
  CLUS_4                1                 64
  CLUS_5               11                 97
  CLUS_6                3                 63
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       44      7      6
  19P LOSS WILD-TYPE    179    143    151
D75V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               44                179
  CLUS_2                7                143
  CLUS_3                6                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
  19P LOSS MUTATED       23      0      3     31
  19P LOSS WILD-TYPE    196     58    134     85
D75V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               23                196
  CLUS_2                0                 58
  CLUS_3                3                134
  CLUS_4               31                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       33      8     10
  19P LOSS WILD-TYPE    139     88    120
D75V11, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               33                139
  CLUS_2                8                 88
  CLUS_3               10                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
  19P LOSS MUTATED       37      3     11
  19P LOSS WILD-TYPE    107    112    128
D75V12, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               37                107
  CLUS_2                3                112
  CLUS_3               11                128
[1] 3 2
[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 = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        0      3      1      0
  19Q LOSS WILD-TYPE     14     14     11     10
D76V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                1                 11
  CLUS_4                0                 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 CLUS_5
  19Q LOSS MUTATED        0      3      1      0      0
  19Q LOSS WILD-TYPE     14      6      6      7     16
D76V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                  6
  CLUS_3                1                  6
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       49      1      4      1      1
  19Q LOSS WILD-TYPE    120    304     15      8     36
D76V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               49                120
  CLUS_2                1                304
  CLUS_3                4                 15
  CLUS_4                1                  8
  CLUS_5                1                 36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       37      8      4
  19Q LOSS WILD-TYPE    128     81    167
D76V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               37                128
  CLUS_2                8                 81
  CLUS_3                4                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 CLUS_5 CLUS_6
  19Q LOSS MUTATED        3      3      1      0      1      4
  19Q LOSS WILD-TYPE     38     34     38     12     40     20
D76V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                3                 34
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                4                 20
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        4      4      2      2
  19Q LOSS WILD-TYPE     63     63     41     15
D76V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                4                 63
  CLUS_3                2                 41
  CLUS_4                2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       45      4      6
  19Q LOSS WILD-TYPE    189    149    144
D76V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               45                189
  CLUS_2                4                149
  CLUS_3                6                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       34      1      6      1      9      4      0
  19Q LOSS WILD-TYPE     89     52     41     64     99     62     75
D76V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               34                 89
  CLUS_2                1                 52
  CLUS_3                6                 41
  CLUS_4                1                 64
  CLUS_5                9                 99
  CLUS_6                4                 62
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       41      6      7
  19Q LOSS WILD-TYPE    182    144    150
D76V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               41                182
  CLUS_2                6                144
  CLUS_3                7                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
  19Q LOSS MUTATED       25      0      4     25
  19Q LOSS WILD-TYPE    194     58    133     91
D76V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               25                194
  CLUS_2                0                 58
  CLUS_3                4                133
  CLUS_4               25                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       30      8      9
  19Q LOSS WILD-TYPE    142     88    121
D76V11, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               30                142
  CLUS_2                8                 88
  CLUS_3                9                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
  19Q LOSS MUTATED       31      4     12
  19Q LOSS WILD-TYPE    113    111    127
D76V12, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               31                113
  CLUS_2                4                111
  CLUS_3               12                127
[1] 3 2
[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 = 20P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        1      1      0      0
  20P LOSS WILD-TYPE     13     16     12     10
D77V1, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P LOSS MUTATED        1      1      0      0      0
  20P LOSS WILD-TYPE     13      8      7      7     16
D77V2, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P LOSS MUTATED       16      1      1      1      0
  20P LOSS WILD-TYPE    153    304     18      8     37
D77V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               16                153
  CLUS_2                1                304
  CLUS_3                1                 18
  CLUS_4                1                  8
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        7      3      2
  20P LOSS WILD-TYPE    158     86    169
D77V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                158
  CLUS_2                3                 86
  CLUS_3                2                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 CLUS_6
  20P LOSS MUTATED        1      2      0      0      1      2
  20P LOSS WILD-TYPE     40     35     39     12     40     22
D77V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                2                 35
  CLUS_3                0                 39
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                2                 22
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        3      1      1      1
  20P LOSS WILD-TYPE     64     66     42     16
D77V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                1                 66
  CLUS_3                1                 42
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       14      2      2
  20P LOSS WILD-TYPE    220    151    148
D77V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               14                220
  CLUS_2                2                151
  CLUS_3                2                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 CLUS_5 CLUS_6 CLUS_7
  20P LOSS MUTATED       10      2      3      0      2      1      0
  20P LOSS WILD-TYPE    113     51     44     65    106     65     75
D77V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               10                113
  CLUS_2                2                 51
  CLUS_3                3                 44
  CLUS_4                0                 65
  CLUS_5                2                106
  CLUS_6                1                 65
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       14      3      1
  20P LOSS WILD-TYPE    209    147    156
D77V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               14                209
  CLUS_2                3                147
  CLUS_3                1                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
  20P LOSS MUTATED        6      1      2      9
  20P LOSS WILD-TYPE    213     57    135    107
D77V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                213
  CLUS_2                1                 57
  CLUS_3                2                135
  CLUS_4                9                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
  20P LOSS MUTATED        7      4      2
  20P LOSS WILD-TYPE    165     92    128
D77V11, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                165
  CLUS_2                4                 92
  CLUS_3                2                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        7      2      4
  20P LOSS WILD-TYPE    137    113    135
D77V12, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                137
  CLUS_2                2                113
  CLUS_3                4                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"

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        1      0      0      0
  20Q LOSS WILD-TYPE     13     17     12     10
D78V1, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q LOSS MUTATED        1      0      0      0      0
  20Q LOSS WILD-TYPE     13      9      7      7     16
D78V2, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q LOSS MUTATED        7      0      1      1      0
  20Q LOSS WILD-TYPE    162    305     18      8     37
D78V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                162
  CLUS_2                0                305
  CLUS_3                1                 18
  CLUS_4                1                  8
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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        4      2      0
  20Q LOSS WILD-TYPE    161     87    171
D78V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                161
  CLUS_2                2                 87
  CLUS_3                0                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 CLUS_6
  20Q LOSS MUTATED        0      2      1      0      1      0
  20Q LOSS WILD-TYPE     41     35     38     12     40     24
D78V5, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                 41
  CLUS_2                2                 35
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                0                 24
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        2      1      1      0
  20Q LOSS WILD-TYPE     65     66     42     17
D78V6, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                1                 66
  CLUS_3                1                 42
  CLUS_4                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7      1      0
  20Q LOSS WILD-TYPE    227    152    150
D78V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                227
  CLUS_2                1                152
  CLUS_3                0                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 CLUS_6 CLUS_7
  20Q LOSS MUTATED        5      1      2      0      0      0      0
  20Q LOSS WILD-TYPE    118     52     45     65    108     66     75
D78V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                5                118
  CLUS_2                1                 52
  CLUS_3                2                 45
  CLUS_4                0                 65
  CLUS_5                0                108
  CLUS_6                0                 66
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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        7      2      0
  20Q LOSS WILD-TYPE    216    148    157
D78V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                216
  CLUS_2                2                148
  CLUS_3                0                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
  20Q LOSS MUTATED        4      0      0      5
  20Q LOSS WILD-TYPE    215     58    137    111
D78V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                215
  CLUS_2                0                 58
  CLUS_3                0                137
  CLUS_4                5                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
  20Q LOSS MUTATED        4      2      0
  20Q LOSS WILD-TYPE    168     94    130
D78V11, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                168
  CLUS_2                2                 94
  CLUS_3                0                130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      0      2
  20Q LOSS WILD-TYPE    140    115    137
D78V12, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                140
  CLUS_2                0                115
  CLUS_3                2                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"

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        0      4      0      0
  21Q LOSS WILD-TYPE     14     13     12     10
D79V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  21Q LOSS MUTATED        1      3      0      0      0
  21Q LOSS WILD-TYPE     13      6      7      7     16
D79V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                  6
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       44      4      2      4      0
  21Q LOSS WILD-TYPE    125    301     17      5     37
D79V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               44                125
  CLUS_2                4                301
  CLUS_3                2                 17
  CLUS_4                4                  5
  CLUS_5                0                 37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       34      7      5
  21Q LOSS WILD-TYPE    131     82    166
D79V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               34                131
  CLUS_2                7                 82
  CLUS_3                5                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 CLUS_6
  21Q LOSS MUTATED        3      5      1      0      1      3
  21Q LOSS WILD-TYPE     38     32     38     12     40     21
D79V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                5                 32
  CLUS_3                1                 38
  CLUS_4                0                 12
  CLUS_5                1                 40
  CLUS_6                3                 21
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        7      4      1      1
  21Q LOSS WILD-TYPE     60     63     42     16
D79V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                4                 63
  CLUS_3                1                 42
  CLUS_4                1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       46      7      1
  21Q LOSS WILD-TYPE    188    146    149
D79V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               46                188
  CLUS_2                7                146
  CLUS_3                1                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 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED       30      1      7      4     10      2      0
  21Q LOSS WILD-TYPE     93     52     40     61     98     64     75
D79V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               30                 93
  CLUS_2                1                 52
  CLUS_3                7                 40
  CLUS_4                4                 61
  CLUS_5               10                 98
  CLUS_6                2                 64
  CLUS_7                0                 75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       43      7      2
  21Q LOSS WILD-TYPE    180    143    155
D79V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               43                180
  CLUS_2                7                143
  CLUS_3                2                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
  21Q LOSS MUTATED       21      1      1     29
  21Q LOSS WILD-TYPE    198     57    136     87
D79V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               21                198
  CLUS_2                1                 57
  CLUS_3                1                136
  CLUS_4               29                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       30      9      7
  21Q LOSS WILD-TYPE    142     87    123
D79V11, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               30                142
  CLUS_2                9                 87
  CLUS_3                7                123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       28      1     17
  21Q LOSS WILD-TYPE    116    114    122
D79V12, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               28                116
  CLUS_2                1                114
  CLUS_3               17                122
[1] 3 2
[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 = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        0      6      0      0
  22Q LOSS WILD-TYPE     14     11     12     10
D80V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 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 CLUS_5
  22Q LOSS MUTATED        2      4      0      0      0
  22Q LOSS WILD-TYPE     12      5      7      7     16
D80V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                  5
  CLUS_3                0                  7
  CLUS_4                0                  7
  CLUS_5                0                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       96      3      4      3      3
  22Q LOSS WILD-TYPE     73    302     15      6     34
D80V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               96                 73
  CLUS_2                3                302
  CLUS_3                4                 15
  CLUS_4                3                  6
  CLUS_5                3                 34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       67     20     13
  22Q LOSS WILD-TYPE     98     69    158
D80V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               67                 98
  CLUS_2               20                 69
  CLUS_3               13                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 CLUS_6
  22Q LOSS MUTATED        4      8      2      1      1      5
  22Q LOSS WILD-TYPE     37     29     37     11     40     19
D80V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                8                 29
  CLUS_3                2                 37
  CLUS_4                1                 11
  CLUS_5                1                 40
  CLUS_6                5                 19
[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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        6      8      3      4
  22Q LOSS WILD-TYPE     61     59     40     13
D80V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                8                 59
  CLUS_3                3                 40
  CLUS_4                4                 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
  22Q LOSS MUTATED       85      6     17
  22Q LOSS WILD-TYPE    149    147    133
D80V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               85                149
  CLUS_2                6                147
  CLUS_3               17                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       62      1      7      1     22     13      2
  22Q LOSS WILD-TYPE     61     52     40     64     86     53     73
D80V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               62                 61
  CLUS_2                1                 52
  CLUS_3                7                 40
  CLUS_4                1                 64
  CLUS_5               22                 86
  CLUS_6               13                 53
  CLUS_7                2                 73
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       79     11     17
  22Q LOSS WILD-TYPE    144    139    140
D80V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               79                144
  CLUS_2               11                139
  CLUS_3               17                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       43      0     13     51
  22Q LOSS WILD-TYPE    176     58    124     65
D80V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               43                176
  CLUS_2                0                 58
  CLUS_3               13                124
  CLUS_4               51                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       51     25     18
  22Q LOSS WILD-TYPE    121     71    112
D80V11, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               51                121
  CLUS_2               25                 71
  CLUS_3               18                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       50     15     29
  22Q LOSS WILD-TYPE     94    100    110
D80V12, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               50                 94
  CLUS_2               15                100
  CLUS_3               29                110
[1] 3 2
[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 = XP LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED        0      6      0      0
  XP LOSS WILD-TYPE     14     11     12     10
D81V1, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               6                11
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  XP LOSS MUTATED        1      5      0      0      0
  XP LOSS WILD-TYPE     13      4      7      7     16
D81V2, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               5                 4
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       76      1      3      2      3
  XP LOSS WILD-TYPE     93    304     16      7     34
D81V3, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              76                93
  CLUS_2               1               304
  CLUS_3               3                16
  CLUS_4               2                 7
  CLUS_5               3                34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       46     16      8
  XP LOSS WILD-TYPE    119     73    163
D81V4, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              46               119
  CLUS_2              16                73
  CLUS_3               8               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 CLUS_6
  XP LOSS MUTATED        2     14      2      1      1      2
  XP LOSS WILD-TYPE     39     23     37     11     40     22
D81V5, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               2                39
  CLUS_2              14                23
  CLUS_3               2                37
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               2                22
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       11      8      3      0
  XP LOSS WILD-TYPE     56     59     40     17
D81V6, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              11                56
  CLUS_2               8                59
  CLUS_3               3                40
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       73      5      6
  XP LOSS WILD-TYPE    161    148    144
D81V7, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              73               161
  CLUS_2               5               148
  CLUS_3               6               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       52      2      6      1     19      4      0
  XP LOSS WILD-TYPE     71     51     41     64     89     62     75
D81V8, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              52                71
  CLUS_2               2                51
  CLUS_3               6                41
  CLUS_4               1                64
  CLUS_5              19                89
  CLUS_6               4                62
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       61     12      9
  XP LOSS WILD-TYPE    162    138    148
D81V9, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              61               162
  CLUS_2              12               138
  CLUS_3               9               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
  XP LOSS MUTATED       34      0      4     44
  XP LOSS WILD-TYPE    185     58    133     72
D81V10, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              34               185
  CLUS_2               0                58
  CLUS_3               4               133
  CLUS_4              44                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED       44     13     12
  XP LOSS WILD-TYPE    128     83    118
D81V11, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              44               128
  CLUS_2              13                83
  CLUS_3              12               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      6     20
  XP LOSS WILD-TYPE    101    109    119
D81V12, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              43               101
  CLUS_2               6               109
  CLUS_3              20               119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        0      5      0      0
  XQ LOSS WILD-TYPE     14     12     12     10
D82V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               5                12
  CLUS_3               0                12
  CLUS_4               0                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 CLUS_5
  XQ LOSS MUTATED        1      4      0      0      0
  XQ LOSS WILD-TYPE     13      5      7      7     16
D82V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                 5
  CLUS_3               0                 7
  CLUS_4               0                 7
  CLUS_5               0                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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       64      1      3      2      1
  XQ LOSS WILD-TYPE    105    304     16      7     36
D82V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              64               105
  CLUS_2               1               304
  CLUS_3               3                16
  CLUS_4               2                 7
  CLUS_5               1                36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table 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       42     12      6
  XQ LOSS WILD-TYPE    123     77    165
D82V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              42               123
  CLUS_2              12                77
  CLUS_3               6               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 CLUS_6
  XQ LOSS MUTATED        3     13      2      1      1      1
  XQ LOSS WILD-TYPE     38     24     37     11     40     23
D82V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                38
  CLUS_2              13                24
  CLUS_3               2                37
  CLUS_4               1                11
  CLUS_5               1                40
  CLUS_6               1                23
[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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED       11      7      3      0
  XQ LOSS WILD-TYPE     56     60     40     17
D82V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              11                56
  CLUS_2               7                60
  CLUS_3               3                40
  CLUS_4               0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       61      4      5
  XQ LOSS WILD-TYPE    173    149    145
D82V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              61               173
  CLUS_2               4               149
  CLUS_3               5               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 CLUS_6 CLUS_7
  XQ LOSS MUTATED       40      2      8      1     15      4      0
  XQ LOSS WILD-TYPE     83     51     39     64     93     62     75
D82V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              40                83
  CLUS_2               2                51
  CLUS_3               8                39
  CLUS_4               1                64
  CLUS_5              15                93
  CLUS_6               4                62
  CLUS_7               0                75
[1] 7 2
[1] TRUE
[1] "dimension of contingency table 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       51      9      8
  XQ LOSS WILD-TYPE    172    141    149
D82V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              51               172
  CLUS_2               9               141
  CLUS_3               8               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
  XQ LOSS MUTATED       26      0      4     38
  XQ LOSS WILD-TYPE    193     58    133     78
D82V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              26               193
  CLUS_2               0                58
  CLUS_3               4               133
  CLUS_4              38                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       37      9     13
  XQ LOSS WILD-TYPE    135     87    117
D82V11, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              37               135
  CLUS_2               9                87
  CLUS_3              13               117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       41      4     14
  XQ LOSS WILD-TYPE    103    111    125
D82V12, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              41               103
  CLUS_2               4               111
  CLUS_3              14               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"
